From a2ce8a320c340a5f1ca18efb412362e0ece22260 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Sat, 15 Jun 2024 17:06:25 +0000
Subject: [PATCH] deploy: 5b9b0588f3c35e0d39cb6a38c4ecf01fd022835a

---
 404.html                                      |  4 ++--
 assets/js/d5df4937.6c24518b.js                |  1 -
 assets/js/d5df4937.e16d5b72.js                |  1 +
 .../js/{main.2c041b40.js => main.ba545c74.js} |  4 ++--
 ...CENSE.txt => main.ba545c74.js.LICENSE.txt} |  0
 ...n.484a9f37.js => runtime~main.df40aa19.js} |  2 +-
 developer-guide/adding-calibration-type.html  |  4 ++--
 developer-guide/adding-plugins-to-ui.html     |  4 ++--
 developer-guide/architecture.html             |  4 ++--
 developer-guide/avoiding-od.html              |  4 ++--
 developer-guide/chart-to-ui.html              |  4 ++--
 developer-guide/data-stores-intro.html        |  4 ++--
 developer-guide/events.html                   |  4 ++--
 developer-guide/filesystem-locations.html     |  4 ++--
 developer-guide/hat-button.html               |  4 ++--
 developer-guide/i2c-addresses.html            |  4 ++--
 developer-guide/important-concepts.html       |  4 ++--
 developer-guide/intro-automations.html        |  4 ++--
 developer-guide/intro-background-jobs.html    |  4 ++--
 developer-guide/intro-plugins.html            |  4 ++--
 developer-guide/introduction.html             |  4 ++--
 developer-guide/local-development.html        |  4 ++--
 developer-guide/local-storage.html            |  4 ++--
 developer-guide/mqtt.html                     |  4 ++--
 developer-guide/pi-development.html           |  4 ++--
 developer-guide/pinout.html                   |  4 ++--
 developer-guide/plugin-as-python-package.html |  4 ++--
 developer-guide/sqlite3.html                  |  4 ++--
 developer-guide/web-ui-api.html               |  4 ++--
 developer-guide/web-ui-introduction.html      |  4 ++--
 developer-guide/writing-automations-1.html    |  4 ++--
 developer-guide/writing-automations-2.html    |  4 ++--
 developer-guide/writing-background-jobs.html  |  4 ++--
 developer-guide/writing-pump-software.html    |  4 ++--
 developer-guide/writing-scripts.html          |  4 ++--
 experiments/algae-day-night-cycle.html        |  4 ++--
 experiments/caffeine-inhibition.html          |  4 ++--
 ...continuous-cultures-using-turbidostat.html |  4 ++--
 experiments/control-testing.html              |  4 ++--
 .../directed-evolution-salt-tolerance.html    |  4 ++--
 experiments/introduction.html                 |  4 ++--
 experiments/low-vs-high-conc-media.html       |  4 ++--
 experiments/salt-stress-on-yeast.html         |  4 ++--
 experiments/tags.html                         |  4 ++--
 experiments/tags/caffeine.html                |  4 ++--
 experiments/tags/continuous-culture.html      |  4 ++--
 experiments/tags/control.html                 |  4 ++--
 experiments/tags/ethanol.html                 |  4 ++--
 experiments/tags/nutrient.html                |  4 ++--
 experiments/tags/salt.html                    |  4 ++--
 experiments/tags/secondary-education.html     |  4 ++--
 experiments/tags/seconday-education.html      |  4 ++--
 experiments/tags/temperature.html             |  4 ++--
 experiments/tags/turbidostat.html             |  4 ++--
 experiments/tags/university-education.html    |  4 ++--
 experiments/tags/yeast.html                   |  4 ++--
 experiments/temp-cycle.html                   |  4 ++--
 experiments/yeast-growth-by-temperature.html  |  4 ++--
 experiments/yeast-in-ethanol.html             |  4 ++--
 index.html                                    |  4 ++--
 search-index.json                             |  2 +-
 search.html                                   |  4 ++--
 user-guide/20ml-v11-hardware-setup-intro.html |  4 ++--
 user-guide/20ml-v11-optics-assembly.html      |  4 ++--
 user-guide/20ml-v11-putting-it-together.html  |  4 ++--
 user-guide/20ml-v11-rpi-hat-assembly.html     |  4 ++--
 user-guide/20ml-v11-wetware-assembly.html     |  4 ++--
 user-guide/accessing-raspberry-pi.html        |  4 ++--
 user-guide/activities.html                    |  4 ++--
 user-guide/addition-hardware-pumps.html       |  4 ++--
 user-guide/available-plugins.html             |  4 ++--
 user-guide/calibrate-od600.html               |  4 ++--
 user-guide/cli.html                           |  4 ++--
 user-guide/common-questions.html              | 22 +++++++++++--------
 user-guide/configuration.html                 |  4 ++--
 user-guide/create-cluster.html                |  4 ++--
 .../create-edit-experiment-profiles.html      |  4 ++--
 user-guide/dosing-automations.html            |  4 ++--
 user-guide/error-codes.html                   |  4 ++--
 user-guide/experiment-profiles-schema.html    |  4 ++--
 user-guide/experiment-profiles.html           |  4 ++--
 user-guide/export-data.html                   |  4 ++--
 user-guide/export-import-existing-data.html   |  4 ++--
 user-guide/external-power.html                |  4 ++--
 user-guide/getting-started.html               |  4 ++--
 user-guide/hardware-calibrations.html         |  4 ++--
 user-guide/hardware-connection-assembly.html  |  4 ++--
 user-guide/hardware-setup-intro.html          |  4 ++--
 user-guide/intro-python-scripting.html        |  4 ++--
 user-guide/intro-to-automations.html          |  4 ++--
 user-guide/introduction.html                  |  4 ++--
 user-guide/led-automations.html               |  4 ++--
 user-guide/local-access-point.html            |  4 ++--
 user-guide/manual-dosing-leds.html            |  4 ++--
 user-guide/monitor-experiment.html            |  4 ++--
 user-guide/networking.html                    |  4 ++--
 user-guide/ngrok-remote-access.html           |  4 ++--
 user-guide/od-normal-growth-rate.html         |  4 ++--
 user-guide/optics-assembly.html               |  4 ++--
 user-guide/pinch-valves.html                  |  4 ++--
 user-guide/prepare-vial-for-cultures.html     |  4 ++--
 user-guide/putting-it-together.html           |  4 ++--
 user-guide/remote-access.html                 |  4 ++--
 user-guide/rpi-hat-assembly.html              |  4 ++--
 user-guide/running-self-test.html             |  4 ++--
 user-guide/set-up-an-experiment.html          |  4 ++--
 user-guide/software-set-up.html               |  4 ++--
 user-guide/tailscale-remote-access.html       |  4 ++--
 user-guide/temperature-automations.html       |  4 ++--
 user-guide/temperature-expansion-kit.html     |  4 ++--
 user-guide/troubleshooting-hardware.html      |  4 ++--
 user-guide/troubleshooting-networks.html      |  4 ++--
 user-guide/troubleshooting-power.html         |  4 ++--
 user-guide/troubleshooting-stirring.html      |  4 ++--
 user-guide/troubleshooting-ui.html            |  4 ++--
 user-guide/updating-software.html             |  4 ++--
 user-guide/using-community-plugins.html       |  4 ++--
 user-guide/using-leds.html                    |  4 ++--
 user-guide/using-pumps.html                   |  4 ++--
 user-guide/using-stemma-qt.html               |  4 ++--
 .../v11-upgrade-building-vial-holder.html     |  4 ++--
 user-guide/v11-upgrade-hardware-setup.html    |  4 ++--
 user-guide/v11-upgrade-optics-assembly.html   |  4 ++--
 .../v11-upgrade-pioreactor-disassembly.html   |  4 ++--
 .../v11-upgrade-pioreactor-reassembly.html    |  4 ++--
 user-guide/wetware-assembly.html              |  4 ++--
 user-guide/write-own-automations.html         |  4 ++--
 127 files changed, 258 insertions(+), 254 deletions(-)
 delete mode 100644 assets/js/d5df4937.6c24518b.js
 create mode 100644 assets/js/d5df4937.e16d5b72.js
 rename assets/js/{main.2c041b40.js => main.ba545c74.js} (98%)
 rename assets/js/{main.2c041b40.js.LICENSE.txt => main.ba545c74.js.LICENSE.txt} (100%)
 rename assets/js/{runtime~main.484a9f37.js => runtime~main.df40aa19.js} (99%)

diff --git a/404.html b/404.html
index 5e02de525..86b2d08e1 100644
--- a/404.html
+++ b/404.html
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-<script src="/assets/js/runtime~main.484a9f37.js" defer="defer"></script>
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+<script src="/assets/js/runtime~main.df40aa19.js" defer="defer"></script>
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diff --git a/assets/js/d5df4937.6c24518b.js b/assets/js/d5df4937.6c24518b.js
deleted file mode 100644
index d7861e683..000000000
--- a/assets/js/d5df4937.6c24518b.js
+++ /dev/null
@@ -1 +0,0 @@
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What is a saturation point?",id:"why-does-my-optical-density-flatten-or-even-decrease-what-is-a-saturation-point",level:4},{value:"What does the effect of the scatter angle have on optical density?",id:"what-does-the-effect-of-the-scatter-angle-have-on-optical-density",level:4},{value:"Can I use my own 5mm LEDs and photodiodes for optical density?",id:"can-i-use-my-own-5mm-leds-and-photodiodes-for-optical-density",level:4},{value:"Is optical density the same as turbidity?",id:"is-optical-density-the-same-as-turbidity",level:4},{value:"Heating and Temperature control",id:"heating-and-temperature-control",level:2},{value:"Why does the Pioreactor only provide a temperature reading every few minutes?",id:"why-does-the-pioreactor-only-provide-a-temperature-reading-every-few-minutes",level:4},{value:"Why does the Pioreactor&#39;s heating keep shutting off?",id:"why-does-the-pioreactors-heating-keep-shutting-off",level:4},{value:"How does heating work on the Pioreactor?",id:"how-does-heating-work-on-the-pioreactor",level:4},{value:"Mixing and stirring in the Pioreactor",id:"mixing-and-stirring-in-the-pioreactor",level:2},{value:"How is mixing / stirring performed in the Pioreactor?",id:"how-is-mixing--stirring-performed-in-the-pioreactor",level:4},{value:"Can I use my own stir bar?",id:"can-i-use-my-own-stir-bar",level:4},{value:"The magnets rubs against the plastic screws above them, causing the stirring performance to be degraded / stop. How do I fix this?",id:"the-magnets-rubs-against-the-plastic-screws-above-them-causing-the-stirring-performance-to-be-degraded--stop-how-do-i-fix-this",level:4},{value:"How can I increase the strength of the magnetic force applied to the stirbar?",id:"how-can-i-increase-the-strength-of-the-magnetic-force-applied-to-the-stirbar",level:4},{value:"How can I improve mixing and aeration?",id:"how-can-i-improve-mixing-and-aeration",level:4},{value:"Raspberry Pi Hardware",id:"raspberry-pi-hardware",level:2},{value:"What Raspberry Pi hardware can I use? I see Raspberry Pi 1, 2, 3, 4, 5, A, B, +, Zero - it&#39;s confusing!",id:"what-raspberry-pi-hardware-can-i-use-i-see-raspberry-pi-1-2-3-4-5-a-b--zero---its-confusing",level:4},{value:"What microSD cards do you recommend?",id:"what-microsd-cards-do-you-recommend",level:4},{value:"What power supply unit (PSU) do I need?",id:"what-power-supply-unit-psu-do-i-need",level:4},{value:"Do I need any cooling for the Raspberry Pi?",id:"do-i-need-any-cooling-for-the-raspberry-pi",level:4},{value:"Could a Raspberry Pi-compatible board work, like Rock Pi 4?",id:"could-a-raspberry-pi-compatible-board-work-like-rock-pi-4",level:4},{value:"Why are the Raspberry Pi LEDs/USB/etc. turned off?",id:"why-are-the-raspberry-pi-ledsusbetc-turned-off",level:4},{value:"What is the username/password for the Raspberry Pi?",id:"what-is-the-usernamepassword-for-the-raspberry-pi",level:4},{value:"Can I use the desktop interface (with a display) with the Pioreactor?",id:"can-i-use-the-desktop-interface-with-a-display-with-the-pioreactor",level:4},{value:"Dosing",id:"dosing",level:2},{value:"Why does the Media card in the UI not update when I run a dosing command?",id:"why-does-the-media-card-in-the-ui-not-update-when-i-run-a-dosing-command",level:4},{value:"Data storage, access and recovery",id:"data-storage-access-and-recovery",level:2},{value:"Where are logs stored?",id:"where-are-logs-stored",level:4},{value:"How do I access raw experiment data?",id:"how-do-i-access-raw-experiment-data",level:4},{value:"My microSD card is corrupted - what can I do?",id:"my-microsd-card-is-corrupted---what-can-i-do",level:4},{value:"Networking",id:"networking",level:2},{value:"How do I change/edit the network the Pioreactor on?",id:"how-do-i-changeedit-the-network-the-pioreactor-on",level:4},{value:"Can I use Ethernet cable connections instead of Wifi connections?",id:"can-i-use-ethernet-cable-connections-instead-of-wifi-connections",level:4},{value:"How can I determine the Pioreactor&#39;s IP address? Or the MAC address?",id:"how-can-i-determine-the-pioreactors-ip-address-or-the-mac-address",level:4},{value:"I&#39;m using a local access point, but I&#39;d like to install plugins, update software, etc.",id:"im-using-a-local-access-point-but-id-like-to-install-plugins-update-software-etc",level:4},{value:"To install a plugin",id:"to-install-a-plugin",level:5},{value:"To upgrade the Pioreactor software",id:"to-upgrade-the-pioreactor-software",level:5},{value:"If I have multiple Pioreactor leaders on my network, what leader does <code>http://pioreactor.local</code> point to?",id:"if-i-have-multiple-pioreactor-leaders-on-my-network-what-leader-does-httppioreactorlocal-point-to",level:4}];function c(e){const t={a:"a",admonition:"admonition",blockquote:"blockquote",code:"code",em:"em",h2:"h2",h4:"h4",h5:"h5",img:"img",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,r.a)(),...e.components};return(0,o.jsxs)(o.Fragment,{children:[(0,o.jsx)(n.Z,{toc:d}),"\n",(0,o.jsx)(t.h2,{id:"pioreactor-operation",children:"Pioreactor operation"}),"\n",(0,o.jsx)(t.h4,{id:"how-can-i-restart-my-pioreactor-is-pulling-the-power-plug-out-safe",children:"How can I restart my Pioreactor? Is pulling the power plug out safe?"}),"\n",(0,o.jsx)(t.p,{children:"We suggest using the UI to reboot a Pioreactor:"}),"\n",(0,o.jsx)(t.p,{children:(0,o.jsx)(t.img,{alt:"Rebooting your pi",src:i(15713).Z+"",width:"3010",height:"1440"})}),"\n",(0,o.jsx)(t.p,{children:"Pulling the plug is usually fine, but try to avoid doing it as much as possible."}),"\n",(0,o.jsx)(t.h4,{id:"can-i-still-use-the-pioreactor-software-without-the-hardware",children:"Can I still use the Pioreactor software without the hardware?"}),"\n",(0,o.jsxs)(t.p,{children:['Yes - the Pioreactor UI and software will still work. We provide a "leader-only" image that is designed to only host a cluster, and not be an active worker. The leader-only image, ',(0,o.jsx)(t.code,{children:"pioreactor_leader.zip "}),", are available ",(0,o.jsx)(t.a,{href:"https://github.com/Pioreactor/CustoPiZer/releases",children:"here"}),"."]}),"\n",(0,o.jsx)(t.h4,{id:"why-does-the-onboard-blue-led-keep-flashing",children:"Why does the onboard blue LED keep flashing?"}),"\n",(0,o.jsxs)(t.p,{children:["There may be a problem. You can diagnose the problem by ",(0,o.jsx)(t.a,{href:"/user-guide/error-codes",children:"counting the number of flashes observed"}),"."]}),"\n",(0,o.jsx)(t.h4,{id:"what-does-the-onboard-button-do",children:"What does the onboard button do?"}),"\n",(0,o.jsx)(t.p,{children:'The button on the Pioreactor HAT sends a signal to the web UI to display a "hello" message. This is useful to know which Pioreactor in a cluster you are interacting with. The button also will republish the state of the Pioreactor.'}),"\n",(0,o.jsxs)(t.p,{children:["The button can be ",(0,o.jsx)(t.a,{href:"/developer-guide/hat-button",children:"reprogrammed"}),", too."]}),"\n",(0,o.jsx)(t.h4,{id:"how-do-i-change-the-date-or-time-on-the-pioreactor",children:"How do I change the date or time on the Pioreactor?"}),"\n",(0,o.jsxs)(t.p,{children:[(0,o.jsx)(t.a,{href:"/user-guide/accessing-raspberry-pi",children:"SSH"})," into your Pioreactor, and run:"]}),"\n",(0,o.jsx)(t.pre,{children:(0,o.jsx)(t.code,{children:'sudo date --set "Thu Nov  2 09:46:50 EDT 2023"\n\n'})}),"\n",(0,o.jsx)(t.h2,{id:"optical-density-and-leds",children:"Optical density and LEDs"}),"\n",(0,o.jsx)(t.h4,{id:"how-does-optical-density-work-on-the-pioreactor",children:"How does optical density work on the Pioreactor?"}),"\n",(0,o.jsxs)(t.p,{children:["The Pioreactor uses turbidity to measure optical density (other systems, like spectrophotometers, use attenuation). Specifically, the Pioreactor uses ",(0,o.jsx)(t.em,{children:"scattering"})," of light. The system will shine infrared light into the culture, and measure the amount of light that is scattered off cells. The scattering has a good linear range (see below for more), and higher saturation point than attenuation for cultures of 20ml volume. If you have an instrument that measures OD600 or some other measurement of optical density, and you wish to calibrate to that, the Pioreactor has a routine to perform a calibration and record in the instruments units. See ",(0,o.jsx)(t.a,{href:"/user-guide/calibrate-od600",children:"docs here"}),"."]}),"\n",(0,o.jsx)(t.h4,{id:"what-are-the-units-of-pioreactors-optical-density",children:"What are the units of Pioreactor's optical density"}),"\n",(0,o.jsxs)(t.p,{children:["The ",(0,o.jsx)(t.em,{children:"uncalibrated"})," optical densities reported the UI and recorded in the database are have an arbitrary unit, and are per Pioreactor (so they can't be compared to each other). However, the ",(0,o.jsx)(t.em,{children:"normalized optical density"}),", generated after starting the activity ",(0,o.jsx)(t.strong,{children:"Growth rate"})," in the UI, is comparable, which is why we suggest using it for inferences (especially if you haven't calibrated to some OD600 machine). Read more about our ",(0,o.jsx)(t.a,{href:"https://docs.pioreactor.com/user-guide/od-normal-growth-rate",children:"optical density measurements here"}),"."]}),"\n",(0,o.jsx)(t.h4,{id:"how-can-i-change-the-frequency-rate-of-optical-density-measurements",children:"How can I change the frequency (rate) of optical density measurements?"}),"\n",(0,o.jsxs)(t.p,{children:["In the configuration, you can edit the parameter ",(0,o.jsx)(t.code,{children:"samples_per_second"}),' to adjust the how often the Pioreactor takes an optical density snapshot. Note that this parameter is the inverse of "duration between readings". For example, if you wish to record a measurement every 60 seconds, then ',(0,o.jsx)(t.code,{children:"samples_per_second=0.01666667"})," (which is 1/60)."]}),"\n",(0,o.jsx)(t.h4,{id:"why-does-the-intensity-for-led-a-turn-on--off-during-an-experiment",children:"Why does the intensity for LED A turn on & off during an experiment?"}),"\n",(0,o.jsx)(t.p,{children:"You may have noticed that the LED labelled A turns on & off every 5 seconds or so. This is (normally) the channel for the infrared (IR) LED, which is used in the optical density measurements. We only take reading every 5 seconds (the default), we don't need the IR LED on all the time. The Pioreactor will only turn on LED when needed. This preserves the strength of the LED over longer periods of time. For more advanced use cases, it also allows other optical measurements to take place without the IR LED interfering with them."}),"\n",(0,o.jsx)(t.h4,{id:"why-does-my-optical-density-flatten-or-even-decrease-what-is-a-saturation-point",children:"Why does my optical density flatten, or even decrease? What is a saturation point?"}),"\n",(0,o.jsxs)(t.p,{children:["For some experiments, especially when using a scatter angle of 135\xb0, you may notice that the optical density starts to flatten, and even decrease, ",(0,o.jsx)(t.em,{children:"when you know the culture should still be growing"}),". This is not a property of the culture, but occurs because the culture is getting too dense, and light is now being interrupted before it reaches the photodiodes. Prior to this point, called the saturation point, the relationship between culture density and optical density is nearly linear. But after this point, there is a flattening, even negative, relationship between culture density and optical density. For all analysis, we recommend only studying when the culture is in the linear regime. You can mitigate the problem by choosing a smaller scatter angle (like 90\xb0 or 45\xb0), diluting the culture using an automation like the turbidostat, or using a lower concentration of nutrient(s) in the media. Read more about Pioreactor's optical system ",(0,o.jsx)(t.a,{href:"https://pioreactor.com/blogs/pioreactor/estimating-growth-rates-with-kalman-filters",children:"here"}),"."]}),"\n",(0,o.jsx)(t.h4,{id:"what-does-the-effect-of-the-scatter-angle-have-on-optical-density",children:"What does the effect of the scatter angle have on optical density?"}),"\n",(0,o.jsxs)(t.p,{children:["The scatter angle is the angle between the IR LED and a photodiode. This angle can be 45\xb0, 90\xb0, or 135\xb0  (although 180\xb0 is possible, we don't consider it here). What is there to consider when choosing an angle. In general, the trend is shorter angles => less sensitive at low densities, but higher saturation point. By default, we suggest 45\xb0 as a good trade off between sensitivity and saturation. You can mix angles, and the Pioreactor's internal algorithm will still combine them into a single growth rate. Read more about Pioreactor's optical system ",(0,o.jsx)(t.a,{href:"https://pioreactor.com/blogs/pioreactor/estimating-growth-rates-with-kalman-filters",children:"here"}),"."]}),"\n",(0,o.jsx)(t.h4,{id:"can-i-use-my-own-5mm-leds-and-photodiodes-for-optical-density",children:"Can I use my own 5mm LEDs and photodiodes for optical density?"}),"\n",(0,o.jsx)(t.p,{children:"Of course! The only two requirements are that the spectrum of the LED overlaps with the spectrum of the photodiode, and that the LED light won't be absorbed by media/culture, nor damage the media/culture. Thus, the often-used 600nm light source works in the Pioreactor. None of our internal algorithms or analytics are dependent on the wavelength of light chosen."}),"\n",(0,o.jsx)(t.p,{children:"When you are using additional LEDs outside of the optical density LED & photodiode pair, you may worry that your additional LEDs will interfere with the optical density measurement. This won't happen, as we turn off all non-optical density LEDs before taking an optical density measurement."}),"\n",(0,o.jsx)(t.h4,{id:"is-optical-density-the-same-as-turbidity",children:"Is optical density the same as turbidity?"}),"\n",(0,o.jsx)(t.p,{children:"Turbidity is a measure of optical density, like how decibels are a measurement of sound intensity. Likewise, absorbance is a measure of optical density."}),"\n",(0,o.jsx)(t.h2,{id:"heating-and-temperature-control",children:"Heating and Temperature control"}),"\n",(0,o.jsx)(t.h4,{id:"why-does-the-pioreactor-only-provide-a-temperature-reading-every-few-minutes",children:"Why does the Pioreactor only provide a temperature reading every few minutes?"}),"\n",(0,o.jsxs)(t.p,{children:["We made a design choice early on to make preparation as error-free as possible. This involved thinking about sensors being ",(0,o.jsx)(t.em,{children:"in situ"})," (in place), versus the sensors being on the outside of the vial. The temperature sensor in the Pioreactor is outside the vial, which means less chance of contamination, but there's a tradeoff (as you could guess): we have to rely on an estimation algorithm that requires a gew minutes to gather data on. We think this is a fair trade-off, as high frequency temperature readings are not that important in an experiment that lasts 12 hours or more."]}),"\n",(0,o.jsx)(t.h4,{id:"why-does-the-pioreactors-heating-keep-shutting-off",children:"Why does the Pioreactor's heating keep shutting off?"}),"\n",(0,o.jsx)(t.p,{children:"If you find that the Pioreactor's heating is shutting off, typically with an accompanying error and flashing blue light, then likely the temperature is becoming too high for safe handling. We restrict the onboard PCB's temperature to be no higher than 63\u2103. Temperature's higher than this can deform the plastic, and possibly cause burns. If the Pioreactor detects a temperature near or above this value, the software will shut off the heating, and possible the entire Raspberry Pi in extreme cases."}),"\n",(0,o.jsxs)(t.p,{children:["To avoid this occurring, we suggest not setting the target temperature too high - not more than 20\u2103 above ambient temperature. Also, reducing the ",(0,o.jsx)(t.code,{children:"Kd"})," parameter in ",(0,o.jsx)(t.code,{children:"[temperature_automation.stable]"})," section in the config.ini would help."]}),"\n",(0,o.jsx)(t.h4,{id:"how-does-heating-work-on-the-pioreactor",children:"How does heating work on the Pioreactor?"}),"\n",(0,o.jsx)(t.p,{children:"The Pioreactor has an onboard PCB, called the heating PCB, that sits below the glass vial. On the PCB are resistors that convert current from PWM outputs into heat. By varying the duty cycle of the PWM, we vary the amount of heat converted."}),"\n",(0,o.jsx)(t.h2,{id:"mixing-and-stirring-in-the-pioreactor",children:"Mixing and stirring in the Pioreactor"}),"\n",(0,o.jsx)(t.h4,{id:"how-is-mixing--stirring-performed-in-the-pioreactor",children:"How is mixing / stirring performed in the Pioreactor?"}),"\n",(0,o.jsx)(t.p,{children:"Stirring is performed with a micro stir bar inside the vial, controlled by a pair of magnets spinning below the vial. The rotation speed, RPM, of the stir bar can be controlled using the Pioreactor software. This stirring is also how aeration is done."}),"\n",(0,o.jsx)(t.h4,{id:"can-i-use-my-own-stir-bar",children:"Can I use my own stir bar?"}),"\n",(0,o.jsx)(t.p,{children:"Of course! The maximum length of a stir bar is 20mm. Keep the height low as to not interfere with the optics. (The provided stir bar is 3mm high). Try using other stir bar shapes / designs!"}),"\n",(0,o.jsx)(t.h4,{id:"the-magnets-rubs-against-the-plastic-screws-above-them-causing-the-stirring-performance-to-be-degraded--stop-how-do-i-fix-this",children:"The magnets rubs against the plastic screws above them, causing the stirring performance to be degraded / stop. How do I fix this?"}),"\n",(0,o.jsx)(t.p,{children:"Dis-attach the top faceplate. Under the faceplate, slightly unscrew each of the four metal screws. This will add more space between the magnets and the plastic screws."}),"\n",(0,o.jsx)(t.h4,{id:"how-can-i-increase-the-strength-of-the-magnetic-force-applied-to-the-stirbar",children:"How can I increase the strength of the magnetic force applied to the stirbar?"}),"\n",(0,o.jsxs)(t.p,{children:[(0,o.jsx)(t.strong,{children:"For Pioreactor 20ml v1.0"}),": Try to reduce the distance between the stirring magnets and the stir bar by carefully raising the stirring fan a small amount. Going even further, you can remove the 4mm screws in the bottom of the vial holder (but find another way to secure the PCB), thereby be able to bring the magnets even closer."]}),"\n",(0,o.jsx)(t.h4,{id:"how-can-i-improve-mixing-and-aeration",children:"How can I improve mixing and aeration?"}),"\n",(0,o.jsx)(t.p,{children:"If the standard mixing and aeration with the stir bar is not enough for your application, you can do a few things, (in increasing order of complication, not necessarily effectiveness):"}),"\n",(0,o.jsxs)(t.ol,{children:["\n",(0,o.jsx)(t.li,{children:"If the tubes in the cap are submerged during operation, this is reduce the transfer of air. Pull them up from the top of the cap to keep them out of the liquid. Even more effective: shorten them with scissors."}),"\n",(0,o.jsx)(t.li,{children:"Increase the RPM of the stirring. This will increase the surface area exposed to the air. Be warned though: too high of an RPM will cause either a large enough vortex to interfere with the optical systems, or will causing the stir bar to fall out of sync."}),"\n",(0,o.jsxs)(t.li,{children:["Add a ",(0,o.jsx)(t.a,{href:"https://www.printables.com/model/575292-baffle-for-pioreactor-vial-cap-a/files",children:"baffle"})," to the vial cap. A simple cylinder that rests into the liquid causes disturbance in the rotating liquid that both mixing and aeration are significantly improved. A tube can be removed from the cap, and a autoclavable rod can be inserted such that it enters the media, but won't interfere with the optics."]}),"\n",(0,o.jsx)(t.li,{children:"Adding external aeration to your Pioreactor. In the simplest case, using an air pump."}),"\n"]}),"\n",(0,o.jsx)(t.h2,{id:"raspberry-pi-hardware",children:"Raspberry Pi Hardware"}),"\n",(0,o.jsx)(t.h4,{id:"what-raspberry-pi-hardware-can-i-use-i-see-raspberry-pi-1-2-3-4-5-a-b--zero---its-confusing",children:"What Raspberry Pi hardware can I use? I see Raspberry Pi 1, 2, 3, 4, 5, A, B, +, Zero - it's confusing!"}),"\n",(0,o.jsx)(t.p,{children:"We've designed the hardware and software to be compatible with any Raspberry Pi that has onboard Wifi and a 40 pin header. That includes (at the time of writing):"}),"\n",(0,o.jsxs)(t.ul,{children:["\n",(0,o.jsx)(t.li,{children:"Raspberry Pi 3 Model B & B+"}),"\n",(0,o.jsx)(t.li,{children:"Raspberry Pi 3 Model A+"}),"\n",(0,o.jsx)(t.li,{children:"Raspberry Pi 4 Model B \xb3"}),"\n",(0,o.jsx)(t.li,{children:"Raspberry Pi 5 Model B"}),"\n",(0,o.jsx)(t.li,{children:"Raspberry Pi Zero W (with header) \xb9"}),"\n",(0,o.jsx)(t.li,{children:"Raspberry Pi Zero 2 W (with header)"}),"\n",(0,o.jsx)(t.li,{children:"Raspberry Pi 400 \xb2"}),"\n"]}),"\n",(0,o.jsxs)(t.p,{children:["Although you can use any above, ",(0,o.jsx)(t.strong,{children:"we like the Raspberry Pi 3 Model A+, and Raspberry Pi Zero 2 W"})," because of their low power consumption, slim build, and low price. Both have the necessary CPU power and memory for the Pioreactor workload, and are generally easy to source. However, they don't have ethernet connections! So talk to your team about if you need to use ethernet or wifi. If you need ethernet, we like the model 3B."]}),"\n",(0,o.jsxs)(t.p,{children:["\xb9 ",(0,o.jsx)(t.em,{children:"Raspberry Pi Zero W"})," is on the list above, and is very low cost compared to the others. They can absolutely be used for Pioreactors ",(0,o.jsx)(t.em,{children:"as workers"})," - we don't recommend them to be your ",(0,o.jsx)(t.em,{children:"leader"})," (note sure what these terms mean? Here's an introduction to ",(0,o.jsx)(t.a,{href:"/user-guide/create-cluster",children:"leader and workers"}),"). As workers, Raspberry Pi Zero W perform just fine, but will respond slower to commands. Note that this does not include the Raspberry Pi Zero ",(0,o.jsx)(t.em,{children:"2"})," W model, which is fine for all roles."]}),"\n",(0,o.jsxs)(t.p,{children:["\xb2 The Raspberry Pi 400 has its 40 pin header exposed in a different orientation, so your Pioreactor won't be able to sit on top like for other RPi versions. Take a ",(0,o.jsx)(t.a,{href:"https://forum.pioreactor.com/t/using-a-raspberry-pi-400/113/8",children:"look at this forum post"})," to see how another user used the Raspberry Pi 400 with their Pioreactor."]}),"\n",(0,o.jsx)(t.p,{children:"\xb3 Note that you don't need a lot of RAM for the Pioreactor, so we recommend getting the lower RAM option RPi 4s (1GB or 2GB) to save some money. However, 4GB and 8GB are fine, too."}),"\n",(0,o.jsx)(t.h4,{id:"what-microsd-cards-do-you-recommend",children:"What microSD cards do you recommend?"}),"\n",(0,o.jsx)(t.p,{children:"At least 16GB. We like 16GB or 32GB SanDisk Edge or Samsung microSD cards for their longevity, but any good quality, class 10 SD card will do."}),"\n",(0,o.jsx)(t.h4,{id:"what-power-supply-unit-psu-do-i-need",children:"What power supply unit (PSU) do I need?"}),"\n",(0,o.jsx)(t.p,{children:"If you look at the power rating, it should be about 5 V and at least 2.25 A, or above 12 W. We really like the official Raspberry Pi PSUs, available at most places you can purchase Raspberry Pis."}),"\n",(0,o.jsx)(t.h4,{id:"do-i-need-any-cooling-for-the-raspberry-pi",children:"Do I need any cooling for the Raspberry Pi?"}),"\n",(0,o.jsx)(t.p,{children:"Nope, you shouldn't, unless you are connecting an external monitor. However, extra heat sinks are never a bad idea!"}),"\n",(0,o.jsx)(t.h4,{id:"could-a-raspberry-pi-compatible-board-work-like-rock-pi-4",children:"Could a Raspberry Pi-compatible board work, like Rock Pi 4?"}),"\n",(0,o.jsx)(t.p,{children:"Maybe? We haven't tested them, but so long as i) the GPIO pins are identical, and ii) Raspberry Pi OS can be installed, it should work."}),"\n",(0,o.jsx)(t.h4,{id:"why-are-the-raspberry-pi-ledsusbetc-turned-off",children:"Why are the Raspberry Pi LEDs/USB/etc. turned off?"}),"\n",(0,o.jsxs)(t.p,{children:['We turn off the "activity" LED (usually the green one) to save some power for the Pioreactor\'s peripherals. You can turn these back on by editing the ',(0,o.jsx)(t.code,{children:"/boot/config.txt"})," file on the RPi."]}),"\n",(0,o.jsx)(t.h4,{id:"what-is-the-usernamepassword-for-the-raspberry-pi",children:"What is the username/password for the Raspberry Pi?"}),"\n",(0,o.jsxs)(t.p,{children:["When setting up your Raspberry Pi with the Pioreactor software, you would have chosen a password. Try the recommended username: ",(0,o.jsx)(t.code,{children:"pioreactor"}),", and password: ",(0,o.jsx)(t.code,{children:"raspberry"}),"."]}),"\n",(0,o.jsx)(t.h4,{id:"can-i-use-the-desktop-interface-with-a-display-with-the-pioreactor",children:"Can I use the desktop interface (with a display) with the Pioreactor?"}),"\n",(0,o.jsx)(t.p,{children:'Not currently. Our software is based of the "headless" operating-system, which doesn\'t have display output.'}),"\n",(0,o.jsx)(t.h2,{id:"dosing",children:"Dosing"}),"\n",(0,o.jsx)(t.h4,{id:"why-does-the-media-card-in-the-ui-not-update-when-i-run-a-dosing-command",children:"Why does the Media card in the UI not update when I run a dosing command?"}),"\n",(0,o.jsxs)(t.p,{children:["The Media card will ",(0,o.jsx)(t.em,{children:"only"})," update when an ",(0,o.jsx)(t.a,{href:"/user-guide/dosing-automations",children:"Dosing Automation"})," is active (even the ",(0,o.jsx)(t.code,{children:"Silent"})," automation). Why is it done this way? Often, you don't want volumes to be recorded there: during cleaning, during testing, etc. Often you only want volumes associated with the experiment to be there."]}),"\n",(0,o.jsx)(t.admonition,{type:"note",children:(0,o.jsxs)(t.p,{children:['All dosing events ares recorded to the database however, and with a record of when the event occurred, and source of action. This data is available in the "Export data" web page, under ',(0,o.jsx)(t.code,{children:"Dosing event log"}),"."]})}),"\n",(0,o.jsx)(t.h2,{id:"data-storage-access-and-recovery",children:"Data storage, access and recovery"}),"\n",(0,o.jsxs)(t.blockquote,{children:["\n",(0,o.jsx)(t.p,{children:"\ud83d\udca1 For any important project, we suggest manually exporting or backing up critical data multiple different places. This doesn't just apply to using the Pioreactor, but is good advice in general."}),"\n"]}),"\n",(0,o.jsx)(t.h4,{id:"where-are-logs-stored",children:"Where are logs stored?"}),"\n",(0,o.jsxs)(t.p,{children:["For the logs that you see in the Log Table in the ",(0,o.jsx)(t.em,{children:"Experiment Overview"})," page, these can be download on the ",(0,o.jsx)(t.em,{children:"Download experiment data"})," page in the Pioreactor web interface. Other logs are also available, including dosing event and algorithm change-logs."]}),"\n",(0,o.jsxs)(t.p,{children:["More granular logs per Pioreactor are available in ",(0,o.jsx)(t.code,{children:"/var/log/pioreactor.log"})," on the Raspberry Pis."]}),"\n",(0,o.jsx)(t.h4,{id:"how-do-i-access-raw-experiment-data",children:"How do I access raw experiment data?"}),"\n",(0,o.jsxs)(t.ol,{children:["\n",(0,o.jsxs)(t.li,{children:["The ",(0,o.jsx)(t.em,{children:"Download experiment data"})," page in the Pioreactor web interface provides CSV exports of common datasets from a pre-selected experiment."]}),"\n",(0,o.jsxs)(t.li,{children:["All data eventually lands in a SQLite3 database on the leader Pioreactor, by default located in ",(0,o.jsx)(t.code,{children:"/home/pioreactor/.pioreactor/storage/pioreactor.sqlite"}),". This can be download using a tool like ",(0,o.jsx)(t.code,{children:"scp"}),"."]}),"\n",(0,o.jsxs)(t.li,{children:["To access the SQLite3 database from the command line, try ",(0,o.jsx)(t.code,{children:"pio db"}),"."]}),"\n"]}),"\n",(0,o.jsx)(t.h4,{id:"my-microsd-card-is-corrupted---what-can-i-do",children:"My microSD card is corrupted - what can I do?"}),"\n",(0,o.jsx)(t.p,{children:"Unfortunately, the microSD card becoming corrupted or damaged is an infrequent but possible risk with using Raspberry Pis."}),"\n",(0,o.jsxs)(t.ul,{children:["\n",(0,o.jsxs)(t.li,{children:["\n",(0,o.jsxs)(t.p,{children:["If the microSD card was inside a non-leader Pioreactor, it's best to try to reformat the microSD card and start fresh (i.e. ",(0,o.jsx)(t.a,{href:"/user-guide/software-set-up#adding-workers-to-your-cluster",children:"reinstall the Pioreactor software and reintroduce it to the cluster"}),"). This is usually okay as no critical data is stored locally in workers, only log files and hardware calibrations will be lost."]}),"\n"]}),"\n",(0,o.jsxs)(t.li,{children:["\n",(0,o.jsxs)(t.p,{children:["If the microSD was inside the leader Raspberry Pi, this is a bigger problem. Likely any running experiment will have to be restarted. Fortunately, if you have more than one Pioreactor in your cluster, then the leader's SQLite database has been periodically backing itself up to other Pioreactors in the cluster every few days. Using the command line, check other Pioreactors' ",(0,o.jsx)(t.code,{children:"/home/pioreactor/.pioreactor/storage"})," directory for the ",(0,o.jsx)(t.em,{children:"latest"})," backup named ",(0,o.jsx)(t.code,{children:"pioreactor.sqlite.backup"})," (should be from within the past few days hours). You can use this database to restart a new leader."]}),"\n"]}),"\n"]}),"\n",(0,o.jsx)(t.h2,{id:"networking",children:"Networking"}),"\n",(0,o.jsx)(t.h4,{id:"how-do-i-changeedit-the-network-the-pioreactor-on",children:"How do I change/edit the network the Pioreactor on?"}),"\n",(0,o.jsx)(t.p,{children:"With modern Raspberry Pis,"}),"\n",(0,o.jsx)(t.h4,{id:"can-i-use-ethernet-cable-connections-instead-of-wifi-connections",children:"Can I use Ethernet cable connections instead of Wifi connections?"}),"\n",(0,o.jsx)(t.p,{children:"Yes, so long as the Raspberry Pi's are connected to the same network and discoverable, this should work. Even mixing Ethernet and Wifi is fine."}),"\n",(0,o.jsx)(t.h4,{id:"how-can-i-determine-the-pioreactors-ip-address-or-the-mac-address",children:"How can I determine the Pioreactor's IP address? Or the MAC address?"}),"\n",(0,o.jsx)(t.p,{children:"Depending on your access to the Pioreactor, there are a few ways:"}),"\n",(0,o.jsxs)(t.ol,{children:["\n",(0,o.jsx)(t.li,{children:"In the UI's Inventory page."}),"\n",(0,o.jsxs)(t.li,{children:["If you can't access the Pioreactor's UI or SSH in: the software will write the IP address to the ",(0,o.jsx)(t.code,{children:"/boot"})," directory on the SD card. After the Pioreactor's blue LED has blinked, you can unplug the Pioreactor, remove the SD card, and place the SD card in another computer. Navigate to the card, and in the directory you should see a file called ",(0,o.jsx)(t.code,{children:"ip"}),". Open this file, and the IP address should be there. Place the SD card back into the Pioreactor and plug it back in."]}),"\n"]}),"\n",(0,o.jsx)(t.h4,{id:"im-using-a-local-access-point-but-id-like-to-install-plugins-update-software-etc",children:"I'm using a local access point, but I'd like to install plugins, update software, etc."}),"\n",(0,o.jsx)(t.h5,{id:"to-install-a-plugin",children:"To install a plugin"}),"\n",(0,o.jsxs)(t.p,{children:["On a computer that is connected to the internet, download the ",(0,o.jsx)(t.code,{children:".whl"})," file from the plugins webpage on PyPI. Then, connect that computer to your Pioreactor's local access point's network. To each Pioreactor you wish to install the plugin on, transfer the ",(0,o.jsx)(t.code,{children:".whl"})," file to the Pioreactor (using SFTP or FTP). Then, run ",(0,o.jsx)(t.code,{children:"pio plugins install <plugin-name> <path/to/local/.whl>"})]}),"\n",(0,o.jsx)(t.h5,{id:"to-upgrade-the-pioreactor-software",children:"To upgrade the Pioreactor software"}),"\n",(0,o.jsxs)(t.p,{children:["See steps ",(0,o.jsx)(t.a,{href:"/user-guide/updating-software#method-2-update-using-a-zip-file-and-the-ui",children:"here"}),"."]}),"\n",(0,o.jsxs)(t.h4,{id:"if-i-have-multiple-pioreactor-leaders-on-my-network-what-leader-does-httppioreactorlocal-point-to",children:["If I have multiple Pioreactor leaders on my network, what leader does ",(0,o.jsx)(t.code,{children:"http://pioreactor.local"})," point to?"]}),"\n",(0,o.jsxs)(t.p,{children:["If there are multiple leaders on the same network, then each will override the other's ",(0,o.jsx)(t.code,{children:"pioreactor.local"})," alias, and the alias will be unreliable. You can either access the leaders by their hostnames: ",(0,o.jsx)(t.code,{children:"http://<leader hostname>.local"}),", or you can change the alias in the config.ini, too, by editing ",(0,o.jsx)(t.code,{children:"domain_alias"})," under section ",(0,o.jsx)(t.code,{children:"[ui]"})," (changing this requires a restart of the machine)."]})]})}function u(e={}){const{wrapper:t}={...(0,r.a)(),...e.components};return t?(0,o.jsx)(t,{...e,children:(0,o.jsx)(c,{...e})}):c(e)}},3901:(e,t,i)=>{i.d(t,{Z:()=>a});i(67294);var o=i(93743);const r={tableOfContentsInline:"tableOfContentsInline_prmo"};var n=i(85893);function a(e){let{toc:t,minHeadingLevel:i,maxHeadingLevel:a}=e;return(0,n.jsx)("div",{className:r.tableOfContentsInline,children:(0,n.jsx)(o.Z,{toc:t,minHeadingLevel:i,maxHeadingLevel:a,className:"table-of-contents",linkClassName:null})})}},93743:(e,t,i)=>{i.d(t,{Z:()=>g});var o=i(67294),r=i(86668);function n(e){const t=e.map((e=>({...e,parentIndex:-1,children:[]}))),i=Array(7).fill(-1);t.forEach(((e,t)=>{const o=i.slice(2,e.level);e.parentIndex=Math.max(...o),i[e.level]=t}));const o=[];return t.forEach((e=>{const{parentIndex:i,...r}=e;i>=0?t[i].children.push(r):o.push(r)})),o}function a(e){let{toc:t,minHeadingLevel:i,maxHeadingLevel:o}=e;return t.flatMap((e=>{const t=a({toc:e.children,minHeadingLevel:i,maxHeadingLevel:o});return function(e){return e.level>=i&&e.level<=o}(e)?[{...e,children:t}]:t}))}function s(e){const t=e.getBoundingClientRect();return t.top===t.bottom?s(e.parentNode):t}function h(e,t){let{anchorTopOffset:i}=t;const o=e.find((e=>s(e).top>=i));if(o){return function(e){return e.top>0&&e.bottom<window.innerHeight/2}(s(o))?o:e[e.indexOf(o)-1]??null}return e[e.length-1]??null}function l(){const e=(0,o.useRef)(0),{navbar:{hideOnScroll:t}}=(0,r.L)();return(0,o.useEffect)((()=>{e.current=t?0:document.querySelector(".navbar").clientHeight}),[t]),e}function d(e){const t=(0,o.useRef)(void 0),i=l();(0,o.useEffect)((()=>{if(!e)return()=>{};const{linkClassName:o,linkActiveClassName:r,minHeadingLevel:n,maxHeadingLevel:a}=e;function s(){const e=function(e){return Array.from(document.getElementsByClassName(e))}(o),s=function(e){let{minHeadingLevel:t,maxHeadingLevel:i}=e;const o=[];for(let r=t;r<=i;r+=1)o.push(`h${r}.anchor`);return Array.from(document.querySelectorAll(o.join()))}({minHeadingLevel:n,maxHeadingLevel:a}),l=h(s,{anchorTopOffset:i.current}),d=e.find((e=>l&&l.id===function(e){return decodeURIComponent(e.href.substring(e.href.indexOf("#")+1))}(e)));e.forEach((e=>{!function(e,i){i?(t.current&&t.current!==e&&t.current.classList.remove(r),e.classList.add(r),t.current=e):e.classList.remove(r)}(e,e===d)}))}return document.addEventListener("scroll",s),document.addEventListener("resize",s),s(),()=>{document.removeEventListener("scroll",s),document.removeEventListener("resize",s)}}),[e,i])}var c=i(39960),u=i(85893);function p(e){let{toc:t,className:i,linkClassName:o,isChild:r}=e;return t.length?(0,u.jsx)("ul",{className:r?void 0:i,children:t.map((e=>(0,u.jsxs)("li",{children:[(0,u.jsx)(c.Z,{to:`#${e.id}`,className:o??void 0,dangerouslySetInnerHTML:{__html:e.value}}),(0,u.jsx)(p,{isChild:!0,toc:e.children,className:i,linkClassName:o})]},e.id)))}):null}const m=o.memo(p);function g(e){let{toc:t,className:i="table-of-contents table-of-contents__left-border",linkClassName:s="table-of-contents__link",linkActiveClassName:h,minHeadingLevel:l,maxHeadingLevel:c,...p}=e;const g=(0,r.L)(),f=l??g.tableOfContents.minHeadingLevel,w=c??g.tableOfContents.maxHeadingLevel,y=function(e){let{toc:t,minHeadingLevel:i,maxHeadingLevel:r}=e;return(0,o.useMemo)((()=>a({toc:n(t),minHeadingLevel:i,maxHeadingLevel:r})),[t,i,r])}({toc:t,minHeadingLevel:f,maxHeadingLevel:w});return d((0,o.useMemo)((()=>{if(s&&h)return{linkClassName:s,linkActiveClassName:h,minHeadingLevel:f,maxHeadingLevel:w}}),[s,h,f,w])),(0,u.jsx)(m,{toc:y,className:i,linkClassName:s,...p})}},15713:(e,t,i)=>{i.d(t,{Z:()=>o});const o=i.p+"assets/images/reboot-76282e6704cc04bdd5fb187efb1986d1.png"},11151:(e,t,i)=>{i.d(t,{Z:()=>s,a:()=>a});var o=i(67294);const r={},n=o.createContext(r);function a(e){const t=o.useContext(n);return o.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function s(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(r):e.components||r:a(e.components),o.createElement(n.Provider,{value:t},e.children)}}}]);
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@@ -0,0 +1 @@
+"use strict";(self.webpackChunkpioreactor=self.webpackChunkpioreactor||[]).push([[1179],{1017:(e,t,i)=>{i.r(t),i.d(t,{assets:()=>l,contentTitle:()=>s,default:()=>u,frontMatter:()=>a,metadata:()=>h,toc:()=>d});var r=i(85893),o=i(11151),n=i(3901);const a={title:"Common questions",slug:"/common-questions"},s=void 0,h={id:"common-questions",title:"Common questions",description:"Pioreactor operation",source:"@site/user-guide/99-common-questions.mdx",sourceDirName:".",slug:"/common-questions",permalink:"/user-guide/common-questions",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:99,frontMatter:{title:"Common questions",slug:"/common-questions"},sidebar:"tutorialSidebar",previous:{title:"User interface",permalink:"/user-guide/troubleshooting-ui"}},l={},d=[{value:"Pioreactor operation",id:"pioreactor-operation",level:2},{value:"How can I restart my Pioreactor? Is pulling the power plug out safe?",id:"how-can-i-restart-my-pioreactor-is-pulling-the-power-plug-out-safe",level:4},{value:"Can I still use the Pioreactor software without the hardware?",id:"can-i-still-use-the-pioreactor-software-without-the-hardware",level:4},{value:"Why does the onboard blue LED keep flashing?",id:"why-does-the-onboard-blue-led-keep-flashing",level:4},{value:"What does the onboard button do?",id:"what-does-the-onboard-button-do",level:4},{value:"How do I change the date or time on the Pioreactor?",id:"how-do-i-change-the-date-or-time-on-the-pioreactor",level:4},{value:"Optical density and LEDs",id:"optical-density-and-leds",level:2},{value:"How does optical density work on the Pioreactor?",id:"how-does-optical-density-work-on-the-pioreactor",level:4},{value:"What are the units of Pioreactor&#39;s optical density",id:"what-are-the-units-of-pioreactors-optical-density",level:4},{value:"How can I change the frequency (rate) of optical density measurements?",id:"how-can-i-change-the-frequency-rate-of-optical-density-measurements",level:4},{value:"Why does the intensity for LED A turn on &amp; off during an experiment?",id:"why-does-the-intensity-for-led-a-turn-on--off-during-an-experiment",level:4},{value:"Why does my optical density flatten, or even decrease? What is a saturation point?",id:"why-does-my-optical-density-flatten-or-even-decrease-what-is-a-saturation-point",level:4},{value:"What does the effect of the scatter angle have on optical density?",id:"what-does-the-effect-of-the-scatter-angle-have-on-optical-density",level:4},{value:"Can I use my own 5mm LEDs and photodiodes for optical density?",id:"can-i-use-my-own-5mm-leds-and-photodiodes-for-optical-density",level:4},{value:"Is optical density the same as turbidity?",id:"is-optical-density-the-same-as-turbidity",level:4},{value:"Heating and Temperature control",id:"heating-and-temperature-control",level:2},{value:"Why does the Pioreactor only provide a temperature reading every few minutes?",id:"why-does-the-pioreactor-only-provide-a-temperature-reading-every-few-minutes",level:4},{value:"Why does the Pioreactor&#39;s heating keep shutting off?",id:"why-does-the-pioreactors-heating-keep-shutting-off",level:4},{value:"How does heating work on the Pioreactor?",id:"how-does-heating-work-on-the-pioreactor",level:4},{value:"Mixing and stirring in the Pioreactor",id:"mixing-and-stirring-in-the-pioreactor",level:2},{value:"How is mixing / stirring performed in the Pioreactor?",id:"how-is-mixing--stirring-performed-in-the-pioreactor",level:4},{value:"Can I use my own stir bar?",id:"can-i-use-my-own-stir-bar",level:4},{value:"The magnets rubs against the plastic screws above them, causing the stirring performance to be degraded / stop. How do I fix this?",id:"the-magnets-rubs-against-the-plastic-screws-above-them-causing-the-stirring-performance-to-be-degraded--stop-how-do-i-fix-this",level:4},{value:"How can I increase the strength of the magnetic force applied to the stirbar?",id:"how-can-i-increase-the-strength-of-the-magnetic-force-applied-to-the-stirbar",level:4},{value:"How can I improve mixing and aeration?",id:"how-can-i-improve-mixing-and-aeration",level:4},{value:"Can I plot the RPM in a chart in the UI?",id:"can-i-plot-the-rpm-in-a-chart-in-the-ui",level:3},{value:"Raspberry Pi Hardware",id:"raspberry-pi-hardware",level:2},{value:"What Raspberry Pi hardware can I use? I see Raspberry Pi 1, 2, 3, 4, 5, A, B, +, Zero - it&#39;s confusing!",id:"what-raspberry-pi-hardware-can-i-use-i-see-raspberry-pi-1-2-3-4-5-a-b--zero---its-confusing",level:4},{value:"What microSD cards do you recommend?",id:"what-microsd-cards-do-you-recommend",level:4},{value:"What power supply unit (PSU) do I need?",id:"what-power-supply-unit-psu-do-i-need",level:4},{value:"Do I need any cooling for the Raspberry Pi?",id:"do-i-need-any-cooling-for-the-raspberry-pi",level:4},{value:"Could a Raspberry Pi-compatible board work, like Rock Pi 4?",id:"could-a-raspberry-pi-compatible-board-work-like-rock-pi-4",level:4},{value:"Why are the Raspberry Pi LEDs/USB/etc. turned off?",id:"why-are-the-raspberry-pi-ledsusbetc-turned-off",level:4},{value:"What is the username/password for the Raspberry Pi?",id:"what-is-the-usernamepassword-for-the-raspberry-pi",level:4},{value:"Can I use the desktop interface (with a display) with the Pioreactor?",id:"can-i-use-the-desktop-interface-with-a-display-with-the-pioreactor",level:4},{value:"Dosing",id:"dosing",level:2},{value:"Why does the Media card in the UI not update when I run a dosing command?",id:"why-does-the-media-card-in-the-ui-not-update-when-i-run-a-dosing-command",level:4},{value:"Data storage, access and recovery",id:"data-storage-access-and-recovery",level:2},{value:"Where are logs stored?",id:"where-are-logs-stored",level:4},{value:"How do I access raw experiment data?",id:"how-do-i-access-raw-experiment-data",level:4},{value:"My microSD card is corrupted - what can I do?",id:"my-microsd-card-is-corrupted---what-can-i-do",level:4},{value:"Networking",id:"networking",level:2},{value:"How do I change/edit the network the Pioreactor on?",id:"how-do-i-changeedit-the-network-the-pioreactor-on",level:4},{value:"Can I use Ethernet cable connections instead of Wifi connections?",id:"can-i-use-ethernet-cable-connections-instead-of-wifi-connections",level:4},{value:"How can I determine the Pioreactor&#39;s IP address? Or the MAC address?",id:"how-can-i-determine-the-pioreactors-ip-address-or-the-mac-address",level:4},{value:"I&#39;m using a local access point, but I&#39;d like to install plugins, update software, etc.",id:"im-using-a-local-access-point-but-id-like-to-install-plugins-update-software-etc",level:4},{value:"To install a plugin",id:"to-install-a-plugin",level:5},{value:"To upgrade the Pioreactor software",id:"to-upgrade-the-pioreactor-software",level:5},{value:"If I have multiple Pioreactor leaders on my network, what leader does <code>http://pioreactor.local</code> point to?",id:"if-i-have-multiple-pioreactor-leaders-on-my-network-what-leader-does-httppioreactorlocal-point-to",level:4}];function c(e){const t={a:"a",admonition:"admonition",blockquote:"blockquote",code:"code",em:"em",h2:"h2",h3:"h3",h4:"h4",h5:"h5",img:"img",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,o.a)(),...e.components};return(0,r.jsxs)(r.Fragment,{children:[(0,r.jsx)(n.Z,{toc:d}),"\n",(0,r.jsx)(t.h2,{id:"pioreactor-operation",children:"Pioreactor operation"}),"\n",(0,r.jsx)(t.h4,{id:"how-can-i-restart-my-pioreactor-is-pulling-the-power-plug-out-safe",children:"How can I restart my Pioreactor? Is pulling the power plug out safe?"}),"\n",(0,r.jsx)(t.p,{children:"We suggest using the UI to reboot a Pioreactor:"}),"\n",(0,r.jsx)(t.p,{children:(0,r.jsx)(t.img,{alt:"Rebooting your pi",src:i(15713).Z+"",width:"3010",height:"1440"})}),"\n",(0,r.jsx)(t.p,{children:"Pulling the plug is usually fine, but try to avoid doing it as much as possible."}),"\n",(0,r.jsx)(t.h4,{id:"can-i-still-use-the-pioreactor-software-without-the-hardware",children:"Can I still use the Pioreactor software without the hardware?"}),"\n",(0,r.jsxs)(t.p,{children:['Yes - the Pioreactor UI and software will still work. We provide a "leader-only" image that is designed to only host a cluster, and not be an active worker. The leader-only image, ',(0,r.jsx)(t.code,{children:"pioreactor_leader.zip "}),", are available ",(0,r.jsx)(t.a,{href:"https://github.com/Pioreactor/CustoPiZer/releases",children:"here"}),"."]}),"\n",(0,r.jsx)(t.h4,{id:"why-does-the-onboard-blue-led-keep-flashing",children:"Why does the onboard blue LED keep flashing?"}),"\n",(0,r.jsxs)(t.p,{children:["There may be a problem. You can diagnose the problem by ",(0,r.jsx)(t.a,{href:"/user-guide/error-codes",children:"counting the number of flashes observed"}),"."]}),"\n",(0,r.jsx)(t.h4,{id:"what-does-the-onboard-button-do",children:"What does the onboard button do?"}),"\n",(0,r.jsx)(t.p,{children:'The button on the Pioreactor HAT sends a signal to the web UI to display a "hello" message. This is useful to know which Pioreactor in a cluster you are interacting with. The button also will republish the state of the Pioreactor.'}),"\n",(0,r.jsxs)(t.p,{children:["The button can be ",(0,r.jsx)(t.a,{href:"/developer-guide/hat-button",children:"reprogrammed"}),", too."]}),"\n",(0,r.jsx)(t.h4,{id:"how-do-i-change-the-date-or-time-on-the-pioreactor",children:"How do I change the date or time on the Pioreactor?"}),"\n",(0,r.jsxs)(t.p,{children:[(0,r.jsx)(t.a,{href:"/user-guide/accessing-raspberry-pi",children:"SSH"})," into your Pioreactor, and run:"]}),"\n",(0,r.jsx)(t.pre,{children:(0,r.jsx)(t.code,{children:'sudo date --set "Thu Nov  2 09:46:50 EDT 2023"\n\n'})}),"\n",(0,r.jsx)(t.h2,{id:"optical-density-and-leds",children:"Optical density and LEDs"}),"\n",(0,r.jsx)(t.h4,{id:"how-does-optical-density-work-on-the-pioreactor",children:"How does optical density work on the Pioreactor?"}),"\n",(0,r.jsxs)(t.p,{children:["The Pioreactor uses turbidity to measure optical density (other systems, like spectrophotometers, use attenuation). Specifically, the Pioreactor uses ",(0,r.jsx)(t.em,{children:"scattering"})," of light. The system will shine infrared light into the culture, and measure the amount of light that is scattered off cells. The scattering has a good linear range (see below for more), and higher saturation point than attenuation for cultures of 20ml volume. If you have an instrument that measures OD600 or some other measurement of optical density, and you wish to calibrate to that, the Pioreactor has a routine to perform a calibration and record in the instruments units. See ",(0,r.jsx)(t.a,{href:"/user-guide/calibrate-od600",children:"docs here"}),"."]}),"\n",(0,r.jsx)(t.h4,{id:"what-are-the-units-of-pioreactors-optical-density",children:"What are the units of Pioreactor's optical density"}),"\n",(0,r.jsxs)(t.p,{children:["The ",(0,r.jsx)(t.em,{children:"uncalibrated"})," optical densities reported the UI and recorded in the database are have an arbitrary unit, and are per Pioreactor (so they can't be compared to each other). However, the ",(0,r.jsx)(t.em,{children:"normalized optical density"}),", generated after starting the activity ",(0,r.jsx)(t.strong,{children:"Growth rate"})," in the UI, is comparable, which is why we suggest using it for inferences (especially if you haven't calibrated to some OD600 machine). Read more about our ",(0,r.jsx)(t.a,{href:"https://docs.pioreactor.com/user-guide/od-normal-growth-rate",children:"optical density measurements here"}),"."]}),"\n",(0,r.jsx)(t.h4,{id:"how-can-i-change-the-frequency-rate-of-optical-density-measurements",children:"How can I change the frequency (rate) of optical density measurements?"}),"\n",(0,r.jsxs)(t.p,{children:["In the configuration, you can edit the parameter ",(0,r.jsx)(t.code,{children:"samples_per_second"}),' to adjust the how often the Pioreactor takes an optical density snapshot. Note that this parameter is the inverse of "duration between readings". For example, if you wish to record a measurement every 60 seconds, then ',(0,r.jsx)(t.code,{children:"samples_per_second=0.01666667"})," (which is 1/60)."]}),"\n",(0,r.jsxs)(t.admonition,{type:"tip",children:[(0,r.jsxs)(t.p,{children:["If you put a large gap between readings, like 1 reading / 60 seconds, then we also suggest turning off the ",(0,r.jsx)(t.em,{children:"downsampling"})," on the UI's charts (it's on by default to avoid plotting thousands of points). To do this, ",(0,r.jsx)(t.a,{href:"/user-guide/accessing-raspberry-pi",children:"SSH"})," into your leader, and we'll edit the following files:"]}),(0,r.jsx)(t.pre,{children:(0,r.jsx)(t.code,{children:"nano /var/www/pioreactorui/contrib/charts/05_od.yaml\n"})}),(0,r.jsxs)(t.p,{children:["And change the field ",(0,r.jsx)(t.code,{children:"down_sample"})," from ",(0,r.jsx)(t.code,{children:"true"})," to ",(0,r.jsx)(t.code,{children:"false"}),". Do the same for the following files:"]}),(0,r.jsx)(t.pre,{children:(0,r.jsx)(t.code,{children:"nano /var/www/pioreactorui/contrib/charts/01_implied_growth_rate.yaml\n"})}),(0,r.jsx)(t.pre,{children:(0,r.jsx)(t.code,{children:"nano /var/www/pioreactorui/contrib/charts/04_normalized_od.yaml\n"})})]}),"\n",(0,r.jsx)(t.h4,{id:"why-does-the-intensity-for-led-a-turn-on--off-during-an-experiment",children:"Why does the intensity for LED A turn on & off during an experiment?"}),"\n",(0,r.jsx)(t.p,{children:"You may have noticed that the LED labelled A turns on & off every 5 seconds or so. This is (normally) the channel for the infrared (IR) LED, which is used in the optical density measurements. We only take reading every 5 seconds (the default), we don't need the IR LED on all the time. The Pioreactor will only turn on LED when needed. This preserves the strength of the LED over longer periods of time. For more advanced use cases, it also allows other optical measurements to take place without the IR LED interfering with them."}),"\n",(0,r.jsx)(t.h4,{id:"why-does-my-optical-density-flatten-or-even-decrease-what-is-a-saturation-point",children:"Why does my optical density flatten, or even decrease? What is a saturation point?"}),"\n",(0,r.jsxs)(t.p,{children:["For some experiments, especially when using a scatter angle of 135\xb0, you may notice that the optical density starts to flatten, and even decrease, ",(0,r.jsx)(t.em,{children:"when you know the culture should still be growing"}),". This is not a property of the culture, but occurs because the culture is getting too dense, and light is now being interrupted before it reaches the photodiodes. Prior to this point, called the saturation point, the relationship between culture density and optical density is nearly linear. But after this point, there is a flattening, even negative, relationship between culture density and optical density. For all analysis, we recommend only studying when the culture is in the linear regime. You can mitigate the problem by choosing a smaller scatter angle (like 90\xb0 or 45\xb0), diluting the culture using an automation like the turbidostat, or using a lower concentration of nutrient(s) in the media. Read more about Pioreactor's optical system ",(0,r.jsx)(t.a,{href:"https://pioreactor.com/blogs/pioreactor/estimating-growth-rates-with-kalman-filters",children:"here"}),"."]}),"\n",(0,r.jsx)(t.h4,{id:"what-does-the-effect-of-the-scatter-angle-have-on-optical-density",children:"What does the effect of the scatter angle have on optical density?"}),"\n",(0,r.jsxs)(t.p,{children:["The scatter angle is the angle between the IR LED and a photodiode. This angle can be 45\xb0, 90\xb0, or 135\xb0  (although 180\xb0 is possible, we don't consider it here). What is there to consider when choosing an angle. In general, the trend is shorter angles => less sensitive at low densities, but higher saturation point. By default, we suggest 45\xb0 as a good trade off between sensitivity and saturation. You can mix angles, and the Pioreactor's internal algorithm will still combine them into a single growth rate. Read more about Pioreactor's optical system ",(0,r.jsx)(t.a,{href:"https://pioreactor.com/blogs/pioreactor/estimating-growth-rates-with-kalman-filters",children:"here"}),"."]}),"\n",(0,r.jsx)(t.h4,{id:"can-i-use-my-own-5mm-leds-and-photodiodes-for-optical-density",children:"Can I use my own 5mm LEDs and photodiodes for optical density?"}),"\n",(0,r.jsx)(t.p,{children:"Of course! The only two requirements are that the spectrum of the LED overlaps with the spectrum of the photodiode, and that the LED light won't be absorbed by media/culture, nor damage the media/culture. Thus, the often-used 600nm light source works in the Pioreactor. None of our internal algorithms or analytics are dependent on the wavelength of light chosen."}),"\n",(0,r.jsx)(t.p,{children:"When you are using additional LEDs outside of the optical density LED & photodiode pair, you may worry that your additional LEDs will interfere with the optical density measurement. This won't happen, as we turn off all non-optical density LEDs before taking an optical density measurement."}),"\n",(0,r.jsx)(t.h4,{id:"is-optical-density-the-same-as-turbidity",children:"Is optical density the same as turbidity?"}),"\n",(0,r.jsx)(t.p,{children:"Turbidity is a measure of optical density, like how decibels are a measurement of sound intensity. Similarly, absorbance is a measure of optical density."}),"\n",(0,r.jsx)(t.h2,{id:"heating-and-temperature-control",children:"Heating and Temperature control"}),"\n",(0,r.jsx)(t.h4,{id:"why-does-the-pioreactor-only-provide-a-temperature-reading-every-few-minutes",children:"Why does the Pioreactor only provide a temperature reading every few minutes?"}),"\n",(0,r.jsxs)(t.p,{children:["We made a design choice early on to make preparation as error-free as possible. This involved thinking about sensors being ",(0,r.jsx)(t.em,{children:"in situ"})," (in place), versus the sensors being on the outside of the vial. The temperature sensor in the Pioreactor is outside the vial, which means less chance of contamination, but there's a tradeoff (as you could guess): we have to rely on an estimation algorithm that requires a gew minutes to gather data on. We think this is a fair trade-off, as high frequency temperature readings are not that important in an experiment that lasts 12 hours or more."]}),"\n",(0,r.jsx)(t.h4,{id:"why-does-the-pioreactors-heating-keep-shutting-off",children:"Why does the Pioreactor's heating keep shutting off?"}),"\n",(0,r.jsx)(t.p,{children:"If you find that the Pioreactor's heating is shutting off, typically with an accompanying error and flashing blue light, then likely the temperature is becoming too high for safe handling. We restrict the onboard PCB's temperature to be no higher than 63\u2103. Temperature's higher than this can deform the plastic, and possibly cause burns. If the Pioreactor detects a temperature near or above this value, the software will shut off the heating, and possible the entire Raspberry Pi in extreme cases."}),"\n",(0,r.jsxs)(t.p,{children:["To avoid this occurring, we suggest not setting the target temperature too high - not more than 20\u2103 above ambient temperature. Also, reducing the ",(0,r.jsx)(t.code,{children:"Kd"})," parameter in ",(0,r.jsx)(t.code,{children:"[temperature_automation.stable]"})," section in the config.ini would help."]}),"\n",(0,r.jsx)(t.h4,{id:"how-does-heating-work-on-the-pioreactor",children:"How does heating work on the Pioreactor?"}),"\n",(0,r.jsx)(t.p,{children:"The Pioreactor has an onboard PCB, called the heating PCB, that sits below the glass vial. On the PCB are resistors that convert current from PWM outputs into heat. By varying the duty cycle of the PWM, we vary the amount of energy converted to heat."}),"\n",(0,r.jsx)(t.h2,{id:"mixing-and-stirring-in-the-pioreactor",children:"Mixing and stirring in the Pioreactor"}),"\n",(0,r.jsx)(t.h4,{id:"how-is-mixing--stirring-performed-in-the-pioreactor",children:"How is mixing / stirring performed in the Pioreactor?"}),"\n",(0,r.jsx)(t.p,{children:"Stirring is performed with a micro stir bar inside the vial, controlled by a pair of magnets spinning below the vial. The rotation speed, RPM, of the stir bar can be controlled using the Pioreactor software. This stirring is also how aeration is done."}),"\n",(0,r.jsx)(t.h4,{id:"can-i-use-my-own-stir-bar",children:"Can I use my own stir bar?"}),"\n",(0,r.jsx)(t.p,{children:"Of course! The maximum length of a stir bar is 20mm. Keep the height low as to not interfere with the optics. (The provided stir bar is 3mm high). Try using other stir bar shapes / designs!"}),"\n",(0,r.jsx)(t.h4,{id:"the-magnets-rubs-against-the-plastic-screws-above-them-causing-the-stirring-performance-to-be-degraded--stop-how-do-i-fix-this",children:"The magnets rubs against the plastic screws above them, causing the stirring performance to be degraded / stop. How do I fix this?"}),"\n",(0,r.jsx)(t.p,{children:"Dis-attach the top faceplate. Under the faceplate, slightly unscrew each of the four metal screws. This will add more space between the magnets and the plastic screws."}),"\n",(0,r.jsx)(t.h4,{id:"how-can-i-increase-the-strength-of-the-magnetic-force-applied-to-the-stirbar",children:"How can I increase the strength of the magnetic force applied to the stirbar?"}),"\n",(0,r.jsxs)(t.p,{children:[(0,r.jsx)(t.strong,{children:"For Pioreactor 20ml v1.0"}),": Try to reduce the distance between the stirring magnets and the stir bar by carefully raising the stirring fan a small amount. Going even further, you can remove the 4mm screws in the bottom of the vial holder (but find another way to secure the PCB), thereby be able to bring the magnets even closer."]}),"\n",(0,r.jsx)(t.h4,{id:"how-can-i-improve-mixing-and-aeration",children:"How can I improve mixing and aeration?"}),"\n",(0,r.jsx)(t.p,{children:"If the standard mixing and aeration with the stir bar is not enough for your application, you can do a few things, (in increasing order of complication, not necessarily effectiveness):"}),"\n",(0,r.jsxs)(t.ol,{children:["\n",(0,r.jsx)(t.li,{children:"If the tubes in the cap are submerged during operation, this is reduce the transfer of air. Pull them up from the top of the cap to keep them out of the liquid. Even more effective: shorten them with scissors."}),"\n",(0,r.jsx)(t.li,{children:"Increase the RPM of the stirring. This will increase the surface area exposed to the air. Be warned though: too high of an RPM will cause either a large enough vortex to interfere with the optical systems, or will causing the stir bar to fall out of sync."}),"\n",(0,r.jsxs)(t.li,{children:["Add a ",(0,r.jsx)(t.a,{href:"https://www.printables.com/model/575292-baffle-for-pioreactor-vial-cap-a/files",children:"baffle"})," to the vial cap. A simple cylinder that rests into the liquid causes disturbance in the rotating liquid that both mixing and aeration are significantly improved. A tube can be removed from the cap, and a autoclavable rod can be inserted such that it enters the media, but won't interfere with the optics."]}),"\n",(0,r.jsx)(t.li,{children:"Adding external aeration to your Pioreactor. In the simplest case, using an air pump."}),"\n"]}),"\n",(0,r.jsx)(t.h3,{id:"can-i-plot-the-rpm-in-a-chart-in-the-ui",children:"Can I plot the RPM in a chart in the UI?"}),"\n",(0,r.jsxs)(t.p,{children:["Yes, follow the instructions ",(0,r.jsx)(t.a,{href:"https://forum.pioreactor.com/t/creating-stirring-rpm-and-pwm-duty-cycle-charts-on-the-ui/339",children:"here"}),"."]}),"\n",(0,r.jsx)(t.h2,{id:"raspberry-pi-hardware",children:"Raspberry Pi Hardware"}),"\n",(0,r.jsx)(t.h4,{id:"what-raspberry-pi-hardware-can-i-use-i-see-raspberry-pi-1-2-3-4-5-a-b--zero---its-confusing",children:"What Raspberry Pi hardware can I use? I see Raspberry Pi 1, 2, 3, 4, 5, A, B, +, Zero - it's confusing!"}),"\n",(0,r.jsx)(t.p,{children:"We've designed the hardware and software to be compatible with any Raspberry Pi that has onboard Wifi and a 40 pin header. That includes (at the time of writing):"}),"\n",(0,r.jsxs)(t.ul,{children:["\n",(0,r.jsx)(t.li,{children:"Raspberry Pi 3 Model B & B+"}),"\n",(0,r.jsx)(t.li,{children:"Raspberry Pi 3 Model A+"}),"\n",(0,r.jsx)(t.li,{children:"Raspberry Pi 4 Model B \xb3"}),"\n",(0,r.jsx)(t.li,{children:"Raspberry Pi 5 Model B"}),"\n",(0,r.jsx)(t.li,{children:"Raspberry Pi Zero W (with headers) \xb9"}),"\n",(0,r.jsx)(t.li,{children:"Raspberry Pi Zero 2 (with headers)"}),"\n",(0,r.jsx)(t.li,{children:"Raspberry Pi 400 \xb2"}),"\n"]}),"\n",(0,r.jsxs)(t.p,{children:["Although you can use any above, ",(0,r.jsx)(t.strong,{children:"we like the Raspberry Pi 3 Model A+, and Raspberry Pi Zero 2"})," because of their low power consumption, slim build, and low price. Both have the necessary CPU power and memory for the Pioreactor workload, and are generally easy to source. However, they don't have ethernet connections! So talk to your team about if you need to use ethernet or wifi. If you need ethernet, we like the model RPi\n3B."]}),"\n",(0,r.jsxs)(t.p,{children:["\xb9 ",(0,r.jsx)(t.em,{children:"Raspberry Pi Zero W"})," is on the list above, and is very low cost compared to the others. They can absolutely be used for Pioreactors ",(0,r.jsx)(t.em,{children:"as workers"})," - we don't recommend them to be your ",(0,r.jsx)(t.em,{children:"leader"})," (note sure what these terms mean? Here's an introduction to ",(0,r.jsx)(t.a,{href:"/user-guide/create-cluster",children:"leader and workers"}),"). As workers, Raspberry Pi Zero W perform just fine, but will respond slower to commands. Note that this does not include the Raspberry Pi Zero ",(0,r.jsx)(t.em,{children:"2"})," W model, which is fine for all roles."]}),"\n",(0,r.jsxs)(t.p,{children:["\xb2 The Raspberry Pi 400 has its 40 pin header exposed in a different orientation, so your Pioreactor won't be able to sit on top like for other RPi versions. Take a ",(0,r.jsx)(t.a,{href:"https://forum.pioreactor.com/t/using-a-raspberry-pi-400/113/8",children:"look at this forum post"})," to see how another user used the Raspberry Pi 400 with their Pioreactor."]}),"\n",(0,r.jsx)(t.p,{children:"\xb3 Note that you don't need a lot of RAM for the Pioreactor, so we recommend getting the lower RAM option RPi 4s (1GB or 2GB) to save some money. However, 4GB and 8GB are fine, too."}),"\n",(0,r.jsx)(t.h4,{id:"what-microsd-cards-do-you-recommend",children:"What microSD cards do you recommend?"}),"\n",(0,r.jsx)(t.p,{children:"At least 16GB. We like 16GB or 32GB SanDisk Edge or Samsung microSD cards for their longevity, but any good quality, class 10 SD card will do."}),"\n",(0,r.jsx)(t.h4,{id:"what-power-supply-unit-psu-do-i-need",children:"What power supply unit (PSU) do I need?"}),"\n",(0,r.jsx)(t.p,{children:"If you look at the power rating, it should be about 5 V and at least 2.25 A, or above 12 W. We really like the official Raspberry Pi PSUs, available at most places you can purchase Raspberry Pis."}),"\n",(0,r.jsx)(t.h4,{id:"do-i-need-any-cooling-for-the-raspberry-pi",children:"Do I need any cooling for the Raspberry Pi?"}),"\n",(0,r.jsx)(t.p,{children:"Nope, you shouldn't, unless you are connecting an external monitor. However, extra heat sinks are never a bad idea!"}),"\n",(0,r.jsx)(t.h4,{id:"could-a-raspberry-pi-compatible-board-work-like-rock-pi-4",children:"Could a Raspberry Pi-compatible board work, like Rock Pi 4?"}),"\n",(0,r.jsx)(t.p,{children:"Maybe? We haven't tested them, but so long as i) the GPIO pins are identical, and ii) Raspberry Pi OS can be installed, it should work."}),"\n",(0,r.jsx)(t.h4,{id:"why-are-the-raspberry-pi-ledsusbetc-turned-off",children:"Why are the Raspberry Pi LEDs/USB/etc. turned off?"}),"\n",(0,r.jsxs)(t.p,{children:['We turn off the "activity" LED (usually the green one) to save some power for the Pioreactor\'s peripherals. You can turn these back on by editing the ',(0,r.jsx)(t.code,{children:"/boot/config.txt"})," file on the RPi."]}),"\n",(0,r.jsx)(t.h4,{id:"what-is-the-usernamepassword-for-the-raspberry-pi",children:"What is the username/password for the Raspberry Pi?"}),"\n",(0,r.jsxs)(t.p,{children:["When setting up your Raspberry Pi with the Pioreactor software, you would have chosen a password. Try the recommended username: ",(0,r.jsx)(t.code,{children:"pioreactor"}),", and password: ",(0,r.jsx)(t.code,{children:"raspberry"}),"."]}),"\n",(0,r.jsx)(t.h4,{id:"can-i-use-the-desktop-interface-with-a-display-with-the-pioreactor",children:"Can I use the desktop interface (with a display) with the Pioreactor?"}),"\n",(0,r.jsx)(t.p,{children:'Not currently. Our software is based of the "headless" operating-system, which doesn\'t have display output.'}),"\n",(0,r.jsx)(t.h2,{id:"dosing",children:"Dosing"}),"\n",(0,r.jsx)(t.h4,{id:"why-does-the-media-card-in-the-ui-not-update-when-i-run-a-dosing-command",children:"Why does the Media card in the UI not update when I run a dosing command?"}),"\n",(0,r.jsxs)(t.p,{children:["The Media card will ",(0,r.jsx)(t.em,{children:"only"})," update when an ",(0,r.jsx)(t.a,{href:"/user-guide/dosing-automations",children:"Dosing Automation"})," is active (even the ",(0,r.jsx)(t.code,{children:"Silent"})," automation). Why is it done this way? Often, you don't want volumes to be recorded there: during cleaning, during testing, etc. Often you only want volumes associated with the experiment to be there."]}),"\n",(0,r.jsx)(t.admonition,{type:"note",children:(0,r.jsxs)(t.p,{children:['All dosing events ares recorded to the database however, and with a record of when the event occurred, and source of action. This data is available in the "Export data" web page, under ',(0,r.jsx)(t.code,{children:"Dosing event log"}),"."]})}),"\n",(0,r.jsx)(t.h2,{id:"data-storage-access-and-recovery",children:"Data storage, access and recovery"}),"\n",(0,r.jsxs)(t.blockquote,{children:["\n",(0,r.jsx)(t.p,{children:"\ud83d\udca1 For any important project, we suggest manually exporting or backing up critical data multiple different places. This doesn't just apply to using the Pioreactor, but is good advice in general."}),"\n"]}),"\n",(0,r.jsx)(t.h4,{id:"where-are-logs-stored",children:"Where are logs stored?"}),"\n",(0,r.jsxs)(t.p,{children:["For the logs that you see in the Log Table in the ",(0,r.jsx)(t.em,{children:"Experiment Overview"})," page, these can be download on the ",(0,r.jsx)(t.em,{children:"Download experiment data"})," page in the Pioreactor web interface. Other logs are also available, including dosing event and algorithm change-logs."]}),"\n",(0,r.jsxs)(t.p,{children:["More granular logs per Pioreactor are available in ",(0,r.jsx)(t.code,{children:"/var/log/pioreactor.log"})," on the Raspberry Pis."]}),"\n",(0,r.jsx)(t.h4,{id:"how-do-i-access-raw-experiment-data",children:"How do I access raw experiment data?"}),"\n",(0,r.jsxs)(t.ol,{children:["\n",(0,r.jsxs)(t.li,{children:["The ",(0,r.jsx)(t.em,{children:"Download experiment data"})," page in the Pioreactor web interface provides CSV exports of common datasets from a pre-selected experiment."]}),"\n",(0,r.jsxs)(t.li,{children:["All data eventually lands in a SQLite3 database on the leader Pioreactor, by default located in ",(0,r.jsx)(t.code,{children:"/home/pioreactor/.pioreactor/storage/pioreactor.sqlite"}),". This can be download using a tool like ",(0,r.jsx)(t.code,{children:"scp"}),"."]}),"\n",(0,r.jsxs)(t.li,{children:["To access the SQLite3 database from the command line, try ",(0,r.jsx)(t.code,{children:"pio db"}),"."]}),"\n"]}),"\n",(0,r.jsx)(t.h4,{id:"my-microsd-card-is-corrupted---what-can-i-do",children:"My microSD card is corrupted - what can I do?"}),"\n",(0,r.jsx)(t.p,{children:"Unfortunately, the microSD card becoming corrupted or damaged is an infrequent but possible risk with using Raspberry Pis."}),"\n",(0,r.jsxs)(t.ul,{children:["\n",(0,r.jsxs)(t.li,{children:["\n",(0,r.jsxs)(t.p,{children:["If the microSD card was inside a non-leader Pioreactor, it's best to try to reformat the microSD card and start fresh (i.e. ",(0,r.jsx)(t.a,{href:"/user-guide/software-set-up#adding-workers-to-your-cluster",children:"reinstall the Pioreactor software and reintroduce it to the cluster"}),"). This is usually okay as no critical data is stored locally in workers, only log files and hardware calibrations will be lost."]}),"\n"]}),"\n",(0,r.jsxs)(t.li,{children:["\n",(0,r.jsxs)(t.p,{children:["If the microSD was inside the leader Raspberry Pi, this is a bigger problem. Likely any running experiment will have to be restarted. Fortunately, if you have more than one Pioreactor in your cluster, then the leader's SQLite database has been periodically backing itself up to other Pioreactors in the cluster every few days. Using the command line, check other Pioreactors' ",(0,r.jsx)(t.code,{children:"/home/pioreactor/.pioreactor/storage"})," directory for the ",(0,r.jsx)(t.em,{children:"latest"})," backup named ",(0,r.jsx)(t.code,{children:"pioreactor.sqlite.backup"})," (should be from within the past few days hours). 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rename to assets/js/main.ba545c74.js
index bb61c2ccd..df7aeebf9 100644
--- a/assets/js/main.2c041b40.js
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e=[],t=[{prefix:"",node:this}];t.length;){var n=t.pop(),r=Object.keys(n.node.edges),a=r.length;n.node.final&&(n.prefix.charAt(0),e.push(n.prefix));for(var o=0;o<a;o++){var i=r[o];t.push({prefix:n.prefix.concat(i),node:n.node.edges[i]})}}return e},I.TokenSet.prototype.toString=function(){if(this._str)return this._str;for(var e=this.final?"1":"0",t=Object.keys(this.edges).sort(),n=t.length,r=0;r<n;r++){var a=t[r];e=e+a+this.edges[a].id}return e},I.TokenSet.prototype.intersect=function(e){for(var t=new I.TokenSet,n=void 0,r=[{qNode:e,output:t,node:this}];r.length;){n=r.pop();for(var a=Object.keys(n.qNode.edges),o=a.length,i=Object.keys(n.node.edges),s=i.length,l=0;l<o;l++)for(var u=a[l],c=0;c<s;c++){var d=i[c];if(d==u||"*"==u){var p=n.node.edges[d],f=n.qNode.edges[u],m=p.final&&f.final,g=void 0;d in n.output.edges?(g=n.output.edges[d]).final=g.final||m:((g=new I.TokenSet).final=m,n.output.edges[d]=g),r.push({qNode:f,output:g,node:p})}}}return t},I.TokenSet.Builder=function(){this.previousWord="",this.root=new I.TokenSet,this.uncheckedNodes=[],this.minimizedNodes={}},I.TokenSet.Builder.prototype.insert=function(e){var t,n=0;if(e<this.previousWord)throw new Error("Out of order word insertion");for(var r=0;r<e.length&&r<this.previousWord.length&&e[r]==this.previousWord[r];r++)n++;this.minimize(n),t=0==this.uncheckedNodes.length?this.root:this.uncheckedNodes[this.uncheckedNodes.length-1].child;for(r=n;r<e.length;r++){var a=new I.TokenSet,o=e[r];t.edges[o]=a,this.uncheckedNodes.push({parent:t,char:o,child:a}),t=a}t.final=!0,this.previousWord=e},I.TokenSet.Builder.prototype.finish=function(){this.minimize(0)},I.TokenSet.Builder.prototype.minimize=function(e){for(var t=this.uncheckedNodes.length-1;t>=e;t--){var n=this.uncheckedNodes[t],r=n.child.toString();r in 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g=0;g<l.fields.length;g++){o[A=l.fields[g]]=I.Set.empty}break}for(var h=0;h<m.length;h++){var b=m[h],y=this.invertedIndex[b],v=y._index;for(g=0;g<l.fields.length;g++){var w=y[A=l.fields[g]],x=Object.keys(w),k=b+"/"+A,S=new I.Set(x);if(l.presence==I.Query.presence.REQUIRED&&(c=c.union(S),void 0===o[A]&&(o[A]=I.Set.complete)),l.presence!=I.Query.presence.PROHIBITED){if(r[A].upsert(v,l.boost,(function(e,t){return e+t})),!a[k]){for(var _=0;_<x.length;_++){var E,C=x[_],T=new I.FieldRef(C,A),P=w[C];void 0===(E=n[T])?n[T]=new I.MatchData(b,A,P):E.add(b,A,P)}a[k]=!0}}else void 0===i[A]&&(i[A]=I.Set.empty),i[A]=i[A].union(S)}}}if(l.presence===I.Query.presence.REQUIRED)for(g=0;g<l.fields.length;g++){o[A=l.fields[g]]=o[A].intersect(c)}}var L=I.Set.complete,j=I.Set.empty;for(s=0;s<this.fields.length;s++){var A;o[A=this.fields[s]]&&(L=L.intersect(o[A])),i[A]&&(j=j.union(i[A]))}var R=Object.keys(n),N=[],O=Object.create(null);if(t.isNegated()){R=Object.keys(this.fieldVectors);for(s=0;s<R.length;s++){T=R[s];var D=I.FieldRef.fromString(T);n[T]=new I.MatchData}}for(s=0;s<R.length;s++){var F=(D=I.FieldRef.fromString(R[s])).docRef;if(L.contains(F)&&!j.contains(F)){var M,z=this.fieldVectors[D],B=r[D.fieldName].similarity(z);if(void 0!==(M=O[F]))M.score+=B,M.matchData.combine(n[D]);else{var $={ref:F,score:B,matchData:n[D]};O[F]=$,N.push($)}}}return N.sort((function(e,t){return t.score-e.score}))},I.Index.prototype.toJSON=function(){var e=Object.keys(this.invertedIndex).sort().map((function(e){return[e,this.invertedIndex[e]]}),this),t=Object.keys(this.fieldVectors).map((function(e){return[e,this.fieldVectors[e].toJSON()]}),this);return{version:I.version,fields:this.fields,fieldVectors:t,invertedIndex:e,pipeline:this.pipeline.toJSON()}},I.Index.load=function(e){var t={},n={},r=e.fieldVectors,a=Object.create(null),o=e.invertedIndex,i=new I.TokenSet.Builder,s=I.Pipeline.load(e.pipeline);e.version!=I.version&&I.utils.warn("Version mismatch when loading serialised index. Current version of lunr '"+I.version+"' does not match serialized index '"+e.version+"'");for(var l=0;l<r.length;l++){var u=(d=r[l])[0],c=d[1];n[u]=new I.Vector(c)}for(l=0;l<o.length;l++){var d,p=(d=o[l])[0],f=d[1];i.insert(p),a[p]=f}return i.finish(),t.fields=e.fields,t.fieldVectors=n,t.invertedIndex=a,t.tokenSet=i.root,t.pipeline=s,new I.Index(t)},I.Builder=function(){this._ref="id",this._fields=Object.create(null),this._documents=Object.create(null),this.invertedIndex=Object.create(null),this.fieldTermFrequencies={},this.fieldLengths={},this.tokenizer=I.tokenizer,this.pipeline=new I.Pipeline,this.searchPipeline=new I.Pipeline,this.documentCount=0,this._b=.75,this._k1=1.2,this.termIndex=0,this.metadataWhitelist=[]},I.Builder.prototype.ref=function(e){this._ref=e},I.Builder.prototype.field=function(e,t){if(/\//.test(e))throw new RangeError("Field '"+e+"' contains illegal character '/'");this._fields[e]=t||{}},I.Builder.prototype.b=function(e){this._b=e<0?0:e>1?1:e},I.Builder.prototype.k1=function(e){this._k1=e},I.Builder.prototype.add=function(e,t){var n=e[this._ref],r=Object.keys(this._fields);this._documents[n]=t||{},this.documentCount+=1;for(var a=0;a<r.length;a++){var o=r[a],i=this._fields[o].extractor,s=i?i(e):e[o],l=this.tokenizer(s,{fields:[o]}),u=this.pipeline.run(l),c=new I.FieldRef(n,o),d=Object.create(null);this.fieldTermFrequencies[c]=d,this.fieldLengths[c]=0,this.fieldLengths[c]+=u.length;for(var p=0;p<u.length;p++){var f=u[p];if(null==d[f]&&(d[f]=0),d[f]+=1,null==this.invertedIndex[f]){var m=Object.create(null);m._index=this.termIndex,this.termIndex+=1;for(var g=0;g<r.length;g++)m[r[g]]=Object.create(null);this.invertedIndex[f]=m}null==this.invertedIndex[f][o][n]&&(this.invertedIndex[f][o][n]=Object.create(null));for(var h=0;h<this.metadataWhitelist.length;h++){var b=this.metadataWhitelist[h],y=f.metadata[b];null==this.invertedIndex[f][o][n][b]&&(this.invertedIndex[f][o][n][b]=[]),this.invertedIndex[f][o][n][b].push(y)}}}},I.Builder.prototype.calculateAverageFieldLengths=function(){for(var e=Object.keys(this.fieldLengths),t=e.length,n={},r={},a=0;a<t;a++){var o=I.FieldRef.fromString(e[a]),i=o.fieldName;r[i]||(r[i]=0),r[i]+=1,n[i]||(n[i]=0),n[i]+=this.fieldLengths[o]}var s=Object.keys(this._fields);for(a=0;a<s.length;a++){var l=s[a];n[l]=n[l]/r[l]}this.averageFieldLength=n},I.Builder.prototype.createFieldVectors=function(){for(var e={},t=Object.keys(this.fieldTermFrequencies),n=t.length,r=Object.create(null),a=0;a<n;a++){for(var o=I.FieldRef.fromString(t[a]),i=o.fieldName,s=this.fieldLengths[o],l=new I.Vector,u=this.fieldTermFrequencies[o],c=Object.keys(u),d=c.length,p=this._fields[i].boost||1,f=this._documents[o.docRef].boost||1,m=0;m<d;m++){var g,h,b,y=c[m],v=u[y],w=this.invertedIndex[y]._index;void 0===r[y]?(g=I.idf(this.invertedIndex[y],this.documentCount),r[y]=g):g=r[y],h=g*((this._k1+1)*v)/(this._k1*(1-this._b+this._b*(s/this.averageFieldLength[i]))+v),h*=p,h*=f,b=Math.round(1e3*h)/1e3,l.insert(w,b)}e[o]=l}this.fieldVectors=e},I.Builder.prototype.createTokenSet=function(){this.tokenSet=I.TokenSet.fromArray(Object.keys(this.invertedIndex).sort())},I.Builder.prototype.build=function(){return this.calculateAverageFieldLengths(),this.createFieldVectors(),this.createTokenSet(),new I.Index({invertedIndex:this.invertedIndex,fieldVectors:this.fieldVectors,tokenSet:this.tokenSet,fields:Object.keys(this._fields),pipeline:this.searchPipeline})},I.Builder.prototype.use=function(e){var t=Array.prototype.slice.call(arguments,1);t.unshift(this),e.apply(this,t)},I.MatchData=function(e,t,n){for(var r=Object.create(null),a=Object.keys(n||{}),o=0;o<a.length;o++){var i=a[o];r[i]=n[i].slice()}this.metadata=Object.create(null),void 0!==e&&(this.metadata[e]=Object.create(null),this.metadata[e][t]=r)},I.MatchData.prototype.combine=function(e){for(var t=Object.keys(e.metadata),n=0;n<t.length;n++){var r=t[n],a=Object.keys(e.metadata[r]);null==this.metadata[r]&&(this.metadata[r]=Object.create(null));for(var o=0;o<a.length;o++){var i=a[o],s=Object.keys(e.metadata[r][i]);null==this.metadata[r][i]&&(this.metadata[r][i]=Object.create(null));for(var l=0;l<s.length;l++){var u=s[l];null==this.metadata[r][i][u]?this.metadata[r][i][u]=e.metadata[r][i][u]:this.metadata[r][i][u]=this.metadata[r][i][u].concat(e.metadata[r][i][u])}}}},I.MatchData.prototype.add=function(e,t,n){if(!(e in this.metadata))return this.metadata[e]=Object.create(null),void(this.metadata[e][t]=n);if(t in this.metadata[e])for(var r=Object.keys(n),a=0;a<r.length;a++){var o=r[a];o in this.metadata[e][t]?this.metadata[e][t][o]=this.metadata[e][t][o].concat(n[o]):this.metadata[e][t][o]=n[o]}else this.metadata[e][t]=n},I.Query=function(e){this.clauses=[],this.allFields=e},I.Query.wildcard=new String("*"),I.Query.wildcard.NONE=0,I.Query.wildcard.LEADING=1,I.Query.wildcard.TRAILING=2,I.Query.presence={OPTIONAL:1,REQUIRED:2,PROHIBITED:3},I.Query.prototype.clause=function(e){return"fields"in e||(e.fields=this.allFields),"boost"in e||(e.boost=1),"usePipeline"in e||(e.usePipeline=!0),"wildcard"in e||(e.wildcard=I.Query.wildcard.NONE),e.wildcard&I.Query.wildcard.LEADING&&e.term.charAt(0)!=I.Query.wildcard&&(e.term="*"+e.term),e.wildcard&I.Query.wildcard.TRAILING&&e.term.slice(-1)!=I.Query.wildcard&&(e.term=e.term+"*"),"presence"in e||(e.presence=I.Query.presence.OPTIONAL),this.clauses.push(e),this},I.Query.prototype.isNegated=function(){for(var e=0;e<this.clauses.length;e++)if(this.clauses[e].presence!=I.Query.presence.PROHIBITED)return!1;return!0},I.Query.prototype.term=function(e,t){if(Array.isArray(e))return e.forEach((function(e){this.term(e,I.utils.clone(t))}),this),this;var n=t||{};return n.term=e.toString(),this.clause(n),this},I.QueryParseError=function(e,t,n){this.name="QueryParseError",this.message=e,this.start=t,this.end=n},I.QueryParseError.prototype=new Error,I.QueryLexer=function(e){this.lexemes=[],this.str=e,this.length=e.length,this.pos=0,this.start=0,this.escapeCharPositions=[]},I.QueryLexer.prototype.run=function(){for(var e=I.QueryLexer.lexText;e;)e=e(this)},I.QueryLexer.prototype.sliceString=function(){for(var e=[],t=this.start,n=this.pos,r=0;r<this.escapeCharPositions.length;r++)n=this.escapeCharPositions[r],e.push(this.str.slice(t,n)),t=n+1;return e.push(this.str.slice(t,this.pos)),this.escapeCharPositions.length=0,e.join("")},I.QueryLexer.prototype.emit=function(e){this.lexemes.push({type:e,str:this.sliceString(),start:this.start,end:this.pos}),this.start=this.pos},I.QueryLexer.prototype.escapeCharacter=function(){this.escapeCharPositions.push(this.pos-1),this.pos+=1},I.QueryLexer.prototype.next=function(){if(this.pos>=this.length)return I.QueryLexer.EOS;var e=this.str.charAt(this.pos);return this.pos+=1,e},I.QueryLexer.prototype.width=function(){return this.pos-this.start},I.QueryLexer.prototype.ignore=function(){this.start==this.pos&&(this.pos+=1),this.start=this.pos},I.QueryLexer.prototype.backup=function(){this.pos-=1},I.QueryLexer.prototype.acceptDigitRun=function(){var e,t;do{t=(e=this.next()).charCodeAt(0)}while(t>47&&t<58);e!=I.QueryLexer.EOS&&this.backup()},I.QueryLexer.prototype.more=function(){return this.pos<this.length},I.QueryLexer.EOS="EOS",I.QueryLexer.FIELD="FIELD",I.QueryLexer.TERM="TERM",I.QueryLexer.EDIT_DISTANCE="EDIT_DISTANCE",I.QueryLexer.BOOST="BOOST",I.QueryLexer.PRESENCE="PRESENCE",I.QueryLexer.lexField=function(e){return e.backup(),e.emit(I.QueryLexer.FIELD),e.ignore(),I.QueryLexer.lexText},I.QueryLexer.lexTerm=function(e){if(e.width()>1&&(e.backup(),e.emit(I.QueryLexer.TERM)),e.ignore(),e.more())return I.QueryLexer.lexText},I.QueryLexer.lexEditDistance=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(I.QueryLexer.EDIT_DISTANCE),I.QueryLexer.lexText},I.QueryLexer.lexBoost=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(I.QueryLexer.BOOST),I.QueryLexer.lexText},I.QueryLexer.lexEOS=function(e){e.width()>0&&e.emit(I.QueryLexer.TERM)},I.QueryLexer.termSeparator=I.tokenizer.separator,I.QueryLexer.lexText=function(e){for(;;){var t=e.next();if(t==I.QueryLexer.EOS)return I.QueryLexer.lexEOS;if(92!=t.charCodeAt(0)){if(":"==t)return I.QueryLexer.lexField;if("~"==t)return e.backup(),e.width()>0&&e.emit(I.QueryLexer.TERM),I.QueryLexer.lexEditDistance;if("^"==t)return e.backup(),e.width()>0&&e.emit(I.QueryLexer.TERM),I.QueryLexer.lexBoost;if("+"==t&&1===e.width())return e.emit(I.QueryLexer.PRESENCE),I.QueryLexer.lexText;if("-"==t&&1===e.width())return e.emit(I.QueryLexer.PRESENCE),I.QueryLexer.lexText;if(t.match(I.QueryLexer.termSeparator))return I.QueryLexer.lexTerm}else e.escapeCharacter()}},I.QueryParser=function(e,t){this.lexer=new I.QueryLexer(e),this.query=t,this.currentClause={},this.lexemeIdx=0},I.QueryParser.prototype.parse=function(){this.lexer.run(),this.lexemes=this.lexer.lexemes;for(var e=I.QueryParser.parseClause;e;)e=e(this);return this.query},I.QueryParser.prototype.peekLexeme=function(){return this.lexemes[this.lexemeIdx]},I.QueryParser.prototype.consumeLexeme=function(){var e=this.peekLexeme();return this.lexemeIdx+=1,e},I.QueryParser.prototype.nextClause=function(){var e=this.currentClause;this.query.clause(e),this.currentClause={}},I.QueryParser.parseClause=function(e){var t=e.peekLexeme();if(null!=t)switch(t.type){case I.QueryLexer.PRESENCE:return I.QueryParser.parsePresence;case I.QueryLexer.FIELD:return I.QueryParser.parseField;case I.QueryLexer.TERM:return I.QueryParser.parseTerm;default:var n="expected either a field or a term, found "+t.type;throw t.str.length>=1&&(n+=" with value '"+t.str+"'"),new I.QueryParseError(n,t.start,t.end)}},I.QueryParser.parsePresence=function(e){var t=e.consumeLexeme();if(null!=t){switch(t.str){case"-":e.currentClause.presence=I.Query.presence.PROHIBITED;break;case"+":e.currentClause.presence=I.Query.presence.REQUIRED;break;default:var n="unrecognised presence operator'"+t.str+"'";throw new I.QueryParseError(n,t.start,t.end)}var r=e.peekLexeme();if(null==r){n="expecting term or field, found nothing";throw new I.QueryParseError(n,t.start,t.end)}switch(r.type){case I.QueryLexer.FIELD:return I.QueryParser.parseField;case I.QueryLexer.TERM:return I.QueryParser.parseTerm;default:n="expecting term or field, found '"+r.type+"'";throw new I.QueryParseError(n,r.start,r.end)}}},I.QueryParser.parseField=function(e){var t=e.consumeLexeme();if(null!=t){if(-1==e.query.allFields.indexOf(t.str)){var n=e.query.allFields.map((function(e){return"'"+e+"'"})).join(", "),r="unrecognised field '"+t.str+"', possible fields: "+n;throw new I.QueryParseError(r,t.start,t.end)}e.currentClause.fields=[t.str];var a=e.peekLexeme();if(null==a){r="expecting term, found nothing";throw new I.QueryParseError(r,t.start,t.end)}if(a.type===I.QueryLexer.TERM)return I.QueryParser.parseTerm;r="expecting term, found '"+a.type+"'";throw new I.QueryParseError(r,a.start,a.end)}},I.QueryParser.parseTerm=function(e){var t=e.consumeLexeme();if(null!=t){e.currentClause.term=t.str.toLowerCase(),-1!=t.str.indexOf("*")&&(e.currentClause.usePipeline=!1);var n=e.peekLexeme();if(null!=n)switch(n.type){case I.QueryLexer.TERM:return e.nextClause(),I.QueryParser.parseTerm;case I.QueryLexer.FIELD:return e.nextClause(),I.QueryParser.parseField;case I.QueryLexer.EDIT_DISTANCE:return I.QueryParser.parseEditDistance;case I.QueryLexer.BOOST:return I.QueryParser.parseBoost;case I.QueryLexer.PRESENCE:return e.nextClause(),I.QueryParser.parsePresence;default:var r="Unexpected lexeme type '"+n.type+"'";throw new I.QueryParseError(r,n.start,n.end)}else e.nextClause()}},I.QueryParser.parseEditDistance=function(e){var t=e.consumeLexeme();if(null!=t){var n=parseInt(t.str,10);if(isNaN(n)){var r="edit distance must be numeric";throw new I.QueryParseError(r,t.start,t.end)}e.currentClause.editDistance=n;var a=e.peekLexeme();if(null!=a)switch(a.type){case I.QueryLexer.TERM:return e.nextClause(),I.QueryParser.parseTerm;case I.QueryLexer.FIELD:return e.nextClause(),I.QueryParser.parseField;case I.QueryLexer.EDIT_DISTANCE:return I.QueryParser.parseEditDistance;case I.QueryLexer.BOOST:return I.QueryParser.parseBoost;case I.QueryLexer.PRESENCE:return e.nextClause(),I.QueryParser.parsePresence;default:r="Unexpected lexeme type '"+a.type+"'";throw new I.QueryParseError(r,a.start,a.end)}else e.nextClause()}},I.QueryParser.parseBoost=function(e){var t=e.consumeLexeme();if(null!=t){var n=parseInt(t.str,10);if(isNaN(n)){var r="boost must be numeric";throw new I.QueryParseError(r,t.start,t.end)}e.currentClause.boost=n;var a=e.peekLexeme();if(null!=a)switch(a.type){case I.QueryLexer.TERM:return e.nextClause(),I.QueryParser.parseTerm;case 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e.languages.kotlin["class-name"];var t={"interpolation-punctuation":{pattern:/^\$\{?|\}$/,alias:"punctuation"},expression:{pattern:/[\s\S]+/,inside:e.languages.kotlin}};e.languages.insertBefore("kotlin","string",{"string-literal":[{pattern:/"""(?:[^$]|\$(?:(?!\{)|\{[^{}]*\}))*?"""/,alias:"multiline",inside:{interpolation:{pattern:/\$(?:[a-z_]\w*|\{[^{}]*\})/i,inside:t},string:/[\s\S]+/}},{pattern:/"(?:[^"\\\r\n$]|\\.|\$(?:(?!\{)|\{[^{}]*\}))*"/,alias:"singleline",inside:{interpolation:{pattern:/((?:^|[^\\])(?:\\{2})*)\$(?:[a-z_]\w*|\{[^{}]*\})/i,lookbehind:!0,inside:t},string:/[\s\S]+/}}],char:{pattern:/'(?:[^'\\\r\n]|\\(?:.|u[a-fA-F0-9]{0,4}))'/,greedy:!0}}),delete e.languages.kotlin.string,e.languages.insertBefore("kotlin","keyword",{annotation:{pattern:/\B@(?:\w+:)?(?:[A-Z]\w*|\[[^\]]+\])/,alias:"builtin"}}),e.languages.insertBefore("kotlin","function",{label:{pattern:/\b\w+@|@\w+\b/,alias:"symbol"}}),e.languages.kt=e.languages.kotlin,e.languages.kts=e.languages.kotlin}(T),T.languages.c=T.languages.extend("clike",{comment:{pattern:/\/\/(?:[^\r\n\\]|\\(?:\r\n?|\n|(?![\r\n])))*|\/\*[\s\S]*?(?:\*\/|$)/,greedy:!0},string:{pattern:/"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"/,greedy:!0},"class-name":{pattern:/(\b(?:enum|struct)\s+(?:__attribute__\s*\(\([\s\S]*?\)\)\s*)?)\w+|\b[a-z]\w*_t\b/,lookbehind:!0},keyword:/\b(?:_Alignas|_Alignof|_Atomic|_Bool|_Complex|_Generic|_Imaginary|_Noreturn|_Static_assert|_Thread_local|__attribute__|asm|auto|break|case|char|const|continue|default|do|double|else|enum|extern|float|for|goto|if|inline|int|long|register|return|short|signed|sizeof|static|struct|switch|typedef|typeof|union|unsigned|void|volatile|while)\b/,function:/\b[a-z_]\w*(?=\s*\()/i,number:/(?:\b0x(?:[\da-f]+(?:\.[\da-f]*)?|\.[\da-f]+)(?:p[+-]?\d+)?|(?:\b\d+(?:\.\d*)?|\B\.\d+)(?:e[+-]?\d+)?)[ful]{0,4}/i,operator:/>>=?|<<=?|->|([-+&|:])\1|[?:~]|[-+*/%&|^!=<>]=?/}),T.languages.insertBefore("c","string",{char:{pattern:/'(?:\\(?:\r\n|[\s\S])|[^'\\\r\n]){0,32}'/,greedy:!0}}),T.languages.insertBefore("c","string",{macro:{pattern:/(^[\t 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T.languages.c.boolean,T.languages.objectivec=T.languages.extend("c",{string:{pattern:/@?"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"/,greedy:!0},keyword:/\b(?:asm|auto|break|case|char|const|continue|default|do|double|else|enum|extern|float|for|goto|if|in|inline|int|long|register|return|self|short|signed|sizeof|static|struct|super|switch|typedef|typeof|union|unsigned|void|volatile|while)\b|(?:@interface|@end|@implementation|@protocol|@class|@public|@protected|@private|@property|@try|@catch|@finally|@throw|@synthesize|@dynamic|@selector)\b/,operator:/-[->]?|\+\+?|!=?|<<?=?|>>?=?|==?|&&?|\|\|?|[~^%?*\/@]/}),delete 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t=/\/\*(?:[^*/]|\*(?!\/)|\/(?!\*)|<self>)*\*\//.source,n=0;n<2;n++)t=t.replace(/<self>/g,(function(){return 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T.languages.go["class-name"],function(e){var t=/\b(?:alignas|alignof|asm|auto|bool|break|case|catch|char|char16_t|char32_t|char8_t|class|co_await|co_return|co_yield|compl|concept|const|const_cast|consteval|constexpr|constinit|continue|decltype|default|delete|do|double|dynamic_cast|else|enum|explicit|export|extern|final|float|for|friend|goto|if|import|inline|int|int16_t|int32_t|int64_t|int8_t|long|module|mutable|namespace|new|noexcept|nullptr|operator|override|private|protected|public|register|reinterpret_cast|requires|return|short|signed|sizeof|static|static_assert|static_cast|struct|switch|template|this|thread_local|throw|try|typedef|typeid|typename|uint16_t|uint32_t|uint64_t|uint8_t|union|unsigned|using|virtual|void|volatile|wchar_t|while)\b/,n=/\b(?!<keyword>)\w+(?:\s*\.\s*\w+)*\b/.source.replace(/<keyword>/g,(function(){return 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e=[],t=[{prefix:"",node:this}];t.length;){var n=t.pop(),r=Object.keys(n.node.edges),a=r.length;n.node.final&&(n.prefix.charAt(0),e.push(n.prefix));for(var o=0;o<a;o++){var i=r[o];t.push({prefix:n.prefix.concat(i),node:n.node.edges[i]})}}return e},I.TokenSet.prototype.toString=function(){if(this._str)return this._str;for(var e=this.final?"1":"0",t=Object.keys(this.edges).sort(),n=t.length,r=0;r<n;r++){var a=t[r];e=e+a+this.edges[a].id}return e},I.TokenSet.prototype.intersect=function(e){for(var t=new I.TokenSet,n=void 0,r=[{qNode:e,output:t,node:this}];r.length;){n=r.pop();for(var a=Object.keys(n.qNode.edges),o=a.length,i=Object.keys(n.node.edges),s=i.length,l=0;l<o;l++)for(var u=a[l],c=0;c<s;c++){var d=i[c];if(d==u||"*"==u){var p=n.node.edges[d],f=n.qNode.edges[u],m=p.final&&f.final,g=void 0;d in n.output.edges?(g=n.output.edges[d]).final=g.final||m:((g=new I.TokenSet).final=m,n.output.edges[d]=g),r.push({qNode:f,output:g,node:p})}}}return t},I.TokenSet.Builder=function(){this.previousWord="",this.root=new I.TokenSet,this.uncheckedNodes=[],this.minimizedNodes={}},I.TokenSet.Builder.prototype.insert=function(e){var t,n=0;if(e<this.previousWord)throw new Error("Out of order word insertion");for(var r=0;r<e.length&&r<this.previousWord.length&&e[r]==this.previousWord[r];r++)n++;this.minimize(n),t=0==this.uncheckedNodes.length?this.root:this.uncheckedNodes[this.uncheckedNodes.length-1].child;for(r=n;r<e.length;r++){var a=new I.TokenSet,o=e[r];t.edges[o]=a,this.uncheckedNodes.push({parent:t,char:o,child:a}),t=a}t.final=!0,this.previousWord=e},I.TokenSet.Builder.prototype.finish=function(){this.minimize(0)},I.TokenSet.Builder.prototype.minimize=function(e){for(var t=this.uncheckedNodes.length-1;t>=e;t--){var n=this.uncheckedNodes[t],r=n.child.toString();r in 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g=0;g<l.fields.length;g++){o[A=l.fields[g]]=I.Set.empty}break}for(var h=0;h<m.length;h++){var b=m[h],y=this.invertedIndex[b],v=y._index;for(g=0;g<l.fields.length;g++){var w=y[A=l.fields[g]],x=Object.keys(w),k=b+"/"+A,S=new I.Set(x);if(l.presence==I.Query.presence.REQUIRED&&(c=c.union(S),void 0===o[A]&&(o[A]=I.Set.complete)),l.presence!=I.Query.presence.PROHIBITED){if(r[A].upsert(v,l.boost,(function(e,t){return e+t})),!a[k]){for(var _=0;_<x.length;_++){var E,C=x[_],T=new I.FieldRef(C,A),P=w[C];void 0===(E=n[T])?n[T]=new I.MatchData(b,A,P):E.add(b,A,P)}a[k]=!0}}else void 0===i[A]&&(i[A]=I.Set.empty),i[A]=i[A].union(S)}}}if(l.presence===I.Query.presence.REQUIRED)for(g=0;g<l.fields.length;g++){o[A=l.fields[g]]=o[A].intersect(c)}}var L=I.Set.complete,j=I.Set.empty;for(s=0;s<this.fields.length;s++){var A;o[A=this.fields[s]]&&(L=L.intersect(o[A])),i[A]&&(j=j.union(i[A]))}var R=Object.keys(n),N=[],O=Object.create(null);if(t.isNegated()){R=Object.keys(this.fieldVectors);for(s=0;s<R.length;s++){T=R[s];var D=I.FieldRef.fromString(T);n[T]=new I.MatchData}}for(s=0;s<R.length;s++){var F=(D=I.FieldRef.fromString(R[s])).docRef;if(L.contains(F)&&!j.contains(F)){var M,z=this.fieldVectors[D],B=r[D.fieldName].similarity(z);if(void 0!==(M=O[F]))M.score+=B,M.matchData.combine(n[D]);else{var $={ref:F,score:B,matchData:n[D]};O[F]=$,N.push($)}}}return N.sort((function(e,t){return t.score-e.score}))},I.Index.prototype.toJSON=function(){var e=Object.keys(this.invertedIndex).sort().map((function(e){return[e,this.invertedIndex[e]]}),this),t=Object.keys(this.fieldVectors).map((function(e){return[e,this.fieldVectors[e].toJSON()]}),this);return{version:I.version,fields:this.fields,fieldVectors:t,invertedIndex:e,pipeline:this.pipeline.toJSON()}},I.Index.load=function(e){var t={},n={},r=e.fieldVectors,a=Object.create(null),o=e.invertedIndex,i=new I.TokenSet.Builder,s=I.Pipeline.load(e.pipeline);e.version!=I.version&&I.utils.warn("Version mismatch when loading serialised index. Current version of lunr '"+I.version+"' does not match serialized index '"+e.version+"'");for(var l=0;l<r.length;l++){var u=(d=r[l])[0],c=d[1];n[u]=new I.Vector(c)}for(l=0;l<o.length;l++){var d,p=(d=o[l])[0],f=d[1];i.insert(p),a[p]=f}return i.finish(),t.fields=e.fields,t.fieldVectors=n,t.invertedIndex=a,t.tokenSet=i.root,t.pipeline=s,new I.Index(t)},I.Builder=function(){this._ref="id",this._fields=Object.create(null),this._documents=Object.create(null),this.invertedIndex=Object.create(null),this.fieldTermFrequencies={},this.fieldLengths={},this.tokenizer=I.tokenizer,this.pipeline=new I.Pipeline,this.searchPipeline=new I.Pipeline,this.documentCount=0,this._b=.75,this._k1=1.2,this.termIndex=0,this.metadataWhitelist=[]},I.Builder.prototype.ref=function(e){this._ref=e},I.Builder.prototype.field=function(e,t){if(/\//.test(e))throw new RangeError("Field '"+e+"' contains illegal character '/'");this._fields[e]=t||{}},I.Builder.prototype.b=function(e){this._b=e<0?0:e>1?1:e},I.Builder.prototype.k1=function(e){this._k1=e},I.Builder.prototype.add=function(e,t){var n=e[this._ref],r=Object.keys(this._fields);this._documents[n]=t||{},this.documentCount+=1;for(var a=0;a<r.length;a++){var o=r[a],i=this._fields[o].extractor,s=i?i(e):e[o],l=this.tokenizer(s,{fields:[o]}),u=this.pipeline.run(l),c=new I.FieldRef(n,o),d=Object.create(null);this.fieldTermFrequencies[c]=d,this.fieldLengths[c]=0,this.fieldLengths[c]+=u.length;for(var p=0;p<u.length;p++){var f=u[p];if(null==d[f]&&(d[f]=0),d[f]+=1,null==this.invertedIndex[f]){var m=Object.create(null);m._index=this.termIndex,this.termIndex+=1;for(var g=0;g<r.length;g++)m[r[g]]=Object.create(null);this.invertedIndex[f]=m}null==this.invertedIndex[f][o][n]&&(this.invertedIndex[f][o][n]=Object.create(null));for(var h=0;h<this.metadataWhitelist.length;h++){var b=this.metadataWhitelist[h],y=f.metadata[b];null==this.invertedIndex[f][o][n][b]&&(this.invertedIndex[f][o][n][b]=[]),this.invertedIndex[f][o][n][b].push(y)}}}},I.Builder.prototype.calculateAverageFieldLengths=function(){for(var e=Object.keys(this.fieldLengths),t=e.length,n={},r={},a=0;a<t;a++){var o=I.FieldRef.fromString(e[a]),i=o.fieldName;r[i]||(r[i]=0),r[i]+=1,n[i]||(n[i]=0),n[i]+=this.fieldLengths[o]}var s=Object.keys(this._fields);for(a=0;a<s.length;a++){var l=s[a];n[l]=n[l]/r[l]}this.averageFieldLength=n},I.Builder.prototype.createFieldVectors=function(){for(var e={},t=Object.keys(this.fieldTermFrequencies),n=t.length,r=Object.create(null),a=0;a<n;a++){for(var o=I.FieldRef.fromString(t[a]),i=o.fieldName,s=this.fieldLengths[o],l=new I.Vector,u=this.fieldTermFrequencies[o],c=Object.keys(u),d=c.length,p=this._fields[i].boost||1,f=this._documents[o.docRef].boost||1,m=0;m<d;m++){var g,h,b,y=c[m],v=u[y],w=this.invertedIndex[y]._index;void 0===r[y]?(g=I.idf(this.invertedIndex[y],this.documentCount),r[y]=g):g=r[y],h=g*((this._k1+1)*v)/(this._k1*(1-this._b+this._b*(s/this.averageFieldLength[i]))+v),h*=p,h*=f,b=Math.round(1e3*h)/1e3,l.insert(w,b)}e[o]=l}this.fieldVectors=e},I.Builder.prototype.createTokenSet=function(){this.tokenSet=I.TokenSet.fromArray(Object.keys(this.invertedIndex).sort())},I.Builder.prototype.build=function(){return this.calculateAverageFieldLengths(),this.createFieldVectors(),this.createTokenSet(),new I.Index({invertedIndex:this.invertedIndex,fieldVectors:this.fieldVectors,tokenSet:this.tokenSet,fields:Object.keys(this._fields),pipeline:this.searchPipeline})},I.Builder.prototype.use=function(e){var t=Array.prototype.slice.call(arguments,1);t.unshift(this),e.apply(this,t)},I.MatchData=function(e,t,n){for(var r=Object.create(null),a=Object.keys(n||{}),o=0;o<a.length;o++){var i=a[o];r[i]=n[i].slice()}this.metadata=Object.create(null),void 0!==e&&(this.metadata[e]=Object.create(null),this.metadata[e][t]=r)},I.MatchData.prototype.combine=function(e){for(var t=Object.keys(e.metadata),n=0;n<t.length;n++){var r=t[n],a=Object.keys(e.metadata[r]);null==this.metadata[r]&&(this.metadata[r]=Object.create(null));for(var o=0;o<a.length;o++){var i=a[o],s=Object.keys(e.metadata[r][i]);null==this.metadata[r][i]&&(this.metadata[r][i]=Object.create(null));for(var l=0;l<s.length;l++){var u=s[l];null==this.metadata[r][i][u]?this.metadata[r][i][u]=e.metadata[r][i][u]:this.metadata[r][i][u]=this.metadata[r][i][u].concat(e.metadata[r][i][u])}}}},I.MatchData.prototype.add=function(e,t,n){if(!(e in this.metadata))return this.metadata[e]=Object.create(null),void(this.metadata[e][t]=n);if(t in this.metadata[e])for(var r=Object.keys(n),a=0;a<r.length;a++){var o=r[a];o in this.metadata[e][t]?this.metadata[e][t][o]=this.metadata[e][t][o].concat(n[o]):this.metadata[e][t][o]=n[o]}else this.metadata[e][t]=n},I.Query=function(e){this.clauses=[],this.allFields=e},I.Query.wildcard=new String("*"),I.Query.wildcard.NONE=0,I.Query.wildcard.LEADING=1,I.Query.wildcard.TRAILING=2,I.Query.presence={OPTIONAL:1,REQUIRED:2,PROHIBITED:3},I.Query.prototype.clause=function(e){return"fields"in e||(e.fields=this.allFields),"boost"in e||(e.boost=1),"usePipeline"in e||(e.usePipeline=!0),"wildcard"in e||(e.wildcard=I.Query.wildcard.NONE),e.wildcard&I.Query.wildcard.LEADING&&e.term.charAt(0)!=I.Query.wildcard&&(e.term="*"+e.term),e.wildcard&I.Query.wildcard.TRAILING&&e.term.slice(-1)!=I.Query.wildcard&&(e.term=e.term+"*"),"presence"in e||(e.presence=I.Query.presence.OPTIONAL),this.clauses.push(e),this},I.Query.prototype.isNegated=function(){for(var e=0;e<this.clauses.length;e++)if(this.clauses[e].presence!=I.Query.presence.PROHIBITED)return!1;return!0},I.Query.prototype.term=function(e,t){if(Array.isArray(e))return e.forEach((function(e){this.term(e,I.utils.clone(t))}),this),this;var n=t||{};return n.term=e.toString(),this.clause(n),this},I.QueryParseError=function(e,t,n){this.name="QueryParseError",this.message=e,this.start=t,this.end=n},I.QueryParseError.prototype=new Error,I.QueryLexer=function(e){this.lexemes=[],this.str=e,this.length=e.length,this.pos=0,this.start=0,this.escapeCharPositions=[]},I.QueryLexer.prototype.run=function(){for(var e=I.QueryLexer.lexText;e;)e=e(this)},I.QueryLexer.prototype.sliceString=function(){for(var e=[],t=this.start,n=this.pos,r=0;r<this.escapeCharPositions.length;r++)n=this.escapeCharPositions[r],e.push(this.str.slice(t,n)),t=n+1;return e.push(this.str.slice(t,this.pos)),this.escapeCharPositions.length=0,e.join("")},I.QueryLexer.prototype.emit=function(e){this.lexemes.push({type:e,str:this.sliceString(),start:this.start,end:this.pos}),this.start=this.pos},I.QueryLexer.prototype.escapeCharacter=function(){this.escapeCharPositions.push(this.pos-1),this.pos+=1},I.QueryLexer.prototype.next=function(){if(this.pos>=this.length)return I.QueryLexer.EOS;var e=this.str.charAt(this.pos);return this.pos+=1,e},I.QueryLexer.prototype.width=function(){return this.pos-this.start},I.QueryLexer.prototype.ignore=function(){this.start==this.pos&&(this.pos+=1),this.start=this.pos},I.QueryLexer.prototype.backup=function(){this.pos-=1},I.QueryLexer.prototype.acceptDigitRun=function(){var e,t;do{t=(e=this.next()).charCodeAt(0)}while(t>47&&t<58);e!=I.QueryLexer.EOS&&this.backup()},I.QueryLexer.prototype.more=function(){return this.pos<this.length},I.QueryLexer.EOS="EOS",I.QueryLexer.FIELD="FIELD",I.QueryLexer.TERM="TERM",I.QueryLexer.EDIT_DISTANCE="EDIT_DISTANCE",I.QueryLexer.BOOST="BOOST",I.QueryLexer.PRESENCE="PRESENCE",I.QueryLexer.lexField=function(e){return e.backup(),e.emit(I.QueryLexer.FIELD),e.ignore(),I.QueryLexer.lexText},I.QueryLexer.lexTerm=function(e){if(e.width()>1&&(e.backup(),e.emit(I.QueryLexer.TERM)),e.ignore(),e.more())return I.QueryLexer.lexText},I.QueryLexer.lexEditDistance=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(I.QueryLexer.EDIT_DISTANCE),I.QueryLexer.lexText},I.QueryLexer.lexBoost=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(I.QueryLexer.BOOST),I.QueryLexer.lexText},I.QueryLexer.lexEOS=function(e){e.width()>0&&e.emit(I.QueryLexer.TERM)},I.QueryLexer.termSeparator=I.tokenizer.separator,I.QueryLexer.lexText=function(e){for(;;){var t=e.next();if(t==I.QueryLexer.EOS)return I.QueryLexer.lexEOS;if(92!=t.charCodeAt(0)){if(":"==t)return I.QueryLexer.lexField;if("~"==t)return e.backup(),e.width()>0&&e.emit(I.QueryLexer.TERM),I.QueryLexer.lexEditDistance;if("^"==t)return e.backup(),e.width()>0&&e.emit(I.QueryLexer.TERM),I.QueryLexer.lexBoost;if("+"==t&&1===e.width())return e.emit(I.QueryLexer.PRESENCE),I.QueryLexer.lexText;if("-"==t&&1===e.width())return e.emit(I.QueryLexer.PRESENCE),I.QueryLexer.lexText;if(t.match(I.QueryLexer.termSeparator))return I.QueryLexer.lexTerm}else e.escapeCharacter()}},I.QueryParser=function(e,t){this.lexer=new I.QueryLexer(e),this.query=t,this.currentClause={},this.lexemeIdx=0},I.QueryParser.prototype.parse=function(){this.lexer.run(),this.lexemes=this.lexer.lexemes;for(var e=I.QueryParser.parseClause;e;)e=e(this);return this.query},I.QueryParser.prototype.peekLexeme=function(){return this.lexemes[this.lexemeIdx]},I.QueryParser.prototype.consumeLexeme=function(){var e=this.peekLexeme();return this.lexemeIdx+=1,e},I.QueryParser.prototype.nextClause=function(){var e=this.currentClause;this.query.clause(e),this.currentClause={}},I.QueryParser.parseClause=function(e){var t=e.peekLexeme();if(null!=t)switch(t.type){case I.QueryLexer.PRESENCE:return I.QueryParser.parsePresence;case I.QueryLexer.FIELD:return I.QueryParser.parseField;case I.QueryLexer.TERM:return I.QueryParser.parseTerm;default:var n="expected either a field or a term, found "+t.type;throw t.str.length>=1&&(n+=" with value '"+t.str+"'"),new I.QueryParseError(n,t.start,t.end)}},I.QueryParser.parsePresence=function(e){var t=e.consumeLexeme();if(null!=t){switch(t.str){case"-":e.currentClause.presence=I.Query.presence.PROHIBITED;break;case"+":e.currentClause.presence=I.Query.presence.REQUIRED;break;default:var n="unrecognised presence operator'"+t.str+"'";throw new I.QueryParseError(n,t.start,t.end)}var r=e.peekLexeme();if(null==r){n="expecting term or field, found nothing";throw new I.QueryParseError(n,t.start,t.end)}switch(r.type){case I.QueryLexer.FIELD:return I.QueryParser.parseField;case I.QueryLexer.TERM:return I.QueryParser.parseTerm;default:n="expecting term or field, found '"+r.type+"'";throw new I.QueryParseError(n,r.start,r.end)}}},I.QueryParser.parseField=function(e){var t=e.consumeLexeme();if(null!=t){if(-1==e.query.allFields.indexOf(t.str)){var n=e.query.allFields.map((function(e){return"'"+e+"'"})).join(", "),r="unrecognised field '"+t.str+"', possible fields: "+n;throw new I.QueryParseError(r,t.start,t.end)}e.currentClause.fields=[t.str];var a=e.peekLexeme();if(null==a){r="expecting term, found nothing";throw new I.QueryParseError(r,t.start,t.end)}if(a.type===I.QueryLexer.TERM)return I.QueryParser.parseTerm;r="expecting term, found '"+a.type+"'";throw new I.QueryParseError(r,a.start,a.end)}},I.QueryParser.parseTerm=function(e){var t=e.consumeLexeme();if(null!=t){e.currentClause.term=t.str.toLowerCase(),-1!=t.str.indexOf("*")&&(e.currentClause.usePipeline=!1);var n=e.peekLexeme();if(null!=n)switch(n.type){case I.QueryLexer.TERM:return e.nextClause(),I.QueryParser.parseTerm;case I.QueryLexer.FIELD:return e.nextClause(),I.QueryParser.parseField;case I.QueryLexer.EDIT_DISTANCE:return I.QueryParser.parseEditDistance;case I.QueryLexer.BOOST:return I.QueryParser.parseBoost;case I.QueryLexer.PRESENCE:return e.nextClause(),I.QueryParser.parsePresence;default:var r="Unexpected lexeme type '"+n.type+"'";throw new I.QueryParseError(r,n.start,n.end)}else e.nextClause()}},I.QueryParser.parseEditDistance=function(e){var t=e.consumeLexeme();if(null!=t){var n=parseInt(t.str,10);if(isNaN(n)){var r="edit distance must be numeric";throw new I.QueryParseError(r,t.start,t.end)}e.currentClause.editDistance=n;var a=e.peekLexeme();if(null!=a)switch(a.type){case I.QueryLexer.TERM:return e.nextClause(),I.QueryParser.parseTerm;case I.QueryLexer.FIELD:return e.nextClause(),I.QueryParser.parseField;case I.QueryLexer.EDIT_DISTANCE:return I.QueryParser.parseEditDistance;case I.QueryLexer.BOOST:return I.QueryParser.parseBoost;case I.QueryLexer.PRESENCE:return e.nextClause(),I.QueryParser.parsePresence;default:r="Unexpected lexeme type '"+a.type+"'";throw new I.QueryParseError(r,a.start,a.end)}else e.nextClause()}},I.QueryParser.parseBoost=function(e){var t=e.consumeLexeme();if(null!=t){var n=parseInt(t.str,10);if(isNaN(n)){var r="boost must be numeric";throw new I.QueryParseError(r,t.start,t.end)}e.currentClause.boost=n;var a=e.peekLexeme();if(null!=a)switch(a.type){case I.QueryLexer.TERM:return e.nextClause(),I.QueryParser.parseTerm;case 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e.languages.kotlin["class-name"];var t={"interpolation-punctuation":{pattern:/^\$\{?|\}$/,alias:"punctuation"},expression:{pattern:/[\s\S]+/,inside:e.languages.kotlin}};e.languages.insertBefore("kotlin","string",{"string-literal":[{pattern:/"""(?:[^$]|\$(?:(?!\{)|\{[^{}]*\}))*?"""/,alias:"multiline",inside:{interpolation:{pattern:/\$(?:[a-z_]\w*|\{[^{}]*\})/i,inside:t},string:/[\s\S]+/}},{pattern:/"(?:[^"\\\r\n$]|\\.|\$(?:(?!\{)|\{[^{}]*\}))*"/,alias:"singleline",inside:{interpolation:{pattern:/((?:^|[^\\])(?:\\{2})*)\$(?:[a-z_]\w*|\{[^{}]*\})/i,lookbehind:!0,inside:t},string:/[\s\S]+/}}],char:{pattern:/'(?:[^'\\\r\n]|\\(?:.|u[a-fA-F0-9]{0,4}))'/,greedy:!0}}),delete e.languages.kotlin.string,e.languages.insertBefore("kotlin","keyword",{annotation:{pattern:/\B@(?:\w+:)?(?:[A-Z]\w*|\[[^\]]+\])/,alias:"builtin"}}),e.languages.insertBefore("kotlin","function",{label:{pattern:/\b\w+@|@\w+\b/,alias:"symbol"}}),e.languages.kt=e.languages.kotlin,e.languages.kts=e.languages.kotlin}(T),T.languages.c=T.languages.extend("clike",{comment:{pattern:/\/\/(?:[^\r\n\\]|\\(?:\r\n?|\n|(?![\r\n])))*|\/\*[\s\S]*?(?:\*\/|$)/,greedy:!0},string:{pattern:/"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"/,greedy:!0},"class-name":{pattern:/(\b(?:enum|struct)\s+(?:__attribute__\s*\(\([\s\S]*?\)\)\s*)?)\w+|\b[a-z]\w*_t\b/,lookbehind:!0},keyword:/\b(?:_Alignas|_Alignof|_Atomic|_Bool|_Complex|_Generic|_Imaginary|_Noreturn|_Static_assert|_Thread_local|__attribute__|asm|auto|break|case|char|const|continue|default|do|double|else|enum|extern|float|for|goto|if|inline|int|long|register|return|short|signed|sizeof|static|struct|switch|typedef|typeof|union|unsigned|void|volatile|while)\b/,function:/\b[a-z_]\w*(?=\s*\()/i,number:/(?:\b0x(?:[\da-f]+(?:\.[\da-f]*)?|\.[\da-f]+)(?:p[+-]?\d+)?|(?:\b\d+(?:\.\d*)?|\B\.\d+)(?:e[+-]?\d+)?)[ful]{0,4}/i,operator:/>>=?|<<=?|->|([-+&|:])\1|[?:~]|[-+*/%&|^!=<>]=?/}),T.languages.insertBefore("c","string",{char:{pattern:/'(?:\\(?:\r\n|[\s\S])|[^'\\\r\n]){0,32}'/,greedy:!0}}),T.languages.insertBefore("c","string",{macro:{pattern:/(^[\t 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T.languages.c.boolean,T.languages.objectivec=T.languages.extend("c",{string:{pattern:/@?"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"/,greedy:!0},keyword:/\b(?:asm|auto|break|case|char|const|continue|default|do|double|else|enum|extern|float|for|goto|if|in|inline|int|long|register|return|self|short|signed|sizeof|static|struct|super|switch|typedef|typeof|union|unsigned|void|volatile|while)\b|(?:@interface|@end|@implementation|@protocol|@class|@public|@protected|@private|@property|@try|@catch|@finally|@throw|@synthesize|@dynamic|@selector)\b/,operator:/-[->]?|\+\+?|!=?|<<?=?|>>?=?|==?|&&?|\|\|?|[~^%?*\/@]/}),delete 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t=/\/\*(?:[^*/]|\*(?!\/)|\/(?!\*)|<self>)*\*\//.source,n=0;n<2;n++)t=t.replace(/<self>/g,(function(){return 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T.languages.go["class-name"],function(e){var t=/\b(?:alignas|alignof|asm|auto|bool|break|case|catch|char|char16_t|char32_t|char8_t|class|co_await|co_return|co_yield|compl|concept|const|const_cast|consteval|constexpr|constinit|continue|decltype|default|delete|do|double|dynamic_cast|else|enum|explicit|export|extern|final|float|for|friend|goto|if|import|inline|int|int16_t|int32_t|int64_t|int8_t|long|module|mutable|namespace|new|noexcept|nullptr|operator|override|private|protected|public|register|reinterpret_cast|requires|return|short|signed|sizeof|static|static_assert|static_cast|struct|switch|template|this|thread_local|throw|try|typedef|typeid|typename|uint16_t|uint32_t|uint64_t|uint8_t|union|unsigned|using|virtual|void|volatile|wchar_t|while)\b/,n=/\b(?!<keyword>)\w+(?:\s*\.\s*\w+)*\b/.source.replace(/<keyword>/g,(function(){return 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class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Adding a new calibration type</h1></header><div class="theme-admonition theme-admonition-info admonition_xJq3 alert alert--info"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 14 16"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"></path></svg></span>info</div><div class="admonitionContent_BuS1"><p>This is subject to change! Currently we don&#x27;t like how much a developer has to implement (or copy and paste) to create a new calibration. We want to make it easier to design new calibrations.</p></div></div>
diff --git a/developer-guide/adding-plugins-to-ui.html b/developer-guide/adding-plugins-to-ui.html
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interface, so you and your users don&#x27;t need to use the command line at all. We&#x27;ve built support for easily adding to the web interface.</p>
diff --git a/developer-guide/architecture.html b/developer-guide/architecture.html
index c21f3b7b8..bf73648f2 100644
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For example, if running an air bubbler, you may want to turn it off before an OD reading is taken, and then turn if back on after.</p>
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Below is an example of adding a chart that displays historical and real-time CO2 sensor data.</p>
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href="/developer-guide/data-stores-intro">Storage and the filesystem</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/i2c-addresses">Hardware</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/web-ui-introduction">User interface</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/adding-calibration-type">Calibrations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/local-development">Development</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/developer-guide/architecture">The Big Architecture Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Automation events</h1></header><p>The <code>execute</code> method attached to any automation can return either <code>None</code>, or a <code>AutomationEvent</code>. If the latter, the event will be published to MQTT as a published setting, i.e under the topic <code>pioreactor/&lt;unit&gt;/&lt;experiment&gt;/dosing_automation/latest_event</code>. This can be used to downstream events that want to know about what events are occurring.</p>
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href="/developer-guide/local-development">Development</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/developer-guide/architecture">The Big Architecture Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Important locations on the filesystem</h1></header><p>Below is a list of important locations and files on the filesystem for the Pioreactor:</p>
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For example, you could do things like:</p>
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menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/local-development">Development</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/developer-guide/architecture">The Big Architecture Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Introduction to background jobs</h1></header><p>The core unit of &quot;work&quot; in the Pioreactor software is a background job (called <em>activities</em> in the web interface). Background jobs include <code>od_reading</code>, <code>monitor</code>, automation controllers, all the <em>automations</em> themselves, etc. Often, a community plugin is a background job (or multiple jobs) that gives your bioreactor new abilities. There are a few important features of background jobs to be highlighted if you intend on working with them.</p>
diff --git a/developer-guide/intro-plugins.html b/developer-guide/intro-plugins.html
index 12b33278f..71a07bb30 100644
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@@ -16,8 +16,8 @@
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menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/i2c-addresses">Hardware</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/web-ui-introduction">User interface</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/adding-calibration-type">Calibrations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/local-development">Development</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/developer-guide/architecture">The Big Architecture Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Working with plugins</h1></header><p>Pioreactor plugins are a way to distribute code to others (or yourself), and avoid having to use the command line each time you invoke your custom code - you should be able to just use the web interface.</p>
diff --git a/developer-guide/introduction.html b/developer-guide/introduction.html
index d8be1c334..93c39b776 100644
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href="/developer-guide/local-development">Development</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/developer-guide/architecture">The Big Architecture Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>More about MQTT on the Pioreactor</h1></header><h3 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="how-do-you-structure-topics-for-mqtt">How do you structure topics for MQTT?<a href="#how-do-you-structure-topics-for-mqtt" class="hash-link" aria-label="Direct link to How do you structure topics for MQTT?" 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by creating a Python package and uploading to PyPI. Let&#x27;s walk through this!</p>
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href="/developer-guide/local-development">Development</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/developer-guide/architecture">The Big Architecture Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>More about SQLite3 on the Pioreactor</h1></header><h3 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="how-do-i-access-the-sqlite3-database">How do I access the SQlite3 database?<a href="#how-do-i-access-the-sqlite3-database" class="hash-link" aria-label="Direct link to How do I access the SQlite3 database?" title="Direct link to How do I access the SQlite3 database?">​</a></h3>
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diff --git a/developer-guide/web-ui-introduction.html b/developer-guide/web-ui-introduction.html
index ee49912ce..0ef1d2dfd 100644
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Here are the details:</p>
diff --git a/developer-guide/writing-automations-1.html b/developer-guide/writing-automations-1.html
index 5ae1de5f4..5d2e70238 100644
--- a/developer-guide/writing-automations-1.html
+++ b/developer-guide/writing-automations-1.html
@@ -16,8 +16,8 @@
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href="/developer-guide/adding-calibration-type">Calibrations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/local-development">Development</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/developer-guide/architecture">The Big Architecture Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Writing a new automation</h1></header><p>An automation is a hands-off way to adjust the environment for the microbes. We currently support three types of automations: dosing, LED, and temperature.</p>
diff --git a/developer-guide/writing-automations-2.html b/developer-guide/writing-automations-2.html
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@@ -16,8 +16,8 @@
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href="/developer-guide/adding-calibration-type">Calibrations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/local-development">Development</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/developer-guide/architecture">The Big Architecture Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Another example writing a new automation</h1></header><p>Let&#x27;s design a simple LED automation for Light/Dark cycles. The basic idea is that the LED automation &quot;wakes up&quot; (specifically: it runs its <code>execute</code> method) every hour, and on specific hours, turns on or turns off the white light LEDs.</p>
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Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Custom &amp; additional pumps for dosing automations</h1></header><p>The following provides solutions to:</p>
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aria-expanded="false" href="/developer-guide/web-ui-introduction">User interface</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/adding-calibration-type">Calibrations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/developer-guide/local-development">Development</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/developer-guide/architecture">The Big Architecture Picture</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Writing scripts</h1></header><p>Since the behaviour of the Pioreactor is controlled by Python objects, you can write Python scripts that use those objects. Here&#x27;s a simple example of starting the stirring by creating the <code>Stirrer</code> object:</p>
diff --git a/experiments/algae-day-night-cycle.html b/experiments/algae-day-night-cycle.html
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href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Algae day and night cycles</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success goal</div><div class="admonitionContent_BuS1"><p>This experiment will show the growth curve of algae over a 20h:4h day/night cycle, at two different intensities (4% and 8%).</p></div></div>
diff --git a/experiments/caffeine-inhibition.html b/experiments/caffeine-inhibition.html
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class="menu__link" tabindex="0" href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Caffeine inhibition</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success Goal</div><div class="admonitionContent_BuS1"><p>Use caffeine-containing liquids to inhibit the growth of your culture.</p></div></div>
diff --git a/experiments/continuous-cultures-using-turbidostat.html b/experiments/continuous-cultures-using-turbidostat.html
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href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Continuous cultures using a turbidostat</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success goal</div><div class="admonitionContent_BuS1"><p>Determine the maximum specific growth rate of your culture using turbidostat strategies and pump extentions of the Pioreactor.</p></div></div>
diff --git a/experiments/control-testing.html b/experiments/control-testing.html
index 5fed27070..3bb8a0724 100644
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class="menu__link" tabindex="0" href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Control testing</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success Goal</div><div class="admonitionContent_BuS1"><p>Conduct a simple control test to evaluate results between Pioreactors, using the same media composition, culture, and activities.</p></div></div>
diff --git a/experiments/directed-evolution-salt-tolerance.html b/experiments/directed-evolution-salt-tolerance.html
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href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Directed evolution of salt-tolerant yeast</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success goal</div><div class="admonitionContent_BuS1"><p>Use a turbidostat system with selective pressures to study evolutionary principles.</p></div></div>
diff --git a/experiments/introduction.html b/experiments/introduction.html
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Explore the sidebar for experiments you can perform with your Pioreactor. We encourage you to expand on the sample protocols we provided using your own cultures and media.</p>
diff --git a/experiments/low-vs-high-conc-media.html b/experiments/low-vs-high-conc-media.html
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class="menu__link" tabindex="0" href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Comparing concentrations of media</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success Goal</div><div class="admonitionContent_BuS1"><p>Conduct a simple comparison of yeast growth between a low percent and high percent YPD media.</p></div></div>
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class="menu__link" tabindex="0" href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Osmotic pressure induced by salt</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success Goal</div><div class="admonitionContent_BuS1"><p>Use your Pioreactor to model how cells are affected by high salt (hypertonic) solutions.</p><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>tip</div><div class="admonitionContent_BuS1"><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="requirements">Requirements<a href="#requirements" class="hash-link" aria-label="Direct link to Requirements" title="Direct link to Requirements">​</a></h2><div style="padding:10px;margin:20px 0px 60px 0px;display:flex;flex-wrap:nowrap"><div id="mainImage" style="width:55%;float:left;margin-right:10px"><h2>  <a href="/experiments/salt-stress-on-yeast#">#</a></h2><img maxheight="240" src="/assets/images/salt_materials-31133e7671b00ff3407421b7b84ccf49.jpg"></div><section style="width:44%;float:left;margin-top:40px"><ul>
diff --git a/experiments/tags.html b/experiments/tags.html
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mainWrapper_z2l0"><div class="container margin-vert--lg"><div class="row"><main class="col col--8 col--offset-2"><h1>Tags</h1><section class="margin-vert--lg"><article><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="C">C<a href="#C" class="hash-link" aria-label="Direct link to C" title="Direct link to C">​</a></h2><ul class="padding--none"><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/caffeine">caffeine<span>1</span></a></li><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/continuous-culture">Continuous culture<span>2</span></a></li><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/control">Control<span>1</span></a></li></ul><hr></article><article><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="E">E<a href="#E" class="hash-link" aria-label="Direct link to E" title="Direct link to E">​</a></h2><ul class="padding--none"><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/ethanol">Ethanol<span>1</span></a></li></ul><hr></article><article><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="N">N<a href="#N" class="hash-link" aria-label="Direct link to N" title="Direct link to N">​</a></h2><ul class="padding--none"><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/nutrient">nutrient<span>1</span></a></li></ul><hr></article><article><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="S">S<a href="#S" class="hash-link" aria-label="Direct link to S" title="Direct link to S">​</a></h2><ul class="padding--none"><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/salt">Salt<span>1</span></a></li><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/secondary-education">Secondary education<span>2</span></a></li><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/seconday-education">Seconday education<span>1</span></a></li></ul><hr></article><article><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="T">T<a href="#T" class="hash-link" aria-label="Direct link to T" title="Direct link to T">​</a></h2><ul class="padding--none"><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/temperature">Temperature<span>1</span></a></li><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/turbidostat">Turbidostat<span>2</span></a></li></ul><hr></article><article><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="U">U<a href="#U" class="hash-link" aria-label="Direct link to U" title="Direct link to U">​</a></h2><ul class="padding--none"><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/university-education">University education<span>2</span></a></li></ul><hr></article><article><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="Y">Y<a href="#Y" class="hash-link" aria-label="Direct link to Y" title="Direct link to Y">​</a></h2><ul class="padding--none"><li class="tag_Nnez"><a class="tag_zVej tagWithCount_h2kH" href="/experiments/tags/yeast">Yeast<span>8</span></a></li></ul><hr></article></section></main></div></div></div><footer class="footer footer--dark"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Topics</div><ul class="footer__items clean-list"><li class="footer__item"><a class="footer__link-item" href="/user-guide/introduction">User Guide</a></li><li class="footer__item"><a class="footer__link-item" href="/developer-guide/introduction">Developer Guide</a></li><li class="footer__item"><a class="footer__link-item" href="/experiments/introduction">Experiments</a></li><li class="footer__item"><a href="https://github.com/Pioreactor/pioreactor/blob/master/CHANGELOG.md" target="_blank" rel="noopener noreferrer" 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diff --git a/experiments/tags/temperature.html b/experiments/tags/temperature.html
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mainWrapper_z2l0"><div class="container margin-vert--lg"><div class="row"><main class="col col--8 col--offset-2"><header class="margin-bottom--xl"><h1>8 docs tagged with &quot;Yeast&quot;</h1><a href="/experiments/tags">View All Tags</a></header><section class="margin-vert--lg"><article class="margin-vert--lg"><a href="/experiments/caffeine-inhibition"><h2>Caffeine inhibition</h2></a><p>Use caffeine-containing liquids to inhibit the growth of your culture.</p></article><article class="margin-vert--lg"><a href="/experiments/low-vs-high-conc-media"><h2>Comparing concentrations of media</h2></a><p>Conduct a simple comparison of yeast growth between a low percent and high percent YPD media.</p></article><article class="margin-vert--lg"><a href="/experiments/continuous-cultures-using-turbidostat"><h2>Continuous cultures using a turbidostat</h2></a><p>Determine the maximum specific growth rate of your culture using turbidostat strategies and pump extentions of the Pioreactor.</p></article><article class="margin-vert--lg"><a href="/experiments/control-testing"><h2>Control testing</h2></a><p>Conduct a simple control test to evaluate results between Pioreactors, using the same media composition, culture, and activities.</p></article><article class="margin-vert--lg"><a href="/experiments/directed-evolution-salt-tolerance"><h2>Directed evolution of salt-tolerant yeast</h2></a><p>Use a turbidostat system with selective pressures to study evolutionary principles.</p></article><article class="margin-vert--lg"><a href="/experiments/salt-stress-on-yeast"><h2>Osmotic pressure induced by salt</h2></a><p>Use your Pioreactor to model how cells are affected by high salt (hypertonic) solutions.</p></article><article class="margin-vert--lg"><a href="/experiments/yeast-growth-by-temperature"><h2>Yeast growth at varying temperatures</h2></a><p>Demonstrate the effect of temperature on yeast growth.</p></article><article class="margin-vert--lg"><a href="/experiments/yeast-in-ethanol"><h2>Yeast growth in ethanol</h2></a><p>Explore the ethanol fermentation process and practice dilution calculations for media preparation.</p></article></section></main></div></div></div><footer class="footer footer--dark"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Topics</div><ul class="footer__items clean-list"><li class="footer__item"><a class="footer__link-item" href="/user-guide/introduction">User Guide</a></li><li class="footer__item"><a class="footer__link-item" href="/developer-guide/introduction">Developer Guide</a></li><li class="footer__item"><a class="footer__link-item" href="/experiments/introduction">Experiments</a></li><li class="footer__item"><a href="https://github.com/Pioreactor/pioreactor/blob/master/CHANGELOG.md" target="_blank" rel="noopener noreferrer" class="footer__link-item">Changelog</a></li></ul></div><div class="col footer__col"><div 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href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link menu__link--active" aria-current="page" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Temperature cycling of continuous cultures</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success Goal</div><div class="admonitionContent_BuS1"><p>Apply turbidostat functions with temperature cycling to study yeast behaviour in a more natural temperature environment.</p></div></div>
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class="menu__link" tabindex="0" href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Yeast growth at varying temperatures</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success Goal</div><div class="admonitionContent_BuS1"><p>Demonstrate the effect of temperature on yeast growth.</p><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>tip</div><div class="admonitionContent_BuS1"><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="requirements">Requirements<a href="#requirements" class="hash-link" aria-label="Direct link to Requirements" title="Direct link to Requirements">​</a></h2><div style="padding:10px;margin:20px 0px 60px 0px;display:flex;flex-wrap:nowrap"><div id="mainImage" style="width:55%;float:left;margin-right:10px"><h2>  <a href="/experiments/yeast-growth-by-temperature#">#</a></h2><img maxheight="240" src="/assets/images/two_pio_plus_vials-b3818c4810f006921d74598265ffba4f.jpg"></div><section style="width:44%;float:left;margin-top:40px"><ul>
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class="menu__link" tabindex="0" href="/experiments/directed-evolution-salt-tolerance">Directed evolution of salt-tolerant yeast</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/experiments/temp-cycle">Temperature cycling of continuous cultures</a></li></ul></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Yeast growth in ethanol</h1></header><div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>Success goal</div><div class="admonitionContent_BuS1"><p>Explore the ethanol fermentation process and practice dilution calculations for media preparation.</p></div></div>
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interested in the Pioreactor customizations, API, plugin development, and hacking.</p></div></div><div class="col col--4"><div class="text--center"><a href="/experiments/introduction"><svg width="121" height="86" viewBox="0 0 121 86" xmlns="http://www.w3.org/2000/svg" class="featureSvg__8YW" stroke="#5332CA" fill="#5332CA" alt="Experiments"><title>interface</title><g stroke="current" fill="none" fill-rule="evenodd"><path stroke-width="6.5" d="M3.25 3.25h114.4v79.3H3.25z"></path><path d="m20.8 60.148 24.267-2.755L70.149 41.54 93.6 32.5v2.328L70.149 44.32 45.067 59.802 20.8 62.4m3.9-.65a4.55 4.55 0 1 1-9.1 0 4.55 4.55 0 0 1 9.1 0m24.7-2.6c0 2.513-2.328 4.55-5.2 4.55-2.872 0-5.2-2.037-5.2-4.55s2.328-4.55 5.2-4.55c2.872 0 5.2 2.037 5.2 4.55m26-16.25a5.2 5.2 0 1 1-10.4 0 5.2 5.2 0 0 1 10.4 0m23.4-9.1a5.2 5.2 0 1 1-10.4 0 5.2 5.2 0 0 1 10.4 0Z" fill="current" fill-rule="nonzero"></path><path stroke-width="3.9" d="M4.742 19.349H114.4"></path><circle stroke-width="2.3" fill="current" cx="11.05" cy="12.35" r="1.3"></circle><circle stroke-width="2.3" fill="current" cx="17.55" cy="12.35" r="1.3"></circle><circle stroke-width="2.3" fill="current" cx="24.05" cy="12.35" r="1.3"></circle><path stroke-width="2.6" d="M11.05 26.679V71.32h95.472"></path></g></svg></a></div><div class="text--center padding-horiz--md"><h3><a href="/experiments/introduction" style="text-decoration:none;color:inherit">Experiments</a></h3><p>Implement Pioreactor-based experiments, from classrooms to research-level.</p></div></div></div></div></section></main></div><footer class="footer footer--dark"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Topics</div><ul class="footer__items clean-list"><li class="footer__item"><a class="footer__link-item" href="/user-guide/introduction">User Guide</a></li><li class="footer__item"><a class="footer__link-item" href="/developer-guide/introduction">Developer Guide</a></li><li 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diff --git a/search-index.json b/search-index.json
index 89ad3009a..622aba8e6 100644
--- a/search-index.json
+++ b/search-index.json
@@ -1 +1 @@
-[{"documents":[{"i":1,"t":"The Big Architecture Picture","u":"/developer-guide/architecture","b":[]},{"i":2,"t":"Adding your plugins to the web interface","u":"/developer-guide/adding-plugins-to-ui","b":["Plugins"]},{"i":17,"t":"Introduction","u":"/developer-guide/data-stores-intro","b":["Storage and the filesystem","Data stores in the Pioreactor"]},{"i":25,"t":"Adding basic time series charts","u":"/developer-guide/chart-to-ui","b":["User interface"]},{"i":33,"t":"Automation events","u":"/developer-guide/events","b":["Automations"]},{"i":37,"t":"Important locations on the filesystem","u":"/developer-guide/filesystem-locations","b":["Storage and the filesystem"]},{"i":53,"t":"I²C addresses","u":"/developer-guide/i2c-addresses","b":["Hardware"]},{"i":55,"t":"Adding behaviour to the HAT's button","u":"/developer-guide/hat-button","b":["Hardware"]},{"i":57,"t":"Important concepts","u":"/developer-guide/important-concepts","b":[]},{"i":68,"t":"Avoiding when optical density is run","u":"/developer-guide/avoiding-od","b":["Background jobs"]},{"i":70,"t":"Automations architecture","u":"/developer-guide/intro-automations","b":["Automations"]},{"i":75,"t":"Working with plugins","u":"/developer-guide/intro-plugins","b":["Plugins"]},{"i":87,"t":"Introduction to background jobs","u":"/developer-guide/intro-background-jobs","b":["Background jobs"]},{"i":105,"t":"Introduction for developers","u":"/developer-guide/introduction","b":["Developer Guide"]},{"i":111,"t":"Local development of Pioreactor","u":"/developer-guide/local-development","b":["Development"]},{"i":124,"t":"More about local storage on the Pioreactor","u":"/developer-guide/local-storage","b":["Storage and the filesystem","Data stores in the Pioreactor"]},{"i":129,"t":"More about MQTT on the Pioreactor","u":"/developer-guide/mqtt","b":["Storage and the filesystem","Data stores in the Pioreactor"]},{"i":134,"t":"Development on a Raspberry Pi","u":"/developer-guide/pi-development","b":["Development"]},{"i":137,"t":"Pinout diagram","u":"/developer-guide/pinout","b":["Hardware"]},{"i":138,"t":"Turning your plugins into a Python package to share","u":"/developer-guide/plugin-as-python-package","b":["Plugins"]},{"i":152,"t":"Overview","u":"/developer-guide/web-ui-introduction","b":["User interface"]},{"i":166,"t":"More about SQLite3 on the Pioreactor","u":"/developer-guide/sqlite3","b":["Storage and the filesystem","Data stores in the Pioreactor"]},{"i":175,"t":"Adding a new calibration type","u":"/developer-guide/adding-calibration-type","b":["Calibrations"]},{"i":177,"t":"API","u":"/developer-guide/web-ui-api","b":["User interface"]},{"i":180,"t":"Writing a new automation","u":"/developer-guide/writing-automations-1","b":["Automations"]},{"i":190,"t":"Another example writing a new automation","u":"/developer-guide/writing-automations-2","b":["Automations"]},{"i":200,"t":"Algae day and night 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#","u":"/user-guide/20ml-v11-optics-assembly","h":"","p":365},{"i":367,"t":"Step 2: Secure bulbs into pockets  #","u":"/user-guide/20ml-v11-optics-assembly","h":"","p":365},{"i":368,"t":"Step 3: You're done!  #","u":"/user-guide/20ml-v11-optics-assembly","h":"","p":365},{"i":370,"t":"Step 1: Necessary parts  #","u":"/user-guide/20ml-v11-rpi-hat-assembly","h":"","p":369},{"i":371,"t":"Step 2: Assemble the bottom faceplate  #","u":"/user-guide/20ml-v11-rpi-hat-assembly","h":"","p":369},{"i":372,"t":"Step 3: Placing the HAT PCB on top  #","u":"/user-guide/20ml-v11-rpi-hat-assembly","h":"","p":369},{"i":373,"t":"Step 2: Assemble the bottom faceplate  #","u":"/user-guide/20ml-v11-rpi-hat-assembly","h":"","p":369},{"i":374,"t":"Step 3: Placing the HAT PCB ontop  #","u":"/user-guide/20ml-v11-rpi-hat-assembly","h":"","p":369},{"i":377,"t":"Step 1: Necessary tools  #","u":"/user-guide/20ml-v11-hardware-setup-intro","h":"","p":375},{"i":378,"t":"Step 2: Use all the information available to you  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Using the Command Prompt","u":"/user-guide/accessing-raspberry-pi","h":"#1-using-the-command-prompt","p":381},{"i":387,"t":"2. Using PuTTY","u":"/user-guide/accessing-raspberry-pi","h":"#2-using-putty","p":381},{"i":389,"t":"Access from a Mac","u":"/user-guide/accessing-raspberry-pi","h":"#access-from-a-mac","p":381},{"i":391,"t":"Access from Linux","u":"/user-guide/accessing-raspberry-pi","h":"#access-from-linux","p":381},{"i":393,"t":"Troubleshooting","u":"/user-guide/accessing-raspberry-pi","h":"#troubleshooting","p":381},{"i":396,"t":"Step 1: Inserting the O-rings  #","u":"/user-guide/20ml-v11-wetware-assembly","h":"","p":395},{"i":397,"t":"Step 2: Attach the window cover  #","u":"/user-guide/20ml-v11-wetware-assembly","h":"","p":395},{"i":398,"t":"Step 3: Connect the flex cable  #","u":"/user-guide/20ml-v11-wetware-assembly","h":"","p":395},{"i":399,"t":"Step 4: Place and secure the heater PCB  #","u":"/user-guide/20ml-v11-wetware-assembly","h":"","p":395},{"i":400,"t":"Step 5: Placing the heating pad  #","u":"/user-guide/20ml-v11-wetware-assembly","h":"","p":395},{"i":401,"t":"Step 6: Complete the vial 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like?","u":"/user-guide/experiment-profiles","h":"#what-do-they-look-like","p":472},{"i":479,"t":"Examples","u":"/user-guide/experiment-profiles","h":"#examples","p":472},{"i":482,"t":"Step 1: Necessary parts  #","u":"/user-guide/20ml-v11-putting-it-together","h":"","p":481},{"i":483,"t":"Step 2: Securing the vial holder  #","u":"/user-guide/20ml-v11-putting-it-together","h":"","p":481},{"i":484,"t":"Step 3: Button extension  #","u":"/user-guide/20ml-v11-putting-it-together","h":"","p":481},{"i":485,"t":"Step 4: Putting it all together  #","u":"/user-guide/20ml-v11-putting-it-together","h":"","p":481},{"i":488,"t":"The blue LED is constantly on?","u":"/user-guide/error-codes","h":"#the-blue-led-is-constantly-on","p":486},{"i":492,"t":"Pioreactor Unit Activity Data","u":"/user-guide/export-data","h":"#pioreactor-unit-activity-data","p":490},{"i":495,"t":"Using the UI","u":"/user-guide/create-edit-experiment-profiles","h":"#using-the-ui","p":494},{"i":497,"t":"On the command line","u":"/user-guide/create-edit-experiment-profiles","h":"#on-the-command-line","p":494},{"i":499,"t":"Tips to writing profiles","u":"/user-guide/create-edit-experiment-profiles","h":"#tips-to-writing-profiles","p":494},{"i":500,"t":"hours_elapsed refers to the profile start time","u":"/user-guide/create-edit-experiment-profiles","h":"#hours_elapsed-refers-to-the-profile-start-time","p":494},{"i":502,"t":"How the if directive works","u":"/user-guide/create-edit-experiment-profiles","h":"#how-the-if-directive-works","p":494},{"i":504,"t":"How expressions work","u":"/user-guide/create-edit-experiment-profiles","h":"#how-expressions-work","p":494},{"i":506,"t":"Expressions in options","u":"/user-guide/create-edit-experiment-profiles","h":"#expressions-in-options","p":494},{"i":508,"t":"Expressions in the common block","u":"/user-guide/create-edit-experiment-profiles","h":"#expressions-in-the-common-block","p":494},{"i":510,"t":"The repeat action","u":"/user-guide/create-edit-experiment-profiles","h":"#the-repeat-action","p":494},{"i":512,"t":"Start/stop controllers instead of automations","u":"/user-guide/create-edit-experiment-profiles","h":"#startstop-controllers-instead-of-automations","p":494},{"i":514,"t":"Update automations instead of controllers","u":"/user-guide/create-edit-experiment-profiles","h":"#update-automations-instead-of-controllers","p":494},{"i":516,"t":"YAML syntax check, and indentation problems","u":"/user-guide/create-edit-experiment-profiles","h":"#yaml-syntax-check-and-indentation-problems","p":494},{"i":518,"t":"Expected `object`, got `array` - at ` ... .options`","u":"/user-guide/create-edit-experiment-profiles","h":"#expected-object-got-array---at---options","p":494},{"i":521,"t":"Export your data","u":"/user-guide/export-import-existing-data","h":"#export-your-data","p":520},{"i":523,"t":"Import your data to a new, fresh, Pioreactor","u":"/user-guide/export-import-existing-data","h":"#import-your-data-to-a-new-fresh-pioreactor","p":520},{"i":527,"t":"Power supply for using Pioreactor peristaltic pumps","u":"/user-guide/external-power","h":"#power-supply-for-using-pioreactor-peristaltic-pumps","p":525},{"i":529,"t":"More details on power supply","u":"/user-guide/external-power","h":"#more-details-on-power-supply","p":525},{"i":533,"t":"Stirring calibration (optional)","u":"/user-guide/hardware-calibrations","h":"#stirring-calibration-optional","p":531},{"i":535,"t":"Calibrating the stirring in the UI  #","u":"/user-guide/hardware-calibrations","h":"","p":531},{"i":536,"t":"Pump calibration","u":"/user-guide/hardware-calibrations","h":"#pump-calibration","p":531},{"i":538,"t":"Calibrating the pumps  #","u":"/user-guide/hardware-calibrations","h":"","p":531},{"i":539,"t":"Made a mistake, or want to change some 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help?","u":"/user-guide/introduction","h":"#looking-for-further-help","p":553},{"i":565,"t":"Silent","u":"/user-guide/led-automations","h":"#silent","p":563},{"i":567,"t":"Light/Dark cycle","u":"/user-guide/led-automations","h":"#lightdark-cycle","p":563},{"i":571,"t":"Pioreactor 20ml assembly","u":"/user-guide/getting-started","h":"","p":569},{"i":573,"t":"Pioreactor 20ml v1.1","u":"/user-guide/getting-started","h":"","p":569},{"i":574,"t":"Pioreactor 20ml v1.0","u":"/user-guide/getting-started","h":"","p":569},{"i":575,"t":"Upgrade kits and accessories","u":"/user-guide/getting-started","h":"","p":569},{"i":577,"t":"Pioreactor 20ml v1.0 → v1.1 upgrade kit","u":"/user-guide/getting-started","h":"","p":569},{"i":578,"t":"Temperature Expansion Kit","u":"/user-guide/getting-started","h":"","p":569},{"i":579,"t":"Adding peristaltic pumps","u":"/user-guide/getting-started","h":"","p":569},{"i":580,"t":"Adding more 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SSHing into your Raspberry Pi","u":"/user-guide/intro-python-scripting","h":"#1-sshing-into-your-raspberry-pi","p":584},{"i":588,"t":"2. Writing our first script.","u":"/user-guide/intro-python-scripting","h":"#2-writing-our-first-script","p":584},{"i":590,"t":"3. Running our Python script","u":"/user-guide/intro-python-scripting","h":"#3-running-our-python-script","p":584},{"i":592,"t":"4. Extending our script: more jobs, changing RPM, and adding lights.","u":"/user-guide/intro-python-scripting","h":"#4-extending-our-script-more-jobs-changing-rpm-and-adding-lights","p":584},{"i":594,"t":"5. Adding an automation","u":"/user-guide/intro-python-scripting","h":"#5-adding-an-automation","p":584},{"i":596,"t":"Conclusion","u":"/user-guide/intro-python-scripting","h":"#conclusion","p":584},{"i":600,"t":"General networking tools","u":"/user-guide/networking","h":"#general-networking-tools","p":598},{"i":602,"t":"Connecting to a wifi network using nmcli","u":"/user-guide/networking","h":"#connecting-to-a-wifi-network-using-nmcli","p":598},{"i":604,"t":"Connecting to multiple networks","u":"/user-guide/networking","h":"#connecting-to-multiple-networks","p":598},{"i":606,"t":"Starting the Pioreactor local access point using nmcli","u":"/user-guide/networking","h":"#starting-the-pioreactor-local-access-point-using-nmcli","p":598},{"i":608,"t":"Changing web UI port from 80 to something else","u":"/user-guide/networking","h":"#changing-web-ui-port-from-80-to-something-else","p":598},{"i":610,"t":"Connecting to eduroam","u":"/user-guide/networking","h":"#connecting-to-eduroam","p":598},{"i":614,"t":"Adding Pioreactors to your cluster","u":"/user-guide/create-cluster","h":"#adding-pioreactors-to-your-cluster","p":612},{"i":616,"t":"Active and inactive","u":"/user-guide/create-cluster","h":"#active-and-inactive","p":612},{"i":618,"t":"Possible cluster topologies","u":"/user-guide/create-cluster","h":"#possible-cluster-topologies","p":612},{"i":620,"t":"Common questions","u":"/user-guide/create-cluster","h":"#common-questions","p":612},{"i":624,"t":"Skip first run?","u":"/user-guide/intro-to-automations","h":"#skip-first-run","p":622},{"i":627,"t":"Dosing","u":"/user-guide/manual-dosing-leds","h":"#dosing","p":626},{"i":629,"t":"LEDs","u":"/user-guide/manual-dosing-leds","h":"#leds","p":626},{"i":633,"t":"Starting a local access point","u":"/user-guide/local-access-point","h":"#starting-a-local-access-point","p":631},{"i":635,"t":"Access the local access point","u":"/user-guide/local-access-point","h":"#access-the-local-access-point","p":631},{"i":637,"t":"Connecting more Pioreactors to your local access point","u":"/user-guide/local-access-point","h":"#connecting-more-pioreactors-to-your-local-access-point","p":631},{"i":639,"t":"Adding internet access to your local access point","u":"/user-guide/local-access-point","h":"#adding-internet-access-to-your-local-access-point","p":631},{"i":641,"t":"Turning off a local access point","u":"/user-guide/local-access-point","h":"#turning-off-a-local-access-point","p":631},{"i":643,"t":"Changing SSID name or password for your local access point","u":"/user-guide/local-access-point","h":"#changing-ssid-name-or-password-for-your-local-access-point","p":631},{"i":645,"t":"Troubleshooting","u":"/user-guide/local-access-point","h":"#troubleshooting","p":631},{"i":646,"t":"My computer can't connect to the local-access-point","u":"/user-guide/local-access-point","h":"#my-computer-cant-connect-to-the-local-access-point","p":631},{"i":648,"t":"I'm on the network, but can't load the Pioreactor UI at http://pioreactor.local","u":"/user-guide/local-access-point","h":"#im-on-the-network-but-cant-load-the-pioreactor-ui-at-httppioreactorlocal","p":631},{"i":650,"t":"I can't connect a worker to my local access point","u":"/user-guide/local-access-point","h":"#i-cant-connect-a-worker-to-my-local-access-point","p":631},{"i":652,"t":"I'm pretty sure I'm at the limit of ~4-8 clients on my access point - what can I do?","u":"/user-guide/local-access-point","h":"#im-pretty-sure-im-at-the-limit-of-4-8-clients-on-my-access-point---what-can-i-do","p":631},{"i":656,"t":"Event logs","u":"/user-guide/monitor-experiment","h":"#event-logs","p":654},{"i":658,"t":"Changing settings","u":"/user-guide/monitor-experiment","h":"#changing-settings","p":654},{"i":660,"t":"Identifying Pioreactors in your cluster","u":"/user-guide/monitor-experiment","h":"#identifying-pioreactors-in-your-cluster","p":654},{"i":662,"t":"Troubleshooting","u":"/user-guide/monitor-experiment","h":"#troubleshooting","p":654},{"i":664,"t":"Gradual increase in noise in OD","u":"/user-guide/monitor-experiment","h":"#gradual-increase-in-noise-in-od","p":654},{"i":666,"t":"Initial noise in OD","u":"/user-guide/monitor-experiment","h":"#initial-noise-in-od","p":654},{"i":668,"t":"Random spikes in OD","u":"/user-guide/monitor-experiment","h":"#random-spikes-in-od","p":654},{"i":670,"t":"Temperature fluctuations","u":"/user-guide/monitor-experiment","h":"#temperature-fluctuations","p":654},{"i":672,"t":"Looking for further help?","u":"/user-guide/monitor-experiment","h":"#looking-for-further-help","p":654},{"i":675,"t":"Step 1: Optic cables assembly  #","u":"/user-guide/optics-assembly","h":"","p":674},{"i":676,"t":"Step 2: Inserting the bulbs into the vial holder  #","u":"/user-guide/optics-assembly","h":"","p":674},{"i":677,"t":"Step 3: Add the rest of the LED caps  #","u":"/user-guide/optics-assembly","h":"","p":674},{"i":678,"t":"Step 4: Add the window covering (optional)  #","u":"/user-guide/optics-assembly","h":"","p":674},{"i":679,"t":"Step 4: Your done!  #","u":"/user-guide/optics-assembly","h":"","p":674},{"i":683,"t":"Background on optical density","u":"/user-guide/od-normal-growth-rate","h":"#background-on-optical-density","p":682},{"i":685,"t":"Normalization","u":"/user-guide/od-normal-growth-rate","h":"#normalization","p":682},{"i":687,"t":"Blanking","u":"/user-guide/od-normal-growth-rate","h":"#blanking","p":682},{"i":689,"t":"Growth rate","u":"/user-guide/od-normal-growth-rate","h":"#growth-rate","p":682},{"i":693,"t":"Pinch valve options","u":"/user-guide/pinch-valves","h":"#pinch-valve-options","p":691},{"i":695,"t":"Software","u":"/user-guide/pinch-valves","h":"#software","p":691},{"i":697,"t":"Recommended pinch valves","u":"/user-guide/pinch-valves","h":"#recommended-pinch-valves","p":691},{"i":700,"t":"1. Preparing the vial","u":"/user-guide/prepare-vial-for-cultures","h":"#1-preparing-the-vial","p":699},{"i":702,"t":"2. Preparing media","u":"/user-guide/prepare-vial-for-cultures","h":"#2-preparing-media","p":699},{"i":704,"t":"3. Sterilization","u":"/user-guide/prepare-vial-for-cultures","h":"#3-sterilization","p":699},{"i":706,"t":"4. Inoculation","u":"/user-guide/prepare-vial-for-cultures","h":"#4-inoculation","p":699},{"i":708,"t":"5. Adjusting tube lengths (Optional)","u":"/user-guide/prepare-vial-for-cultures","h":"#5-adjusting-tube-lengths-optional","p":699},{"i":710,"t":"6. Handling the glass","u":"/user-guide/prepare-vial-for-cultures","h":"#6-handling-the-glass","p":699},{"i":712,"t":"7. Positioning glassware in the Pioreactor sleeve","u":"/user-guide/prepare-vial-for-cultures","h":"#7-positioning-glassware-in-the-pioreactor-sleeve","p":699},{"i":714,"t":"Extra","u":"/user-guide/prepare-vial-for-cultures","h":"#extra","p":699},{"i":717,"t":"Step 1: Necessary parts  #","u":"/user-guide/putting-it-together","h":"","p":716},{"i":718,"t":"Step 2: Securing the vial holder  #","u":"/user-guide/putting-it-together","h":"","p":716},{"i":719,"t":"Step 3: Attaching the vial holder to the HAT  #","u":"/user-guide/putting-it-together","h":"","p":716},{"i":720,"t":"Step 4: Connecting heater and stirring to the HAT  #","u":"/user-guide/putting-it-together","h":"","p":716},{"i":722,"t":"Step 1: Necessary parts  #","u":"/user-guide/rpi-hat-assembly","h":"","p":721},{"i":723,"t":"Step 2: Assemble the bottom faceplate  #","u":"/user-guide/rpi-hat-assembly","h":"","p":721},{"i":724,"t":"Step 3: Placing the HAT PCB on top  #","u":"/user-guide/rpi-hat-assembly","h":"","p":721},{"i":725,"t":"Step 2: Assemble the bottom faceplate  #","u":"/user-guide/rpi-hat-assembly","h":"","p":721},{"i":726,"t":"Step 3: Placing the HAT PCB ontop  #","u":"/user-guide/rpi-hat-assembly","h":"","p":721},{"i":728,"t":"Introduction to remote access","u":"/user-guide/remote-access","h":"#introduction-to-remote-access","p":727},{"i":730,"t":"Security","u":"/user-guide/remote-access","h":"#security","p":727},{"i":734,"t":"How to run the self-test routine","u":"/user-guide/running-self-test","h":"#how-to-run-the-self-test-routine","p":732},{"i":736,"t":"Explanation of each test","u":"/user-guide/running-self-test","h":"#explanation-of-each-test","p":732},{"i":739,"t":"Creating an experiment","u":"/user-guide/set-up-an-experiment","h":"#creating-an-experiment","p":738},{"i":741,"t":"Assigning Pioreactors to your experiment","u":"/user-guide/set-up-an-experiment","h":"#assigning-pioreactors-to-your-experiment","p":738},{"i":743,"t":"(Optional) Blanking","u":"/user-guide/set-up-an-experiment","h":"#optional-blanking","p":738},{"i":745,"t":"How to record a blank  #","u":"/user-guide/set-up-an-experiment","h":"","p":738},{"i":746,"t":"Start activities from the Pioreactors page","u":"/user-guide/set-up-an-experiment","h":"#start-activities-from-the-pioreactors-page","p":738},{"i":748,"t":"Changing settings","u":"/user-guide/set-up-an-experiment","h":"#changing-settings","p":738},{"i":751,"t":"Before you begin","u":"/user-guide/software-set-up","h":"#before-you-begin","p":750},{"i":753,"t":"Setting up your Raspberry Pi","u":"/user-guide/software-set-up","h":"#setting-up-your-raspberry-pi","p":750},{"i":755,"t":"Adding additional workers to your cluster","u":"/user-guide/software-set-up","h":"#adding-additional-workers-to-your-cluster","p":750},{"i":757,"t":"Troubleshooting","u":"/user-guide/software-set-up","h":"#troubleshooting","p":750},{"i":763,"t":"Thermostat","u":"/user-guide/temperature-automations","h":"#thermostat","p":761},{"i":765,"t":"Only record temperature","u":"/user-guide/temperature-automations","h":"#only-record-temperature","p":761},{"i":768,"t":"My Pioreactor isn't responsive anymore","u":"/user-guide/troubleshooting-hardware","h":"#my-pioreactor-isnt-responsive-anymore","p":767},{"i":770,"t":"I see a \"Pioreactor HAT must be present\" error, but the HAT is definitely attached.","u":"/user-guide/troubleshooting-hardware","h":"#i-see-a-pioreactor-hat-must-be-present-error-but-the-hat-is-definitely-attached","p":767},{"i":772,"t":"I see \"The internal ADC/DAC is not responding. Exiting.\"","u":"/user-guide/troubleshooting-hardware","h":"#i-see-the-internal-adcdac-is-not-responding-exiting","p":767},{"i":774,"t":"I see \"Heating PCB must be attached to Pioreactor HAT\" or Heating PCB must be present to measure RPM.\" errors.","u":"/user-guide/troubleshooting-hardware","h":"#i-see-heating-pcb-must-be-attached-to-pioreactor-hat-or-heating-pcb-must-be-present-to-measure-rpm-errors","p":767},{"i":776,"t":"I'm having trouble with Pioreactor's stirring.","u":"/user-guide/troubleshooting-hardware","h":"#im-having-trouble-with-pioreactors-stirring","p":767},{"i":780,"t":"Step 0: before you begin  #","u":"/user-guide/temperature-expansion-kit","h":"","p":778},{"i":781,"t":"Step 1: Expose the Pioreactor HAT  #","u":"/user-guide/temperature-expansion-kit","h":"","p":778},{"i":782,"t":"Step 2: Attach the new HAT  #","u":"/user-guide/temperature-expansion-kit","h":"","p":778},{"i":783,"t":"Step 3: Attach the Pt1000  #","u":"/user-guide/temperature-expansion-kit","h":"","p":778},{"i":784,"t":"Step 4: Install the software  #","u":"/user-guide/temperature-expansion-kit","h":"","p":778},{"i":785,"t":"Troubleshooting","u":"/user-guide/temperature-expansion-kit","h":"#troubleshooting","p":778},{"i":786,"t":"I don't have internet access - how can I install the plugin?","u":"/user-guide/temperature-expansion-kit","h":"#i-dont-have-internet-access---how-can-i-install-the-plugin","p":778},{"i":788,"t":"I'm seeing \"Record null temperature. Is the Pt1000 probe connected?\" and the wire is connected.","u":"/user-guide/temperature-expansion-kit","h":"#im-seeing-record-null-temperature-is-the-pt1000-probe-connected-and-the-wire-is-connected","p":778},{"i":791,"t":"My Pioreactor activities start very slowly from the UI","u":"/user-guide/troubleshooting-networks","h":"#my-pioreactor-activities-start-very-slowly-from-the-ui","p":790},{"i":793,"t":"I'm having trouble with the local access point","u":"/user-guide/troubleshooting-networks","h":"#im-having-trouble-with-the-local-access-point","p":790},{"i":798,"t":"Stirring is making a grinding noise.","u":"/user-guide/troubleshooting-stirring","h":"#stirring-is-making-a-grinding-noise","p":797},{"i":800,"t":"UI is reporting \"Stirring RPM is 0\", or stirring self-test failed.","u":"/user-guide/troubleshooting-stirring","h":"#ui-is-reporting-stirring-rpm-is-0-or-stirring-self-test-failed","p":797},{"i":802,"t":"The magnets rub against the plastic screws above them, causing the stirring performance to be degraded / stop.","u":"/user-guide/troubleshooting-stirring","h":"#the-magnets-rub-against-the-plastic-screws-above-them-causing-the-stirring-performance-to-be-degraded--stop","p":797},{"i":804,"t":"Stir bar is not spinning","u":"/user-guide/troubleshooting-stirring","h":"#stir-bar-is-not-spinning","p":797},{"i":806,"t":"Stirring is not able to keep a steady RPM","u":"/user-guide/troubleshooting-stirring","h":"#stirring-is-not-able-to-keep-a-steady-rpm","p":797},{"i":808,"t":"My stir bar keeps skipping. How can I reduce that?","u":"/user-guide/troubleshooting-stirring","h":"#my-stir-bar-keeps-skipping-how-can-i-reduce-that","p":797},{"i":810,"t":"Raspberry Pi shuts off or restarts when stirring is turned on","u":"/user-guide/troubleshooting-stirring","h":"#raspberry-pi-shuts-off-or-restarts-when-stirring-is-turned-on","p":797},{"i":813,"t":"I'm not able to access http://pioreactor.local","u":"/user-guide/troubleshooting-ui","h":"#im-not-able-to-access-httppioreactorlocal","p":812},{"i":815,"t":"I see \"Failed to connect to MQTT. ...\" in a pop-up - what can I do?","u":"/user-guide/troubleshooting-ui","h":"#i-see-failed-to-connect-to-mqtt--in-a-pop-up---what-can-i-do","p":812},{"i":817,"t":"When I click an action in the UI, I don't see any response. Or the button just spins and does nothing.","u":"/user-guide/troubleshooting-ui","h":"#when-i-click-an-action-in-the-ui-i-dont-see-any-response-or-the-button-just-spins-and-does-nothing","p":812},{"i":821,"t":"Adding LEDs to your Pioreactor  #","u":"/user-guide/using-leds","h":"","p":819},{"i":824,"t":"Installing plugins","u":"/user-guide/using-community-plugins","h":"#installing-plugins","p":822},{"i":826,"t":"Automations installed via plugins","u":"/user-guide/using-community-plugins","h":"#automations-installed-via-plugins","p":822},{"i":828,"t":"Activities installed via plugins","u":"/user-guide/using-community-plugins","h":"#activities-installed-via-plugins","p":822},{"i":830,"t":"Uninstalling plugins","u":"/user-guide/using-community-plugins","h":"#uninstalling-plugins","p":822},{"i":832,"t":"Alternative: putting Python files in the the plugins folder","u":"/user-guide/using-community-plugins","h":"#alternative-putting-python-files-in-the-the-plugins-folder","p":822},{"i":836,"t":"Example","u":"/user-guide/using-stemma-qt","h":"#example","p":834},{"i":839,"t":"Step 1: Inserting the O-rings  #","u":"/user-guide/v11-upgrade-building-vial-holder","h":"","p":838},{"i":840,"t":"Step 2: Attach the window cover  #","u":"/user-guide/v11-upgrade-building-vial-holder","h":"","p":838},{"i":841,"t":"Step 3: Place and secure the heater PCB  #","u":"/user-guide/v11-upgrade-building-vial-holder","h":"","p":838},{"i":842,"t":"Step 4: Complete the vial holder  #","u":"/user-guide/v11-upgrade-building-vial-holder","h":"","p":838},{"i":845,"t":"Method 1: Updating over the internet","u":"/user-guide/updating-software","h":"#method-1-updating-over-the-internet","p":843},{"i":847,"t":"Method 2: Update using a zip file and the UI","u":"/user-guide/updating-software","h":"#method-2-update-using-a-zip-file-and-the-ui","p":843},{"i":849,"t":"Method 3: Update using a zip file over scp or sftp","u":"/user-guide/updating-software","h":"#method-3-update-using-a-zip-file-over-scp-or-sftp","p":843},{"i":852,"t":"Step 1: Upgrade parts  #","u":"/user-guide/v11-upgrade-hardware-setup","h":"","p":851},{"i":853,"t":"Step 2: Use all the information available to you  #","u":"/user-guide/v11-upgrade-hardware-setup","h":"","p":851},{"i":854,"t":"Step 3: Electronics protection  #","u":"/user-guide/v11-upgrade-hardware-setup","h":"","p":851},{"i":855,"t":"Step 4: We are here for you!  #","u":"/user-guide/v11-upgrade-hardware-setup","h":"","p":851},{"i":857,"t":"Step 1: Insert optic cables into channels  #","u":"/user-guide/v11-upgrade-optics-assembly","h":"","p":856},{"i":858,"t":"Step 2: Secure bulbs into pockets  #","u":"/user-guide/v11-upgrade-optics-assembly","h":"","p":856},{"i":859,"t":"Step 3: You're done!  #","u":"/user-guide/v11-upgrade-optics-assembly","h":"","p":856},{"i":861,"t":"Step 1: Unplug and disassemble the optics system  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":860},{"i":862,"t":"Step 2: Remove the top assembly from the base  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":860},{"i":863,"t":"Step 3: Remove the heater PCB from the vial holder  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":860},{"i":864,"t":"Step 4: Remove the window cover  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":860},{"i":865,"t":"Step 5: Items to be reused  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":860},{"i":867,"t":"Viewing pump configuration in config.ini","u":"/user-guide/using-pumps","h":"#viewing-pump-configuration-in-configini","p":866},{"i":869,"t":"Setting up the dosing platform  #","u":"/user-guide/using-pumps","h":"","p":866},{"i":870,"t":"Connecting the tubes  #","u":"/user-guide/using-pumps","h":"","p":866},{"i":871,"t":"Calibrating pumps","u":"/user-guide/using-pumps","h":"#calibrating-pumps","p":866},{"i":873,"t":"Using pumps in experiments","u":"/user-guide/using-pumps","h":"#using-pumps-in-experiments","p":866},{"i":875,"t":"Sterilizing the pumps before and after experiments","u":"/user-guide/using-pumps","h":"#sterilizing-the-pumps-before-and-after-experiments","p":866},{"i":877,"t":"Preparing for experiments","u":"/user-guide/using-pumps","h":"#preparing-for-experiments","p":866},{"i":879,"t":"Running pumps from the web interface","u":"/user-guide/using-pumps","h":"#running-pumps-from-the-web-interface","p":866},{"i":881,"t":"Running pumps from the command line","u":"/user-guide/using-pumps","h":"#running-pumps-from-the-command-line","p":866},{"i":883,"t":"Programmatically run pumps using automations","u":"/user-guide/using-pumps","h":"#programmatically-run-pumps-using-automations","p":866},{"i":886,"t":"Step 1: Necessary parts  #","u":"/user-guide/wetware-assembly","h":"","p":885},{"i":887,"t":"Step 2: Placing the heating pad  #","u":"/user-guide/wetware-assembly","h":"","p":885},{"i":888,"t":"Step 3: Securing the heating PCB into the vial holder  #","u":"/user-guide/wetware-assembly","h":"","p":885},{"i":890,"t":"Step 1: Necessary parts  #","u":"/user-guide/v11-upgrade-pioreactor-reassembly","h":"","p":889},{"i":891,"t":"Step 2: Complete the top assembly  #","u":"/user-guide/v11-upgrade-pioreactor-reassembly","h":"","p":889},{"i":892,"t":"Step 3: Button extension  #","u":"/user-guide/v11-upgrade-pioreactor-reassembly","h":"","p":889},{"i":893,"t":"Step 4: Putting it all together  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Placing your yaml file in either folder above will populate the dropdown list in the UI with your new automation. Here's an example example.yaml file: --- display_name: My Automations Name # human readable name automation_name: my_automations_name # the corresponding name of the automation from the Python code. source: my_plugin_name description: Provide a meaningful description of what the automation does, when to use it, how it works... fields: - key: duration # key is the same as the keyword in the Python code. default: 30 unit: min label: Duration between events - key: target_od default: 1.5 unit: AU label: Target OD - key: volume default: 0.75 unit: mL label: Max volume - key: intensity default: 50 unit: \"%\" # note: percent signs needs to be quoted. label: Intensity of PWM If this file was saved to the folder /home/pioreactor/.pioreactor/plugins/ui/contrib/automations/dosing, we would see the following in the web interface (after refreshing): More examples of automation yaml files here.","s":"Adding a custom automation to the drop-down of automations","u":"/developer-guide/adding-plugins-to-ui","h":"#adding-a-custom-automation-to-the-drop-down-of-automations","p":2},{"i":14,"t":"If your plugin produces data (or is some novel transformation of existing data), you can also add a new chart to the Overview page. See documentation here.","s":"Adding a chart to display a new data source","u":"/developer-guide/adding-plugins-to-ui","h":"#adding-a-chart-to-display-a-new-data-source","p":2},{"i":16,"t":"If the UI isn't display the data from your yaml, you may have introduced a yaml file that is not being read correctly. Look for error logs on the Overview page. There is a 30sec cache, so it may take up to 30sec to see new changes in the UI.","s":"Troubleshooting","u":"/developer-guide/adding-plugins-to-ui","h":"#troubleshooting","p":2},{"i":18,"t":"The Pioreactor has a few different ways to store data (depending on the requirements). They are:","s":"Introduction","u":"/developer-guide/data-stores-intro","h":"","p":17},{"i":20,"t":"The most important datastore is the SQLite3 database on the leader, located at /home/pioreactor/.pioreactor/storage/. This database stores historical data, jobs changes, logs, experiments, etc. The background job mqtt_to_db_streaming picks up data from MQTT (like OD readings), and puts them into the database. The CLI command pio db will open up the SQLite terminal to query the database directly. Backups of the database​ The Pioreactor software will automatically backup the SQLite database via a scheduale cron job. The backup is hosted locally on the Raspberry Pi, however if there if the cluster has active worker Pioreactors, the database backup is duplicated to (at most) two workers as well. This level of redundancy means that if the leader's microSD card fails, the database can be recovered from backups stored off the card.","s":"SQLite3","u":"/developer-guide/data-stores-intro","h":"#sqlite3","p":17},{"i":22,"t":"SQLite3 is also used by the library diskcache. This is essentially a fast key-value store on the Raspberry Pi. For Pioreactor, we use it to store \"machine-specific\" data, like calibration curves, locks on GPIOs, state of LEDs, jobs running, etc. Instead of one large file containing all these keys, we have split them into multiple locations based on category and level of persistence. The persistent databases are stored in /home/pioreactor/.pioreactor/storage and the temporary databases are in /tmp. You can access them from Python using pioreactor.utils.local_persistant_storage and pioreactor.utils.local_intermittent_storage, respectively. info What are temporary and persistent? Something like GPIO locks or LED state are physically reset between cycles of the Raspberry Pi. So when the Pi power-cycles, the state is wiped, and by have the database in /tmp, the databases are wiped as well. You can use pio view-cache <name> to view the contents of <name>, and pio clear-cache <name> <key> to clear contents.","s":"Local key-value datastore","u":"/developer-guide/data-stores-intro","h":"#local-key-value-datastore","p":17},{"i":24,"t":"The inter- and intra-Pioreactor communications are handled by MQTT, a pub/sub service. The MQTT broker is on the leader Pioreactor (pio mqtt will stream the latest messages to your terminal). MQTT is used to transfer data between workers and leader, and even between process on the workers (ex: OD readings are created on worker, send to leader, and then sent back to worker's growth_rate_calculating job. This does create minor latency, and certainly more risk of data loss, but simplifies the design of the system overall). A principle we have stood by is to not let MQTT turn into our database. That is, we shouldn't store important information in MQTT only (also use mqtt_to_db_streaming job to store important data in the SQLite3 database, or handle it locally using local_intermitant_storage or local_persistance_storage), we shouldn't store information in MQTT that is \"machine-specific\", like calibrations (better to use local_intermitant_storage or local_persistance_storage) we shouldn't use MQTT as a source of truth (trust the database, local_intermitant_storage or local_persistance_storage more). Serialization of MQTT messages​ We make a configuration change so MQTT data is not persisted through leader power-cycles. Authentication​ The Mosquitto broker has a username/password of pioreactor / raspberry.","s":"MQTT","u":"/developer-guide/data-stores-intro","h":"#mqtt","p":17},{"i":26,"t":"You can add custom charts to the UI. Below is an example of adding a chart that displays historical and real-time CO2 sensor data.","s":"Adding basic time series charts","u":"/developer-guide/chart-to-ui","h":"","p":25},{"i":28,"t":"Create a yaml file with the following fields, and place it in /home/pioreactor/.pioreactor/plugins/ui/contrib/charts. (Plugins can put the yaml file under ui/contrib/charts in there project folder - it will be added upon installation.) chart_key: a unique identifier for the chart being added, string. data_source: the SQL table to read historical data from. The data source must have a timestamp, pioreactor_unit, and experiment column, along with a numeric column to plot (see below), string. data_source_column: the column in data_source to read and display, string. title: title on the chart, string y_axis_label: the y-axis label, string fixed_decimals: How many decimals to display, integer. mqtt_topic: a truncated MQTT topic to read live data from - stripped of the pioreactor/<unit>/<experiment> part. Ex: co2_readings/ppm if the entire MQTT topic is pioreactor/<unit>/<experiment>/co2_readings/ppm, string. payload_key: (Optional) If the MQTT topic is json blobs, use the payload_key to retrieve the data from the blob, string. interpolation: (Optional) the interpolation to use between points, default is stepAfter, string. y_axis_domain: (Optional) specify a starting y-axis domain. Must be an array, like [0.0, 0.5]. y_transformation: (Optional) an inline JS function to transform the y data. Default is the identity function, string. See examples of yaml files here and here.","s":"Step 1","u":"/developer-guide/chart-to-ui","h":"#step-1","p":25},{"i":30,"t":"In your config.ini, add your chart key under [ui.overview.charts] and assign it 1. Example: [ui.overview.charts] # show/hide charts on the PioreactorUI dashboard # 1 is show, 0 is hide ... co2_readings=1 ...","s":"Step 2","u":"/developer-guide/chart-to-ui","h":"#step-2","p":25},{"i":32,"t":"If the UI stops displaying data, you may have introduced a yaml file that is not being read correctly. Check out the Pioreactor UI logs by sshing into the leader, and running: tail /var/log/pioreactorui.log The last few lines should tell you about if a field is missing, a wrong type, etc. There is a 30sec cache, so it may take up to 30sec to see new changes in the UI.","s":"Troubleshooting","u":"/developer-guide/chart-to-ui","h":"#troubleshooting","p":25},{"i":34,"t":"The execute method attached to any automation can return either None, or a AutomationEvent. If the latter, the event will be published to MQTT as a published setting, i.e under the topic pioreactor/<unit>/<experiment>/dosing_automation/latest_event. This can be used to downstream events that want to know about what events are occurring. It may make more sense to look at a specific execute. This is from the builtin Turbidostat automation: class Turbidostat(DosingAutomationJob): ... def execute(self) -> Optional[events.DilutionEvent]: if self.latest_od >= self.target_od: self.execute_io_action(media_ml=self.volume, waste_ml=self.volume) return events.DilutionEvent( f\"latest OD={self.latest_od:.2f} >= target OD={self.target_od:.2f}\", {'latest_od': self.latest_od, 'target_od': self.target_od} ) else: return When execute runs, either a DilutionEvent or nothing is returned. All events take up two (optional) arguments: a message, and a dictionary of arbitrary data. In this case, we've included a small message of why the dosing did or did not occur, and included some metadata about the optical densities. After execute returns an event, it will be published to MQTT. For example: pioreactor/unit/demo_exp/dosing_automation/latest_event {\"event_name\":\"NoEvent\",\"message\":\"latest OD=0.98 < target OD=1.00\",\"data\":{\"latest_od\":0.98,\"target_od\":1.0}} This can be listed in other jobs, and acted on, if needed.","s":"Automation events","u":"/developer-guide/events","h":"","p":33},{"i":36,"t":"Pioreactor ships with some default events. They are located in pioreactor.automation.events. Events are simple subclass of events.AutomationEvent, so events behave and look the same, except for their name. You can create custom automations, too: From pioreactor.automations.events import AutomationEvent class MyExampleEvent(AutomationEvent): pass class MyAutomation(...): ... def execute(self): ... event = MyExampleEvent(\"my message\", {'some_data': 1.0}) return event","s":"Using events, and creating your own","u":"/developer-guide/events","h":"#using-events-and-creating-your-own","p":33},{"i":38,"t":"Below is a list of important locations and files on the filesystem for the Pioreactor:","s":"Important locations on the filesystem","u":"/developer-guide/filesystem-locations","h":"","p":37},{"i":40,"t":"/var/www/pioreactorui/ is the source of the web-app. /var/www/pioreactorui/.env holds some configuration for the UI. /var/www/pioreactorui/contrib/ holds yaml files that display automation data, job data, and chart data. /home/pioreactor/.pioreactor/plugins/ui/contrib/ also holds yaml files, like the above.","s":"UI","u":"/developer-guide/filesystem-locations","h":"#ui","p":37},{"i":42,"t":"/var/log/pioreactor.log is the log file for the Pioreactor app /var/log/pioreactorui.log is the log file for the Pioreactor UI","s":"Logs","u":"/developer-guide/filesystem-locations","h":"#logs","p":37},{"i":44,"t":"/home/pioreactor/.pioreactor/storage/ holds the main database, backup of the database, and persistent caches. /tmp/ holds temporary caches. Files in here are not kept between reboots.","s":"Storage","u":"/developer-guide/filesystem-locations","h":"#storage","p":37},{"i":46,"t":"/usr/local/bin/ store bash scripts that are used when working with the filesystem: installing plugins, updating code, etc.","s":"Bash scripts","u":"/developer-guide/filesystem-locations","h":"#bash-scripts","p":37},{"i":48,"t":"/home/pioreactor/.pioreactor/ holds all configuration files for the Pioreactor UI and app, the main one being config.ini","s":"Config","u":"/developer-guide/filesystem-locations","h":"#config","p":37},{"i":50,"t":"/home/pioreactor/.pioreactor/plugins/ is where Python files can be added. /home/pioreactor/.pioreactor/plugins/ui/contrib/ also holds UI yaml files for custom Python code.","s":"Plugins","u":"/developer-guide/filesystem-locations","h":"#plugins","p":37},{"i":52,"t":"/home/pioreactor/.pioreactor/experiment_profiles/ is where experiment profiles (yaml) are stored.","s":"Experiment profiles","u":"/developer-guide/filesystem-locations","h":"#experiment-profiles","p":37},{"i":54,"t":"Name Chip Address ADC RP2040 0x30 DAC RP2040 0x30 TEMP TMP1075 0x4F","s":"I²C addresses","u":"/developer-guide/i2c-addresses","h":"","p":53},{"i":56,"t":"You can add a hook to what happens when the button is pressed on the Pioreactor HAT. For example, you could do things like: Flash an LED on when the button is pressed Cycle media: turn on both media and waste pumps for as long as the button is compressed for Pause a job, example: pause OD reading so you can take the vial out of the sleeve to inspect Spike the culture via dosing To do this, you need to write a small plugin that can be placed in the Pioreactor's /home/pioreactor/.pioreactor/plugins folder. Here's an example on how to turn on LED channel B for as long as the button is compressed: \"\"\" The background job Monitor is the job that listens to button state changes. There are hooks in that class to add callbacks for button down and button up. \"\"\" from pioreactor.background_jobs.monitor import Monitor from pioreactor.actions.led_intensity import led_intensity def on(*args): led_intensity({'B': 20}, verbose=False, source_of_event=\"button\") def off(*args): led_intensity({'B': 0}, verbose=False, source_of_event=\"button\") Monitor.add_pre_button_callback(on) Monitor.add_post_button_callback(off) An example to pause a job over MQTT: from pioreactor.background_jobs.monitor import Monitor from pioreactor.pubsub import publish from pioreactor.whoami import get_latest_experiment_name, get_unit_name target=\"od_reading\" def pause(*args): publish(f\"pioreactor/{get_unit_name()}/{get_latest_experiment_name()}/{target}/$state/set\", \"sleeping\") def unpause(*args): publish(f\"pioreactor/{get_unit_name()}/{get_latest_experiment_name()}/{target}/$state/set\", \"ready\") Monitor.add_pre_button_callback(pause) Monitor.add_post_button_callback(unpause)","s":"Adding behaviour to the HAT's button","u":"/developer-guide/hat-button","h":"","p":55},{"i":59,"t":"The Pioreactor runs ontop of a Raspberry Pi. We provide the operating system that runs on the Raspberry Pi as downloadable images. The operating system the latest version of Raspberry Pi OS (a fork of Debian Bookworm at the time of writing) with our custom modifications.","s":"Operating system","u":"/developer-guide/important-concepts","h":"#operating-system","p":57},{"i":61,"t":"The Pioreactor software works as follows: Different jobs, like stirring, OD reading, dosing, etc. are controlled by separate Python objects. Some jobs will passively listen for events from other jobs, and change their behavior in response, for example, dosing automations listen to OD readings, and may respond by dosing or not dosing. The main \"control plane\" for the Pioreactor software is the command line interface, pio. For example, when the user starts a activity from the UI, the web server will run pio run <some activity> --arguments, which launches a Python process that will instantiate the object the controls the activity. Because each activity is a separate Python process, we can modify an activity before running it by changing files on the filesystem.","s":"An initial mental model of Pioreactor software","u":"/developer-guide/important-concepts","h":"#an-initial-mental-model-of-pioreactor-software","p":57},{"i":63,"t":"One of the Raspberry Pi's is assigned as the \"leader\", and this hosts most of the services: web server, MQTT broker, database, etc. It also sends commands to any \"workers\". The leader can also be a worker. Together, the leader and all the workers are called a \"cluster\". A cluster can be a small as a single leader+worker. See more information about clusters here.","s":"Cluster topology","u":"/developer-guide/important-concepts","h":"#cluster-topology","p":57},{"i":65,"t":"The Raspberry Pis communicate through the local network (in more advanced cases, this network is hosted on the leader). Users control the Pioreactor cluster while being on the same network, and accessing the web UI or the command line of the Pioreactors.","s":"Networking","u":"/developer-guide/important-concepts","h":"#networking","p":57},{"i":67,"t":"MQTT is message-broker system that the Pioreactor uses to communicate between Pioreactors and between processes. Think of it as an in-memory event log, and any software in the cluster can interact with it. The leader Pioreactor hosts the message-broker (using the software Mosquitto), and worker Pioreactors (which are called MQTT clients) will read and write to it. On the leader's command line, you can view the event log with pio mqtt. The Pioreactor UI also connects to MQTT, and uses it to push and pull live data from the activities in each Pioreactor (states of activities, settings, graphs, etc).","s":"MQTT","u":"/developer-guide/important-concepts","h":"#mqtt","p":57},{"i":69,"t":"It's common to want a feature to turn off, or more generally change behaviour, when a sensitive optical density reading is taken. For example, if running an air bubbler, you may want to turn it off before an OD reading is taken, and then turn if back on after. This behaviour is so common, we've added a helper class to take care of it for you. In pioreactor.background_jobs.base is the class BackgroundJobWithDodgingContrib that implements most of the \"dodging\" behaviour for you. you'll only need to do three things: Inherit from BackgroundJobWithDodgingContrib, instead of BackgroundJobContrib from pioreactor.background_jobs.base import BackgroundJobWithDodgingContrib class JustPause(BackgroundJobWithDodgingContrib): ... Fill in what to do before, and after, an OD reading takes place by implementing method action_to_do_before_od_reading and action_to_do_after_od_reading, respectively. class JustPause(BackgroundJobWithDodgingContrib): ... def action_to_do_before_od_reading(self): # example self.logger.debug(\"Pausing\") self.stop_pumping() def action_to_do_after_od_reading(self): # example self.logger.debug(\"Unpausing\") self.start_pumping() We also want some \"buffer\" time before and after an OD reading. For example, if using a bubbler, we want the bubbles to dissipate completely before taking an OD reading. We should stop bubbling early then. To set these times, add the following to your config.ini: [<job_name>] pre_delay_duration=<float> post_delay_duration=<float> enable_dodging_od=1 # 1 if you want the behaviour, 0 to disable it. The diagram of timing, actions, and OD reading, looks like the following: And you're done!","s":"Avoiding when optical density is run","u":"/developer-guide/avoiding-od","h":"","p":68},{"i":72,"t":"Automations are specialized background jobs with a simplified interface for controlling some part of the Pioreactor. Whereas there is really only one way to control stirring in the Pioreactor (on, off, and constant), there are many ways to modify dosing to get different microbiological outcomes. Similarly with LEDs: there are many ways researchers want to control LEDs to change microorganisms. Same with temperature. For that reason, we've built an automation interface to make developing automations easier. You'll see an example of this simplified design when we build one in the next page.","s":"Automations","u":"/developer-guide/intro-automations","h":"#automations","p":70},{"i":74,"t":"Because we often want to change automations during an experiment, there is a Controller object (a background job) that initializes and teardowns automations during an experiment. For each automation type: dosing, temperature, and LED, there is a corresponding controller: DosingController, TemperatureController, and LEDController, respectively. Running these looks like: from pioreactor.background_jobs.dosing_control import DosingController dc = DosingController( dosing_automation=\"turbidostat\", # name of the automation, see next page duration=30, # how often `execute` runs, in minutes target_od=2.0, # kwarg that the turbidostat automation needs volume=0.5, # kwarg that the turbidostat automation needs ) The controller will start the automation (and publish information about to MQTT via published_settings), and if requested, will stop the automation and start a new one. Using the controllers is the preferred way to start and stop automations, rather than invoking the automations directly. Since the automation in the controller is part of published_settings, you can change the automation over MQTT by publishing to a MQTT topic. For example, if you wish to change the dosing automation from turbidostat to chemostat, publish the following JSON payload to pioreactor/<unit>/<experiment>/dosing_control/automation/set { \"automation_name\":\"chemostat\", \"args\": { \"volume: 1, \"duration\": 20 } }","s":"Controllers","u":"/developer-guide/intro-automations","h":"#controllers","p":70},{"i":76,"t":"Pioreactor plugins are a way to distribute code to others (or yourself), and avoid having to use the command line each time you invoke your custom code - you should be able to just use the web interface. There are two ways to distribute a plugin:","s":"Working with plugins","u":"/developer-guide/intro-plugins","h":"","p":75},{"i":78,"t":"On each Pioreactor's Raspberry Pi is a folder at /home/pioreactor/.pioreactor/plugins. When the Pioreactor software starts, any Python files in this folder are read and loaded into memory. If you were to include an automation in here, or a background job (with the click CLI component), they would be available globally. Why would you want to distribute code this way? It's a great way to test or develop your code instead of committing to other distribution methods: short iterations times, tight feedback loop, and code runs in the production environment. Two downsides are that it's harder to distribute your code to the rest of the community, and that it doesn't have the same deployment pipeline (adding configs, etc.) caution The Pioreactor software will load and run each Python file in /plugins on each invocation of pio. Don't have long-running or blocking code without wrapping it in a function or if __name__ == \"__main__\". For example: # my plugin code.py #❌ don't do this import time time.sleep(100) # ✅ this is okay import time def sleep(): time.sleep(100) # ✅ also is okay import time if __name__ == \"__main__\": time.sleep(100)","s":"1. Adding Python files to plugins folder","u":"/developer-guide/intro-plugins","h":"#1-adding-python-files-to-plugins-folder","p":75},{"i":80,"t":"Here's an example: place the following code into the file /home/pioreactor/.pioreactor/plugins/demo_job.py # -*- coding: utf-8 -*- import click from pioreactor.whoami import get_unit_name, get_latest_experiment_name from pioreactor.background_jobs.base import BackgroundJob __plugin_summary__ = \"Just a demo job\" __plugin_version__ = \"0.0.1\" __plugin_name__ = \"Demo job\" __plugin_author__ = \"Cam Davidson-Pilon\" __plugin_homepage__ = \"https://docs.pioreactor.com\" class DemoJob(BackgroundJob): job_name=\"demo_job\" def __init__(self, unit, experiment, **kwargs): super().__init__(unit=unit, experiment=experiment) def on_ready(self): self.logger.debug(\"Hello, world!\") def on_disconnected(self): self.logger.debug(\"Goodbye, world!\") @click.command(name=\"demo_job\", help=__plugin_summary__) def click_demo_job(): job = DemoJob( unit=get_unit_name(), experiment=get_latest_experiment_name(), ) job.block_until_disconnected() You should be able to execute the following from the command line now: pio run demo_job. Finally, in your web interface under plugins, you should see \"Demo Job\" installed. info A full introduction to writing jobs is available. info How do you add this to your /pioreactors page in the UI? See here.","s":"Custom background jobs","u":"/developer-guide/intro-plugins","h":"#custom-background-jobs","p":75},{"i":82,"t":"If you are interested in creating a Python script to control multiple jobs, like in a previous Python scripting example, you can create a file called example_script.py in the /home/pioreactor/.pioreactor/plugins/ folder: import time import click from pioreactor.background_jobs.stirring import start_stirring from pioreactor.background_jobs.od_reading import start_od_reading from pioreactor.actions.led_intensity import led_intensity from pioreactor.background_jobs.temperature_control import start_temperature_control __plugin_summary__ = \"My example script to control stirring, OD and temperature\" __plugin_version__ = \"0.0.1\" __plugin_name__ = \"Example Script\" __plugin_author__ = \"Cam Davidson-Pilon\" __plugin_homepage__ = \"https://docs.pioreactor.com\" @click.command(name=\"my_script\", help=__plugin_summary__) # the name field is used in the invocation `pio run X` def click_my_script(): led_intensity({\"B\": 50}) stirrer = start_stirring(target_rpm=400) od_reader = start_od_reading(\"90\", \"REF\") temp_controller = start_temperature_control(\"thermostat\", target_temperature=32) time.sleep(10) stirrer.set_target_rpm(300) stirrer.block_until_disconnected() You should be able to execute the following from the command line now: pio run my_script. (The my_script is from the @click.command line, you can change it there). important The function that click.command wraps should have it's name prepended by click_. Ex: def click_my_script is okay, but def my_script is not. info How do you add this to your /pioreactors page in the UI? See here.","s":"Custom scripts","u":"/developer-guide/intro-plugins","h":"#custom-scripts","p":75},{"i":84,"t":"Here's an example of adding a custom automation: place the following code into the file /home/pioreactor/.pioreactor/plugins/demo_automation.py # -*- coding: utf-8 -*- from pioreactor.automations.dosing.base import DosingAutomationContrib __plugin_summary__ = \"A demo dosing automation\" __plugin_version__ = \"0.0.1\" __plugin_name__ = \"Demo Dosing Automation\" __plugin_author__ = \"Cam Davidson-Pilon\" __plugin_homepage__ = \"https://docs.pioreactor.com\" class DemoAutomation(DosingAutomationContrib): automation_name = \"demo\" def __init__(self, volume, **kwargs): super().__init__(**kwargs) self.volume = volume def execute(self): self.logger(\"Here I would execute...\") You should be able to execute the following from the command line now: pio run dosing_control --automation-name demo --volume 10 info A full introduction to writing automations is available. info How do you add this to your /pioreactors page in the UI? See here.","s":"Custom automations","u":"/developer-guide/intro-plugins","h":"#custom-automations","p":75},{"i":86,"t":"An alternative to placing Python files in the plugins folder is to bundle your code into a Python package that can be installed over the internet. This is the best way to ship your code to many users, and is pretty easy! We have a full guide on how to create a Pioreactor Python package.","s":"2. pip-installable plugins","u":"/developer-guide/intro-plugins","h":"#2-pip-installable-plugins","p":75},{"i":88,"t":"The core unit of \"work\" in the Pioreactor software is a background job (called activities in the web interface). Background jobs include od_reading, monitor, automation controllers, all the automations themselves, etc. Often, a community plugin is a background job (or multiple jobs) that gives your bioreactor new abilities. There are a few important features of background jobs to be highlighted if you intend on working with them.","s":"Introduction to background jobs","u":"/developer-guide/intro-background-jobs","h":"","p":87},{"i":90,"t":"All background jobs inherit from the base class pioreactor.background_jobs.base.BackgroundJob. This class controls most of the behind-the-scenes behaviour of the class. Typically, we structure background job code such that the Python file has a single background job class and a command-line interface. See examples here.","s":"Inheritance and file structure","u":"/developer-guide/intro-background-jobs","h":"#inheritance-and-file-structure","p":87},{"i":92,"t":"All subclasses of BackgroundJob have the logger attribute that can be used to log messages. These messages are printed to the console, sent to MQTT, sometimes displayed in the UI, and all are stored permanently in the Pioreactor database. Here's how: # use for debugging job.logger.debug(\"A debug message - displayed in the console\") # use for providing relevant updates job.logger.info(\"An info message - this is display in the Recent Logs table in the UI\") # use for successes or important updates job.logger.notice(\"A notice message - this is displayed in the UI in a green popup\") # use for when something doesn't look correct, but will continue. job.logger.warning(\"A debug message - this is displayed in the UI in a yellow popup\") # use for when something is wrong and you take over control from the user job.logger.error(\"A debug message - this is displayed in the UI in a red popup\")","s":"Logging","u":"/developer-guide/intro-background-jobs","h":"#logging","p":87},{"i":94,"t":"A background job can be in one of five different states: init: the job is initializing. The job starts in this state. ready: the job is prepared to do \"work\", or currently doing \"work\" sleeping: the job's work is paused (ex: when the stirring job is in state sleeping, it turns off its power.) This state is called \"paused\" in the web interface. disconnected: the job has disconnected from services (MQTT, databases, etc.) and cleaned itself up successfully. lost: the job did not disconnect gracefully. Something may be wrong. Here's how the states can transition to each other: ┌──────────┐ │ │ ┌──────────────────────┬───────► lost ◄────────┐ │ │ │ │ │ │ │ └─────▲────┘ │ │ │ │ │ ┌────┴─────┐ ┌─────┴──────┐ │ ┌───────┴──────┐ │ │ │ │ │ │ │ │ init ├──────────► ready ├──────┼─────► disconnected │ │ │ │ │ │ │ │ └──────────┘ └────┬──▲────┘ │ └──────▲───────┘ │ │ │ │ │ │ │ │ │ │ │ │ ┌────▼──┴────┬──────┘ │ │ │ │ │ sleeping ├───────────────────┘ │ │ └────────────┘ The author can optionally define hooks when a job moves between states, and when it enters a new state. For example, the method .on_ready_to_sleeping() is called when the job moves from ready to sleeping. Similarly, the method .on_sleeping() is called when the jobs enters state sleeping. By default, these methods are empty. The recommended way to move a job between states is with job.set_state(job.READY). This will invoke any hooks that exist between the states. State can also be changed remotely over MQTT - we'll get to that point later.","s":"State of a job","u":"/developer-guide/intro-background-jobs","h":"#state-of-a-job","p":87},{"i":96,"t":"On job creation, the job will connect to MQTT to allow for publishing and subscribing. The attribute sub_client is for subscribing from MQTT, and pub_client is for publishing to MQTT. Internally, sub_client and pub_client are Paho client objects. Since publishing is so common, we also expose a .publish method: job = SomeBackgroundJob(unit, experiment) job.publish(f\"pioreactor/{job.unit}/{job.experiment}/...\", payload) Another common pattern is to subscribe to a MQTT topic, and execute a threaded callback whenever a message comes in from that topic. This is done with the .subscribe_and_callback method. By convention, this is most often used in a .start_passive_listeners method: from pioreactor.background_jobs.base import BackgroundJob class SomeBackgroundJob(BackgroundJob): def __init__(self, ...): ... self.start_passive_listeners() def response_to_dosing_event(self, msg): # change self in response, etc. ... def start_passive_listeners(self): self.subscribe_and_callback( self.response_to_dosing_event, f\"pioreactor/{self.unit}/{self.experiment}/dosing_events\", )","s":"Publish & subscribe, also known as pub/sub","u":"/developer-guide/intro-background-jobs","h":"#publish--subscribe-also-known-as-pubsub","p":87},{"i":98,"t":"A common task is when we have a job running, say stirring job, and we want to dynamically update an attribute, like the target RPM, without restarting the job. We also want to know the value of a job's attribute when it changes. For example, in the stirring job, we'd like to know what the actual RPM is. This can't be edited externally (it's a measured value...), but we want the value available for other jobs to use, for the web interface to display, or to sink it into a database. These two tasks, updating attributes and reading attributes in real-time, are so common that we've wrapped the logic into the parent BackgroundJob class, and allow job authors to tell us what attributes they wish to update and/or read. In the class definition, the attribute published_settings defines which class attributes they would like to track. For example, the job responsible for stirring looks like: class Stirrer(BackgroundJob): published_settings = { \"target_rpm\": {\"datatype\": \"json\", \"settable\": True, \"unit\": \"RPM\"}, \"measured_rpm\": {\"datatype\": \"json\", \"settable\": False, \"unit\": \"RPM\"}, \"duty_cycle\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"%\"}, } ... Thus the attributes target_rpm, measured_rpm, duty_cycle are all published to MQTT when they change, but only duty_cycle and target_rpm are able to be updated over MQTT (as defined by settable). The \"datatype\" field is normally one of: \"string\", \"float\", \"integer\", \"json\", \"boolean\" (full list in pioreactor/types.py). The \"settable\" field sets whether this attribute can be changed externally. The \"unit\" field is the unit of measurement, if any. This key is optional, and can be omitted. Also, there is an optional \"persist\" key (not shown above), which contains a boolean describing if the value should be kept in MQTT after the job exits, default False. When a class' attribute that's present in published_settings changes, a MQTT message is published under the topic pioreactor/{self.unit}/{self.experiment}/{self.job_name}/{attr} with payload equal to the new value of the attribute. This is how the web interface is provided real-time data. For updating an attribute, the BackgroundJob parent class listens to the MQTT topic: pioreactor/{self.unit}/{self.experiment}/{self.job_name}/+/set (the + is a MQTT wildcard), and when a message comes in, the class will check if the attribute (defined by +) is settable. If so, a lookup is done to see if a class method called set_<attr> is defined, and if present, calls that, with the only argument the message's payload. Otherwise, a simple assignment is done: self.<attr> = payload. The utility of a set_<attr> method is when changing the attribute requires more logic (ex: changing a PID controller's set point, see example here). info state is special attribute that is automatically appended to published_settings (with settable: True and persist: True) so the state of the job can always be updated and read from MQTT. Over MQTT, the field is called referenced as pioreactor/{unit}/{experiment}/{job_name}/$state - note the $. When the job disconnects and cleans up, the published settings in MQTT are removed by sending an empty payload to the respective topics (unless persist: True, see above.)","s":"Publishing attributes to MQTT","u":"/developer-guide/intro-background-jobs","h":"#publishing-attributes-to-mqtt","p":87},{"i":100,"t":"Only a single instance of a background job, indexed by the job's name, can be running on a Raspberry Pi. For example, only a single Monitor background job can run, likewise only a single ODReading can run. (It's not clear what running multiple ODReadings means, or how they will interact with the hardware - poorly we expect). The uniqueness is across processes, too. So if a script is running ODReading, then pio run od_reading will fail. note This uniqueness constraint is enforced in the current version of the software. It's possible we will see a reason to remove the uniqueness constraint in a future version - let us know if you want to see this, too!","s":"Uniqueness","u":"/developer-guide/intro-background-jobs","h":"#uniqueness","p":87},{"i":102,"t":"Background jobs make lots of connections to MQTT, GPIOs, hardware, and other external systems. It's important to treat background jobs as objects that need to be cleaned up these connections properly. If your jobs needs to clean up something, you can put it into the on_disconnected function: from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class HappyJob(BackgroundJob): def __init__(self, ...): # connect to a hardware self.hardware_connection = Hardware() self.hardware_connection.connect() # set LED on, too led_intensity({\"A\": 10}) def on_disconnected(self): self.hardware_connection.disconnect() led_intensity({\"A\": 0}) on_disconnected is called and connections are closed when the job exits (see below). There are two ways to use a background job that will ensure jobs are cleaned up correctly on exit: job = SomeBackgroundJob(unit, experiment) ... job.clean_up() # all cleaned up - state is set to disconnected alternatively, with a context manager: with SomeBackgroundJob(unit, experiment) as job: ... # all cleaned up - state is set to disconnected The job is also cleaned up when the Python process exits. caution The following will cause problems: #❌ don't do this def function_that_doesnt_clean_up(): job = SomeBackgroundJob(unit, experiment) # job not cleaned up return True value = function_that_doesnt_clean_up() ... In the above, the job SomeBackgroundJob isn't disconnected, and state hasn't changed - nor can you access the job anymore (no accessible references). Do this instead: # ✅ this is okay def function_that_does_clean_up(): with SomeBackgroundJob(unit, experiment) as job: ... return True value = function_that_does_clean_up() Blocking​ Often we want the job to wait and blocks, so as to wait for user commands or MQTT messages. We can accomplish this with job.block_until_disconnected() This blocks the execution until the job is disconnected (either a MQTT state change, or a signal from the OS).","s":"Entry & exit","u":"/developer-guide/intro-background-jobs","h":"#entry--exit","p":87},{"i":104,"t":"Often we want the job to wait and blocks, so as to wait for user commands or MQTT messages. We can accomplish this with job.block_until_disconnected() This blocks the execution until the job is disconnected (either a MQTT state change, or a signal from the OS).","s":"Blocking","u":"/developer-guide/intro-background-jobs","h":"#blocking","p":87},{"i":106,"t":"This documentation is for those who want to get the most customization out of their Pioreactor, use the Pioreactor core software for their own project, understand how the pieces work, contribute back code to the open-source Pioreactor software.","s":"Introduction for developers","u":"/developer-guide/introduction","h":"","p":105},{"i":108,"t":"Our code base is all open source, and available on GitHub. Pioreactor core, written in Python. Pioreactor user interface, a React app written in JS.","s":"Open source","u":"/developer-guide/introduction","h":"#open-source","p":105},{"i":110,"t":"Any suggestions or comments can be added to our Issue Tracker. If you're up for it, feel free to send a pull request, too!","s":"Have edits, corrections, or suggestions?","u":"/developer-guide/introduction","h":"#have-edits-corrections-or-suggestions","p":105},{"i":113,"t":"Confirm that Python3 is installed, and is greater or equal to version 3.9. python3 --version will print the version. To install the Pioreactor codebase locally, it should be enough to clone the repo pioreactor/pioreactor. git clone https://github.com/Pioreactor/pioreactor.git && cd pioreactor Install the core software are necessary packages (useful to do this in a virtualenv!): pip3 install -e . pip3 install -r requirements/requirements_dev.txt In the pioreactor folder, create a folder called .pioreactor/ and .pioreactor/storage. mkdir .pioreactor mkdir .pioreactor/storage The configuration file that is used is config.dev.ini, and is provided in the repository.","s":"Local development","u":"/developer-guide/local-development","h":"#local-development","p":111},{"i":115,"t":"You will need to install MQTT and have a broker running locally. On OSX, homebrew can be used to install the MQTT broker mosquitto. On Windows, it can be installed from this download page. info The mosquitto broker should be running whenever you invoke the Pioreactor software locally, else you'll likely get some connection refused error. The CLI tools mosquitto_pub and mosquitto_sub should work as well.","s":"MQTT","u":"/developer-guide/local-development","h":"#mqtt","p":111},{"i":117,"t":"With pio TESTING=1 pio run <job name> You can also modify to hostname and experiment with TESTING=1 \\ HOSTNAME=<whatever> \\ EXPERIMENT=<up to you> \\ pio run <job name> With python TESTING=1 python <your script>.py You can also modify to hostname and experiment with TESTING=1 \\ HOSTNAME=<whatever> \\ EXPERIMENT=<up to you> \\ python <your script>.py info If invoking from a different directory from pioreactor/, you'll need to have a config.dev.ini file locally. I usually copy my pioreactor/config.dev.ini to wherever I am working. Or you can use an environment argument GLOBAL_CONFIG=./config.dev.ini pio ...","s":"Running jobs locally","u":"/developer-guide/local-development","h":"#running-jobs-locally","p":111},{"i":119,"t":"py.test pioreactor/tests","s":"Testing","u":"/developer-guide/local-development","h":"#testing","p":111},{"i":121,"t":"Create a folder in the pioreactor folder called plugins_dev. In this folder, you can place python files that will run whenever pio is invoked (similar to the plugins folder at .pioreactor/plugins on the Raspberry Pi, see docs here)","s":"Plugins development","u":"/developer-guide/local-development","h":"#plugins-development","p":111},{"i":123,"t":"Raspberry Pi images are built in the Pioreactor/CustoPizer repo. Nightly builds are available at nightly.pioreactor.com.","s":"Raspberry Pi Images","u":"/developer-guide/local-development","h":"#raspberry-pi-images","p":111},{"i":126,"t":"Here's an example: from pioreactor.utils import local_intermittent_storage, local_peristant_storage with local_intermittent_storage(\"my_cache\") as cache: cache['key'] = \"value\" print(cache['key']) with local_peristant_storage(\"my_longterm_storage\") as cache: cache['key'] = \"value\" You can use pio view-cache <name> to view the contents of <name>, and pio clear-cache <name> <key> to clear contents.","s":"How do I write and read from the local storage?","u":"/developer-guide/local-storage","h":"#how-do-i-write-and-read-from-the-local-storage","p":124},{"i":128,"t":"local_intermittent_storage is data that won't, or shouldn't, exist after a reboot. For example: the state of GPIO pins. At a hardware level, this is reset after each reboot, and so should data associated with it. Whereas local_peristant_storage is data that should exist between reboots. This is data like calibration data, or OD blank data.","s":"What's the difference between local_intermittent_storage and local_peristant_storage?","u":"/developer-guide/local-storage","h":"#whats-the-difference-between-local_intermittent_storage-and-local_peristant_storage","p":124},{"i":131,"t":"We suggest using the following prefix: pioreactor/{unit name or $broadcast}/{experiment name or $experiment}/ ...","s":"How do you structure topics for MQTT?","u":"/developer-guide/mqtt","h":"#how-do-you-structure-topics-for-mqtt","p":129},{"i":133,"t":"If you're writing code for Job, you can simply use Job's methods: def some_method(self, ...): ... self.publish(f\"pioreactor/{self.unit}/{self.experiment}/{self.job_name}/more/topics\", payload) If writing a script: from pioreactor.utils import publish publish(f\"pioreactor/{unit}/{experiment}/more/topics\", payload)","s":"How do I publish data to MQTT?","u":"/developer-guide/mqtt","h":"#how-do-i-publish-data-to-mqtt","p":129},{"i":136,"t":"If you have a Raspberry Pi available, you can quickly boot up a near-exact environment to a Pioreactor. We can mock out the hardware needed, but everything else will work: networking, the Pioreactor UI, MQTT, running jobs, plugins, etc. Install the Pioreactor software on to a microSD card by following the instructions here. Power the Raspberry Pi. Since there's no HAT hardware, there won't be a blue blinking LED. The Raspberry Pi will still connect to the network you provided in the setup. SSH into the Raspberry Pi. Instructions on how to SSH in. You should also be able to visit http://pioreactor.local Once SSH'ed in, we need to add some \"mocking\" packages. Enter the following: sudo pip3 install fake-rpi The environment variable TESTING will determine if the Pioreactor should run in \"testing\" mode (i.e. mock out hardware required, and fake some data). We also need to specify the location of the config.ini file with the GLOBAL_CONFIG env variable. For example, we can mock the stirring job by entering: TESTING=1 GLOBAL_CONFIG=/home/pioreactor/.pioreactor/config.ini pio run stirring However, the experiment needs to be mocked out too: TESTING=1 \\ GLOBAL_CONFIG=/home/pioreactor/.pioreactor/config.ini \\ EXPERMENT=\"Demo Experiment\" \\ pio run stirring That's a lot of typing variables, so you could move these environment variables to ~/.profile: nano ~/.profile And add anywhere: export TESTING=1 export GLOBAL_CONFIG=/home/pioreactor/.pioreactor/config.ini export EXPERMENT=\"Demo Experiment\" And finally enter: source ~/.profile Now you can do pio run stirring without having to enter in the environment variables.","s":"Developing without hardware","u":"/developer-guide/pi-development","h":"#developing-without-hardware","p":134},{"i":139,"t":"If you'd like to contribute your plugin to the community, this is done easily by creating a Python package and uploading to PyPI. Let's walk through this!","s":"Turning your plugins into a Python package to share","u":"/developer-guide/plugin-as-python-package","h":"","p":138},{"i":141,"t":"Your plugin name should be all lowercase, and have underscores divide any words. Example: pireactor_relay_plugin is fine, but pioreactor-relay-plugin is not, nor is Pioreactor-Relay-Plugin. However, your distribution package name should be lowercase and have dashes instead of underscores (it's a Python thing: I agree, this is confusing, I'll walk you through it). You can just replace any underscores with dashes: so our example distribution package name is pioreactor-relay-plugin. Later in these steps, we'll reference these names as follows: PLUGIN_NAME: should be the name in all lowercase with underscores. Example: pioreactor_relay_plugin DISTRIBUTION-NAME: should be the name in all lowercase with dashes. Example: pioreactor-relay-plugin","s":"Choosing a plugin name","u":"/developer-guide/plugin-as-python-package","h":"#choosing-a-plugin-name","p":138},{"i":143,"t":"tip Note that the way files are organized may depend on if your plugin is an automation or a background job. Plugins can install both automations and jobs. Consider an example plugin: a plugin named pioreactor_relay_plugin that implements a background job which just turns on or off a PWM channel. Follow the file organization here: CamDavidsonPilon/pioreactor-relay-plugin. Here's a general directory outline of how your files should be organized for a job: 📁 <DISTRIBUTION-NAME (with dashes)> ├─ 📁 <PLUGIN_NAME> │ ├─ 📁 ui │ │ ├─ 📁 contrib │ │ │ ├─ 📁 jobs │ │ │ │ ├─ 📝 <PLUGIN_NAME>.yaml │ ├─ 📝 __init__.py │ ├─ 📝 additional_config.ini │ ├─ 📝 my_plugin_code.py ├─ 📝 LICENSE.txt ├─ 📝 MANIFEST.in ├─ 📝 README.md ├─ 📝 setup.py The directory outline is very similar for an automation plugin &#151 the only difference is the location of the .yaml file. 📁 <DISTRIBUTION-NAME with dashes> ├─ 📁 <PLUGIN_NAME> │ ├─ 📁 ui │ │ ├─ 📁 contrib │ │ │ ├─ 📁 automations │ │ │ │ ├─ 📁 <AUTOMATION TYPE (one of {dosing, led, temperature})> │ │ │ │ │ ├─ 📝 <PLUGIN_NAME>.yaml │ ├─ 📝 __init__.py │ ├─ 📝 additional_config.ini │ ├─ 📝 my_plugin_code.py ├─ 📝 LICENSE.txt ├─ 📝 README.md ├─ 📝 MANIFEST.in ├─ 📝 setup.py Start by creating a new folder for your plugin, equal to the distribution name (the name with dashes). In our case, we named it pioreactor-relay-plugin. This top level folder will contain five important parts: 1. The subfolder <PLUGIN_NAME> containing your plugin's code​ Within the top level directory, we created a sub-directory called <PLUGIN_NAME>. 2. A license text file, named LICENSE.txt​ A common license for software is the MIT license. 3. A MANIFEST file, named MANIFEST.in​ When creating a Python package, there's a default set of files that are included. To assure that our additional configuration and yaml files are included, create a MANIFEST.in file and paste the following: recursive-include <PLUGIN_NAME>/ui/ *.yaml include <PLUGIN_NAME>/additional_config.ini 4. A README.md​ Write a few notes with general information on your plugin to guide users. Call out any additional installation steps, or hardware required. This is a markdown document. 5. A Python setup.py file​ Create a Python file called setup.py and copy & paste the following. Make changes based on your own plugin information. # -*- coding: utf-8 -*- from setuptools import setup, find_packages setup( name=\"<DISTRIBUTION-NAME (with dashes)>\", version=\"<VERSION>\", license_files = ('LICENSE.txt',), description=\"<DESCRIPTION OF PLUGIN>\", long_description=open(\"README.md\").read(), long_description_content_type=\"text/markdown\", author_email=\"<EMAIL>\", author=\"<NAME>\", url=\"<A HOMEPAGE>\", packages=find_packages(), include_package_data=True, install_requires=[], # PROVIDE OTHER PYTHON REQUIREMENTS, ex: \"pioreactor>=23.6.0\", \"numpy>=1.0\" entry_points={ \"pioreactor.plugins\": \"<PLUGIN_NAME> = <PLUGIN_NAME>\" }, )","s":"Organizing your files","u":"/developer-guide/plugin-as-python-package","h":"#organizing-your-files","p":138},{"i":145,"t":"1. Your plugins Python files​ This Python file contains the core code for your plugin. If your plugin is implementing a background job, then there should be a function decorated with @click.command at the bottom of the file. See example here. For discovery reasons, this function's name should start with click_. 2. A Python __init__.py file​ If implementing an automation: Import the Class of your automation file: from <SUBFOLDER CONTAINING PLUGIN>.<PYTHON FILE NAME> import <CLASS NAME> If implementing a job: This will contain an import statement such as the following: from <PLUGIN_NAME>.<PYTHON FILE NAME> import <PLUGIN CLICK FUNCTION> This imports the function within our plugin file that executes our plugin action. Example for the relay plugin: from pioreactor_relay_plugin.relay import click_relay where click_relay is the function decorated with @click.command. 3. Optional: A configuration file, named additional_config.ini​ This configuration file will contain additional configs that we want to add to our list of existing Configurations on the Pioreactor web interface. This file will be merged with the existing config.ini when the plugin is installed. tip A convention we've tried to follow is to use the section name convention of [<job_name>.config] or [<automation_name>.config] in the configuration files. For example, our relay job has [relay.config] in its additional_config.ini and settings under it. 4. Optional: Adding details for the UI​ If implementing a job:​ Within <PLUGIN_NAME> folder, create subfolders named ui/contrib/jobs. For a job, create a .yaml file that looks like the following format. The name of the yaml can be anything, but convention is to use the <job_name>.yaml: --- display_name: # human readable name job_name: # `job_name` as defined in your Python file display: # bool; true to display on the /Pioreactors card source: # name of your plugin description: # description of what your plugin does published_settings: - key: # as defined in Python unit: # unit (ml, lux, AU, etc.) label: # human readable name description: # description of your setting type: # one of numeric, boolean, string, json default: # provide a default value, often null display: # bool; true to display on the /Pioreactors card - key: ... unit: ... ... There are lots of examples of job yaml files here. If implementing an automation:​ In the case of creating an automation plugin, create subfolder(s) with ui/contrib/automations/<AUTOMATION TYPE>, where AUTOMATION TYPE is one of dosing, led, or temperature depending on your automation type. Create a yaml file with the following convention. The name of the yaml file can be anything, but by convention it's <automation_name>.yaml. --- display_name: # human readable name automation_name: # automation name as defined in your Python files source: # name of your plugin description: # description of your plugin fields: - key: # as defined in Python unit: # unit of your key label: # human readable name description: # description of your key - key: ... unit: ... There are lots of examples of automation yaml files here. 5. Optional: adding tables to the SQL store​ You can also add a file called additional_sql.sql that will run against the SQLite database. For example, a CO₂ sensor may want to create a new table in the database to store its sensor data. It's additional_sql.sql may look like: CREATE TABLE IF NOT EXISTS co2_readings ( experiment TEXT NOT NULL, pioreactor_unit TEXT NOT NULL, timestamp TEXT NOT NULL, co2_reading_ppm REAL ); You also need to tell Pioreactor software how to populate this table from your source of data. Include the following in your code such that it executes when the plugin is loaded: a parser function that accepts a MQTT topic and payload, and returns a dictionary that maps to the new tables schema. a TopicToParserToTable object is created with the MQTT topics to listen to, the parser, and the table name to load to. This TopicToParserToTable is provided to register_source_to_sink. Example below for a CO2 sensor: ... from pioreactor.background_jobs.leader.mqtt_to_db_streaming import produce_metadata from pioreactor.background_jobs.leader.mqtt_to_db_streaming import register_source_to_sink from pioreactor.background_jobs.leader.mqtt_to_db_streaming import TopicToParserToTable from pioreactor.utils import timing ... def parser(topic, payload) -> dict: metadata = produce_metadata(topic) return { \"experiment\": metadata.experiment, \"pioreactor_unit\": metadata.pioreactor_unit, \"timestamp\": timing.current_utc_timestamp(), \"co2_reading_ppm\": float(payload), } register_source_to_sink( TopicToParserToTable( [\"pioreactor/+/+/scd_reading/co2\", \"pioreactor/+/+/co2_reading/co2\"], parser, \"co2_readings\", ) ) ... note You also need to add the following to your MANIFEST.in: ... include <PLUGIN_NAME>/additional_sql.sql See an example plugin that uses this idea here. 6. Optional: adding a custom chart to the UI​ To add a chart that display real-time and historical data (provided by MQTT and SQL store respectively), you can do the following: In a new folder named ui/contrib/charts in your project, add a YAML file as described here. The name of the file can by the chart_key field, append with .yaml. In your additional_config.ini, add a new entry to be merged: [ui.overview.charts] <your chart key>=1 info You'll need to make sure your database table has the necessary fields. See details under data_source in the docs here. See an example plugin that uses this idea here. 7. Optional: adding post_install and pre_uninstall bash scripts.​ If your plugin needs to edit the operating system, you can include either of the following files: post_install.sh, or pre_uninstall.sh. We have used these files to enable systemd services such that the job being installed will start at startup. Example post_install.sh and pre_uninstall.sh. You'll need to append to your MANIFEST.in, too: include <PLUGIN_NAME>/post_install.sh include <PLUGIN_NAME>/pre_uninstall.sh For an example, see the logs2slack plugin's repository. 8. Optional: only installing on leader Pioreactor.​ Some plugins may only want to be installed on the leader. For example, if they are changing the UI or database. To signal that a plugin should only be installed on the leader (and no-op on workers), add an empty file named LEADER_ONLY to the folder. You'll need to append to your MANIFEST.in, too: include <PLUGIN_NAME>/LEADER_ONLY For an example, see the logs2slack plugin's repository.","s":"Contents of the subfolder, <PLUGIN_NAME>","u":"/developer-guide/plugin-as-python-package","h":"#contents-of-the-subfolder-plugin_name","p":138},{"i":147,"t":"Create an account on https://pypi.org/. Make sure to verify your email. On your command line, type the following: pip install twine pip install --upgrade build python -m build --wheel This creates a .whl file in a dist/ folder (that will be created). Next, we upload the whl file to PyPI: twine upload dist/<THE .WHL FILE> You will then be prompted for a username and password. Use the credentials for your PyPI account. Then, your package is uploaded and viewable at the link provided in the output! Note Before you build a new wheel, it's good practice to clean up your previous build. This can be done using python setup.py clean --all on the command line.","s":"Create a Python package on PyPI","u":"/developer-guide/plugin-as-python-package","h":"#create-a-python-package-on-pypi","p":138},{"i":149,"t":"A plugin can be installed through the command line on a leader using pio: pio plugin install <DISTRIBUTION-NAME OR PLUGIN_NAME> To install a given plugin on the leader and all workers connected to the leader in a cluster, pios plugins install can be used. pios plugin install <DISTRIBUTION-NAME OR PLUGIN_NAME>","s":"Installing your Python package on your cluster","u":"/developer-guide/plugin-as-python-package","h":"#installing-your-python-package-on-your-cluster","p":138},{"i":151,"t":"To give your plugin further reach, we've provided an option to add it to the web interface. You will need to edit the plugins.json file within our Pioreactor repository, list-of-plugins. There are two ways to do this: Create an issue to have us edit the plugins.json file for you. Fork from our repository to edit the plugins.json file, then create a pull request. In both cases, we will evaluate your plugin to ensure code quality and all requirements are met. Once your plugin is accepted, it will appear on the Plugins tab on the Pioreactor web interface. Users in the community can now easily click Install to download your plugin onto their Pioreactors!","s":"Sharing your plugin with the community","u":"/developer-guide/plugin-as-python-package","h":"#sharing-your-plugin-with-the-community","p":138},{"i":153,"t":"The web UI is hosted on the leader Pioreactor. Here are the details:","s":"Overview","u":"/developer-guide/web-ui-introduction","h":"","p":152},{"i":155,"t":"The web server we use is lighttpd, and hosted from /var/www/pioreactorui. This folder is actually a git repo, and pulls from pioreactorui GH repo. Systemd controls starting and restarting lighttpd. The lighttpd conf file is located in /etc/lighttpd/conf-enabled/50-pioreactorui.conf. Error logs (though not helpful) are in /var/log/lighttpd/error.log. The default protocol is http served on port 80. To use https requires a certificate, and is out of scope for this project. If you'd change the protocol or the port, you'll need up tell the software too: look in the config.ini under [ui] section. How to change the web UI port","s":"Web server","u":"/developer-guide/web-ui-introduction","h":"#web-server","p":152},{"i":157,"t":"The backend app is a Flask app, with entry point in /var/www/pioreactorui/main.fcgi. The app uses Huey as background workers to perform pio tasks, save to disk, etc. Huey is controlled by systemd huey.service. The API is available here","s":"Backend","u":"/developer-guide/web-ui-introduction","h":"#backend","p":152},{"i":159,"t":"The frontend is a React app, built with Material UI components. The source code is at pioreactorui_frontend. A lot of the \"data\" for the frontend comes from YAML files on the RPi's filesystem. For example, all the charts, activities, and automations are defined in their own YAML file in a contrib folder on the filesystem. This way, it's easy to add new data to the frontend without having to write new JS.","s":"Frontend","u":"/developer-guide/web-ui-introduction","h":"#frontend","p":152},{"i":161,"t":"To allow for pioreactor.local to be an alias for <leader hostname>.local, we use mdns provided by avahi. There is a systemd service, avahi_alias.service, that will point pioreactor.local to <leader hostname>.local.","s":"DNS name resolution to pioreactor.local","u":"/developer-guide/web-ui-introduction","h":"#dns-name-resolution-to-pioreactorlocal","p":152},{"i":163,"t":"To update on the UI on Pioreactor leader, use pio update ui. This also restarts the server. To restart: sudo systemctl restart lighttp && sudo systemctl restart huey","s":"Updating and restarting the web UI","u":"/developer-guide/web-ui-introduction","h":"#updating-and-restarting-the-web-ui","p":152},{"i":165,"t":"Start up logs from systemd are in sudo systemctl status lighttpd.service. Logs for the backend and background workers are located in /var/log/pioreactorui.log.","s":"Logs","u":"/developer-guide/web-ui-introduction","h":"#logs","p":152},{"i":168,"t":"Runpio db on the leader to open up the database shell. You can quit with .q.","s":"How do I access the SQlite3 database?","u":"/developer-guide/sqlite3","h":"#how-do-i-access-the-sqlite3-database","p":166},{"i":170,"t":"You can either use .tables in the sqlite shell, or visit all the tables schemas here.","s":"Where is a list of tables on the database?","u":"/developer-guide/sqlite3","h":"#where-is-a-list-of-tables-on-the-database","p":166},{"i":172,"t":"Using the sqlite shell (pio db), you can execute any SQL statements, including creating new tables. Plugins can also automatically create new tables when installed, see instructions here.","s":"How can I add new SQL tables?","u":"/developer-guide/sqlite3","h":"#how-can-i-add-new-sql-tables","p":166},{"i":174,"t":"The Pioreactor job mqtt_to_db_streaming handles how to get data into the sqlite3 database. This job listens to specific topics in MQTT, and writes it to the database. We've implemented hooks into mqtt_to_db_streaming job for you to added your own topics. In your code: a parser, usually called parser, function that accepts a MQTT topic and payload, and returns a dictionary that maps to the tables schema. a TopicToParserToTable object is created with the MQTT topics to listen to, the parser, and the table name to load to. This TopicToParserToTable is provided to register_source_to_sink. Example below for a CO2 sensor: ... from pioreactor.background_jobs.leader.mqtt_to_db_streaming import produce_metadata from pioreactor.background_jobs.leader.mqtt_to_db_streaming import register_source_to_sink from pioreactor.background_jobs.leader.mqtt_to_db_streaming import TopicToParserToTable from pioreactor.utils import timing ... def parser(topic, payload) -> dict: metadata = produce_metadata(topic) return { \"experiment\": metadata.experiment, \"pioreactor_unit\": metadata.pioreactor_unit, \"timestamp\": timing.current_utc_timestamp(), \"co2_reading_ppm\": float(payload), } register_source_to_sink( TopicToParserToTable( [\"pioreactor/+/+/scd_reading/co2\", \"pioreactor/+/+/co2_reading/co2\"], parser, \"co2_readings\", ) ) You can place this into the ~/.pioreactor/plugins folder. The next time mqtt_to_db_streaming starts, it will starts listening to the specific topics.","s":"How do I populate my own SQL tables?","u":"/developer-guide/sqlite3","h":"#how-do-i-populate-my-own-sql-tables","p":166},{"i":176,"t":"info This is subject to change! Currently we don't like how much a developer has to implement (or copy and paste) to create a new calibration. We want to make it easier to design new calibrations. Ideally, all calibrations, including od_calibration and pump_calibration, should behave similarly: Interface should have the following: pio run <x>_calibration starts the calibration and saves it keyed by a unique name (see 2. for storage) pio run <x>_calibration list lists all saved calibrations, keyed by their unique name. pio run <x>_calibration display ?name? displays information about the current calibration to be used, or the calibration ?name? if provided pio run <x>_calibration change_current <name> changes the current calibration to <name> calibration. pio run <x>_calibration publish <name> publishes the calibration to the leader. On disk, all run calibrations should be stored in local persistent storage under <x>_calibrations keyed by a unique name, and the current calibration should be stored in <x>_current_calibration, with appropriate key (can use <calibration_type>) that is not the unique name, but something consistent. Note: The name cannot be current. A struct should be created / sub-classed from structs.Calibration that will encode / decode the calibration data blob. When a new calibration is created, a PUT request to /api/calibrations/ should be sent. The body is the json-encoded Calibration struct. When a new calibration is set as current (change_current), a PATCH request to /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name> should be sent. Creating a new calibration should both publish to leader and set as current. For example, for pump_calibration, the three default calibration types are: media_pump_calibration, alt_media_pump_calibration, and waste_pump_calibration.","s":"Adding a new calibration type","u":"/developer-guide/adding-calibration-type","h":"","p":175},{"i":179,"t":"Endpoint Methods Rule --------------------------------------- ------- ------------------------------------------------------------------------- able_to_install_plugins_from_ui GET /api/allow_ui_installs create_or_update_new_calibrations PUT /api/calibrations get_available_calibrations_type_by_unit GET /api/calibrations/<pioreactor_unit> get_available_calibrations_of_type GET /api/calibrations/<pioreactor_unit>/<calibration_type> get_calibration_by_name GET /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name> patch_calibrations PATCH /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name> get_current_calibrations_of_type GET /api/calibrations/<pioreactor_unit>/<calibration_type>/current get_configs GET /api/configs get_config GET /api/configs/<filename> update_config PATCH /api/configs/<filename> get_automation_contrib GET /api/contrib/automations/<automation_type> get_charts_contrib GET /api/contrib/charts create_experiment_profile POST /api/contrib/experiment_profiles get_experiment_profiles GET /api/contrib/experiment_profiles get_experiment_profile GET /api/contrib/experiment_profiles/<filename> delete_experiment_profile DELETE /api/contrib/experiment_profiles/<filename> get_job_contrib GET /api/contrib/jobs get_experiments GET /api/experiments create_experiment POST /api/experiments delete_experiment DELETE /api/experiments/<experiment> update_experiment PATCH /api/experiments/<experiment> get_logs GET /api/experiments/<experiment>/logs get_media_rates GET /api/experiments/<experiment>/media_rates get_fallback_time_series GET /api/experiments/<experiment>/time_series/<data_source>/<column> get_growth_rates GET /api/experiments/<experiment>/time_series/growth_rates get_od_readings GET /api/experiments/<experiment>/time_series/od_readings get_od_readings_filtered GET /api/experiments/<experiment>/time_series/od_readings_filtered get_temperature_readings GET /api/experiments/<experiment>/time_series/temperature_readings get_unit_labels GET /api/experiments/<experiment>/unit_labels upsert_unit_labels PUT /api/experiments/<experiment>/unit_labels get_logs_for_unit_and_experiment GET /api/experiments/<experiment>/units/<unit>/logs get_list_of_workers_for_experiment GET /api/experiments/<experiment>/workers add_worker_to_experiment PUT /api/experiments/<experiment>/workers remove_workers_from_experiment DELETE /api/experiments/<experiment>/workers remove_worker_from_experiment DELETE /api/experiments/<experiment>/workers/<pioreactor_unit> stop_worker_in_experiment POST /api/experiments/<experiment>/workers/<worker>/stop stop_all_in_experiment POST /api/experiments/<experiment>/workers/stop get_experiments_worker_assignments GET /api/experiments/assignment_count get_latest_experiment GET /api/experiments/latest export_datasets POST /api/export_datasets get_historical_config_for GET /api/historical_configs/<filename> get_historical_media_used GET /api/historical_media get_historical_organisms_used GET /api/historical_organisms is_local_access_point_active GET /api/is_local_access_point_active install_plugin POST /api/plugins/install get_installed_plugins GET /api/plugins/installed get_plugin GET /api/plugins/installed/<filename> uninstall_plugin POST /api/plugins/uninstall setup_worker_pioreactor POST /api/setup_worker_pioreactor reboot_unit POST /api/units/<unit>/reboot shutdown_unit POST /api/units/<unit>/shutdown update_app POST /api/update_app update_app_from_release_archive POST /api/update_app_from_release_archive update_app_to_develop POST /api/update_app_to_develop upload POST /api/upload get_app_version GET /api/versions/app get_ui_version GET /api/versions/ui get_list_of_workers GET /api/workers add_worker PUT /api/workers delete_worker DELETE /api/workers/<pioreactor_unit> get_worker GET /api/workers/<pioreactor_unit> get_experiment_assignment_for_worker GET /api/workers/<pioreactor_unit>/experiment change_worker_status PUT /api/workers/<pioreactor_unit>/is_active run_job_on_unit PATCH /api/workers/<unit>/experiments/<experiment>/jobs/<job>/run stop_job_on_unit PATCH /api/workers/<unit>/jobs/<job>/stop get_workers_and_experiment_assignments GET /api/workers/assignments static GET /static/<path:filename> From python3 -m flask --debug --app main routes -s rule","s":"All endpoints","u":"/developer-guide/web-ui-api","h":"#all-endpoints","p":177},{"i":181,"t":"An automation is a hands-off way to adjust the environment for the microbes. We currently support three types of automations: dosing, LED, and temperature. In this section, we'll develop a simple dosing automation.","s":"Writing a new automation","u":"/developer-guide/writing-automations-1","h":"","p":180},{"i":183,"t":"Writing an automation involves creating a Python class and overriding specific methods. It would be helpful to be somewhat familiar with Python classes before beginning. Here's an example of a (naive) turbidostat automation, i.e. it will add fresh media and remove old media when an optical density threshold is exceeded. The full code is below, and we'll go through each line of code after: from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): automation_name = \"naive_turbidostat\" published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, } def __init__(self, target_od, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) def execute(self): if self.latest_od > self.target_od: self.execute_io_action(media_ml=1.0, waste_ml=1.0) First important thing is to subclass from DosingAutomationJobContrib: from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): ... The DosingAutomationJobContrib is a subclass of a BackgroundJob. The -Contrib part is a small detail to specify that it's a third-party automation (i.e. you are developing it, not us.) We need a \"key\" to i) distinguish this from other automations, and ii) be able to be communicate between systems (think: the web UI in JavaScript to Python, and back). The automation_name attribute does this for us. Normally, it's the snakecase of the class name. automation_name = \"naive_turbidostat\" The published_settings tells the Pioreactor software what class attributes are published to MQTT, and if they are editable via MQTT (we will try editing over MQTT later). This is important if you wish to dynamically change attributes of an automation during an experiment, for example: from the web interface. Our class has the following: ... published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, } ... The associated metadata says that the class attribute target_od is a float, is editable via MQTT (so it can be changed using the web interface), and it has units od. Next, we define how to initialize our automation class. Here we can add settings we want to accept from the user: what is our initial target optical density. Note the boilerplate **kwargs, and super() are important. def __init__(self, target_od, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) Finally, every duration (specified in the controller, later in this section) minutes, the function execute will run. duration can be kept low (ex: to often check for some condition), or used to set some periodic task (ex: a chemostat doses every X minutes). The execute contains the core logic of the automation. In our simple case, we want to dilute the vial if we have exceed the latest_od: def execute(self): if self.latest_od > self.target_od: self.execute_io_action(media_ml=1.0, waste_ml=1.0) Since we are working with a fixed volume, media_ml must equal waste_ml, else an error will be thrown. What is latest_od attribute? Our class, when active, is listening to new optical densities being recorded. Hence when execute runs, we'll have access to the most up-to-date value of optical density. Likewise, there are also latest_normalized_od and latest_growth_rate attributes that update when a new growth-rate value is calculated. All three attributes are defined and maintained in the parent class.","s":"Creating our first custom automation","u":"/developer-guide/writing-automations-1","h":"#creating-our-first-custom-automation","p":180},{"i":185,"t":"How do we run this automation now? Let's copy the code into a file called naive_turbidostat.py and place it into the folder ~/.pioreactor/plugins. info You can create this file on your Pioreactor's Raspberry Pi: after accessing the Raspberry Pi's command line, typing nano ~/.pioreactor/plugins/naive_turbidostat.py, and pasting in the code below. # -*- coding: utf-8 -*- from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): automation_name = \"naive_turbidostat\" published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, } def __init__(self, target_od, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) def execute(self): if self.latest_od > self.target_od: self.execute_io_action(media_ml=1.0, waste_ml=1.0) Run the script with pio run dosing_control --automation-name naive_turbidostat --target-od 0.5. This will start the job. After a moment, you may notice that warnings are thrown - that's because there's no optical density measurements being produced! You can use crtl-c to stop the job. Editing attributes over MQTT (optional)​ We'll demonstrate the ability to dynamically change the target_od attribute using MQTT. For each member of published_settings, the DosingAutomationJobContrib class listens to the MQTT topic: pioreactor/<unit name>/<experiment>/dosing_automation/<attribute>/set We'll use mosquitto_pub to publish a message to this topic. So, with the Python script running, open a new command line, and enter the following: mosquitto_pub -t \"pioreactor/test_unit/test_experiment/dosing_automation/target_od/set\" -m 5.0 -u pioreactor -P raspberry You should see some logs in the Python console report that the target_od was changed. Also, a the value of 5.0 is published and retained to the topic pioreactor/test_unit/test_experiment/dosing_automation/target_od Why is this useful? This is how the web interface updates settings in running activities. Other Pioreactor activities can update each other's settings. External programs or apps can monitor and update settings this way, too.","s":"Running the automation","u":"/developer-guide/writing-automations-1","h":"#running-the-automation","p":180},{"i":187,"t":"To add your automation to the UI so it appears in the automation drop-down, follow the the steps here.","s":"Adding the automation to the UI","u":"/developer-guide/writing-automations-1","h":"#adding-the-automation-to-the-ui","p":180},{"i":189,"t":"Below are some extensions, with additions highlighted. Dynamic volume exchanged​ Exchanging 1ml each time may not be enough, so we add volume to the published_settings. Now, from the UI, we can dynamically adjust the volume. from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): automation_name = \"naive_turbidostat\" published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, \"volume\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"mL\"}, } def __init__(self, target_od, volume, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) self.volume = float(volume) def execute(self): if self.latest_od > self.target_od: self.execute_io_action(media_ml=self.volume, waste_ml=self.volume) Using latest_growth_rate​ If our growth rate is high, we may want to modify the volume exchanged to keep up. A naive solution: we can bump up the exchanged volume if the growth rate is high. Much better would be a dynamic solution, or a feedback loop. from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): automation_name = \"naive_turbidostat\" published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, \"volume\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"mL\"}, } def __init__(self, target_od, volume, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) self.volume = float(volume) def execute(self): if self.latest_od > self.target_od: if self.latest_growth_rate > 0.2: self.execute_io_action(media_ml=2 * self.volume, waste_ml=2 * self.volume) else: self.execute_io_action(media_ml=self.volume, waste_ml=self.volume)","s":"Extensions of our custom automation","u":"/developer-guide/writing-automations-1","h":"#extensions-of-our-custom-automation","p":180},{"i":191,"t":"Let's design a simple LED automation for Light/Dark cycles. The basic idea is that the LED automation \"wakes up\" (specifically: it runs its execute method) every hour, and on specific hours, turns on or turns off the white light LEDs.","s":"Another example writing a new automation","u":"/developer-guide/writing-automations-2","h":"","p":190},{"i":193,"t":"Imports at the top of the file! # -*- coding: utf-8 -*- from __future__ import annotations from pioreactor.automations.led.base import LEDAutomationJobContrib from pioreactor.whoami import get_unit_name, get_latest_experiment_name from pioreactor.automations import events Define a new class as a subclass of LEDAutomationJobContrib. We use LEDAutomationJobContrib since this is a 3rd party automation. We give the new class a descriptive name. The automation_name attribute is necessary - and is often just the camel case version of the class name. class LightDarkCycle(LEDAutomationJobContrib): automation_name = \"light_dark_cycle\" Define our published_settings for this class. This is a dictionary of LightDarkCycle attributes that we can modify/inspect from MQTT (and hence from the UI, or from the leader Pioreactor). Not all attributes need to go in here - only the ones that users may want to modify mid-experiment. Later in this post, we'll see what each of these attributes does. published_settings = { \"duration\": {\"datatype\": \"float\", \"settable\": False, \"unit\": \"min\"}, \"light_intensity\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"%\"}, \"light_duration_hours\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"h\"}, \"dark_duration_hours\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"h\"}, } Create the __init__, with the attributes we'll need. def __init__(self, light_intensity: float, light_duration_hours: int, dark_duration_hours: int, **kwargs): super().__init__(**kwargs) self.hours_online = -1 self.light_active = False self.channels = [\"B\", \"C\"] self.set_light_intensity(light_intensity) self.light_duration_hours = float(light_duration_hours) self.dark_duration_hours = float(dark_duration_hours) hours_online will keep track of how many elapsed hours have gone by. light_active keeps track of whether the LEDs are currently on or off channels refers to which LED channels on the Pioreactor HAT we are using. light_duration_hours: the number of hours to keep the light on for, typically 16 dark_duration_hours: the number of hours to keep the light off for, typically 8 light_intensity: the level of intensity, as a percent, of the LEDs when turned on. We define the execute function, which is what runs every duration minutes. In the function, we increment hours_online by 1 (since it runs every 60 minutes), and ask a separate function, trigger_leds, to handle turning on and off LEDs. The execute can return an Event, which is useful for logging and testing purposes. def execute(self): self.hours_online += 1 event = self.trigger_leds(self.hours_online) return event The other class function, trigger_leds, role is to: determine if we should turn on LEDs, turn off LEDs, or do nothing. If we are changing LEDs status (on to off, or off to on), perform that task. return an Event, with some description of what occurred (even if nothing changed). To do 1., we think about the total hours passed modulo how long our cycle is. That is, if our cycle lasts 24 hours (which might be the result of choosing 16h light + 8h dark), then the hour 33 is really the same as hour 9, likewise the hour 123 is the same as hour 3: we take the hour modulo the duration. We then ask, is this hour in the dark period, or the light period, of the cycle? We also ask if the lights_active is on, or off, respectively? If so, we change the status of the LEDs. For example, if we should be in the dark period, but our LEDs are on, well, we turn them off, and return a ChangeLEDIntensity event. The function set_led_intensity is from the parent class, and is a helper function. def trigger_leds(self, hours: int) -> events.Event: cycle_duration: int = self.light_duration_hours + self.dark_duration_hours if ((hours % cycle_duration) < self.light_duration_hours) and (not self.light_active): self.light_active = True for channel in self.channels: self.set_led_intensity(channel, self.light_intensity) return events.ChangedLedIntensity(f\"{hours}h: turned on LEDs\") elif ((hours % cycle_duration) >= self.light_duration_hours) and (self.light_active): self.light_active = False for channel in self.channels: self.set_led_intensity(channel, 0) return events.ChangedLedIntensity(f\"{hours}h: turned off LEDs\") else: return events.NoEvent(f\"{hours}h: no change\") We also need to define that set_light_intensity function above. This function is automatically called whenever we change light_intensity (see note below). We need additional logic to immediately change the light_intensity when asked, otherwise, the LEDs wouldn't actually update until the next execute is called, which could be an hour away. def set_light_intensity(self, intensity) -> None: self.light_intensity = float(intensity) if self.light_active: # update now! for channel in self.channels: self.set_led_intensity(channel, self.light_intensity) else: pass info Updates over MQTT either update the attribute directly, i.e. :self.<attr> = new_value, or, if defined, the method set_<attr>(new_value) is called instead. This is what is happening with set_light_intensity. Using set_<attr> methods is useful when you have additional logic that needs to be accomplished when an attribute changes. That's the end of the class! In total, our file looks like: # -*- coding: utf-8 -*- from __future__ import annotations from pioreactor.automations.led.base import LEDAutomationJobContrib from pioreactor.automations import events class LightDarkCycle(LEDAutomationJobContrib): \"\"\" Follows as h light / h dark cycle. Starts dark. \"\"\" automation_name = \"light_dark_cycle\" published_settings = { \"duration\": {\"datatype\": \"float\", \"settable\": False, \"unit\": \"min\"}, # doesn't make sense to change duration. \"light_intensity\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"%\"}, \"light_duration_hours\": {\"datatype\": \"int\", \"settable\": True, \"unit\": \"h\"}, \"dark_duration_hours\": {\"datatype\": \"int\", \"settable\": True, \"unit\": \"h\"}, } def __init__(self, light_intensity: float, light_duration_hours: int, dark_duration_hours: int, **kwargs): super().__init__(**kwargs) self.hours_online: int = -1 self.light_active: bool = False self.channels = [\"B\", \"C\"] self.set_light_intensity(light_intensity) self.light_duration_hours = float(light_duration_hours) self.dark_duration_hours = float(dark_duration_hours) def trigger_leds(self, hours: int) -> events.Event: cycle_duration: int = self.light_duration_hours + self.dark_duration_hours if ((hours % cycle_duration) < self.light_duration_hours) and (not self.light_active): self.light_active = True for channel in self.channels: self.set_led_intensity(channel, self.light_intensity) return events.ChangedLedIntensity(f\"{hours}h: turned on LEDs\") elif ((hours % cycle_duration) >= self.light_duration_hours) and (self.light_active): self.light_active = False for channel in self.channels: self.set_led_intensity(channel, 0) return events.ChangedLedIntensity(f\"{hours}h: turned off LEDs\") else: return events.NoEvent(f\"{hours}h: no change\") def set_light_intensity(self, intensity) -> None: self.light_intensity = float(intensity) if self.light_active: # update now! for channel in self.channels: self.set_led_intensity(channel, self.light_intensity) else: pass def execute(self) -> events.Event: self.hours_online += 1 event = self.trigger_leds(self.hours_online) return event","s":"The Code","u":"/developer-guide/writing-automations-2","h":"#the-code","p":190},{"i":195,"t":"Setting up your Pioreactor is easy: attach LEDs to LED channels B and C, and stick them in pockets X2 and X3.","s":"Setting up the Pioreactor","u":"/developer-guide/writing-automations-2","h":"#setting-up-the-pioreactor","p":190},{"i":197,"t":"Let's save this file to our Pioreactor plugin folder, by accessing the Pioreactor's command line, typing nano ~/.pioreactor/plugins/light_dark_cycle.py, and pasting in the code above. You can test the automation from the Pioreactor's command line by executing: pio run led_control --automation-name light_dark_cycle --light_intensity 45 --light_duration_hours 16 --dark_duration_hours 8","s":"Running the automation","u":"/developer-guide/writing-automations-2","h":"#running-the-automation","p":190},{"i":199,"t":"To add your automation to the UI so it appears in the automation drop-down, follow the the steps here.","s":"Adding the automation to the UI","u":"/developer-guide/writing-automations-2","h":"#adding-the-automation-to-the-ui","p":190},{"i":201,"t":"Success goal This experiment will show the growth curve of algae over a 20h:4h day/night cycle, at two different intensities (4% and 8%).","s":"Algae day and night cycles","u":"/experiments/algae-day-night-cycle","h":"","p":200},{"i":203,"t":"# At least one available Pioreactor Algae Media for algae; for ex. Bold's Basal Medium (BBM) Two LED cables per Pioreactor.","s":"Requirements","u":"/experiments/algae-day-night-cycle","h":"#requirements","p":200},{"i":206,"t":"Adding two LED bulbs onto your base Pioreactor will transform it into a photo-bioreactor, giving you the ability to grow species that require light! In this experiment, we will monitor algae using our Day/Night plugin. There are two main phases that will be observed between the light being on (\"day\") and off (\"night\"). Exponential growth will occur during the “day” as algae biomass is accumulated through photosynthesis), and stalled growth will occur “overnight”, where algae reproduce, but don't accumulate biomass. This should make for some interestingly patterned OD readings!","s":"Introduction","u":"/experiments/algae-day-night-cycle","h":"#introduction","p":200},{"i":208,"t":"We started off with a culture of Chlorella vulgaris that we grew in a tissue culture flask using Bold's Basal Medium. We then used 10 mL of BBM per vial, then inoculated with 1 mL of our culture. With two Pioreactors, we started our experiment using the Day/Night plugin and chose light intensities of 4% and 8%. We kept stirring high to avoid formation of flocculants that could impede our OD readings. Typical experiments use a 16h:8h day night cycle, but we've adjusted the time period to 20h:4h. The experiment takes place over a few days, so results were seen after a week.","s":"Experiment","u":"/experiments/algae-day-night-cycle","h":"#experiment","p":200},{"i":210,"t":"For this style of experiment, let's investigate our normalized OD results: Adjusting just one factor (light intensity) where one is twice as high as the other yielded an approximate doubling of growth in the vial subjected to higher light intensity!","s":"Results","u":"/experiments/algae-day-night-cycle","h":"#results","p":200},{"i":212,"t":"Your Pioreactor is capable of controling a wide diversity of lighting effects on algae or other photosynthesizing microorganisms. The addition of the Day/Night cycle plugin and the ability to use LEDs opens a range of photobioreactor experiments! You can adjust intensities, photoperiods, and even switch out types of bulbs across the light spectrum to study effects of colours or UV lights.","s":"Recommendations","u":"/experiments/algae-day-night-cycle","h":"#recommendations","p":200},{"i":214,"t":"Attach two LED cables into channels C and D. Insert the bulbs into the X2 and X3 pockets and secure them in place with the pocket caps. While on, some light leaking is acceptable. Prepare a sterile stock of media for algae. We used Bold’s Basal Medium (BBM). Aim for 10 to 12 mL of media per each vial/Pioreactor you will be using. This is to allow more headspace for oxygen! Add 1 mL of your algae culture to each vial. Wipe the vials and place them in the Pioreactor. Visit pioreactor.local and start a new experiment. Click the Plugins tab on the left and install the led_cycle plugin. This will add the Day/Night feature when you begin LED automations. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start Stirring activity and OD reading activity. Optional Start the Temperature automation activity set on an optimal temperature. Start the LED automation at the bottom of the Activities list in Manage. Select Day/Night Cycle from the drop down menu, and set your desired Intensity (no more than 12% works best!) or Light and Dark duration (16h:8h is optimal). This automation creates a day/night cycle ideal for algae growth. Confirm that everything looks normal on the Overview page (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Optional Change the names of the Pioreactor in the UI to organize your vials. Watch the growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/algae-day-night-cycle","h":"#detailed-procedure","p":200},{"i":216,"t":"Success Goal Use caffeine-containing liquids to inhibit the growth of your culture.","s":"Caffeine inhibition","u":"/experiments/caffeine-inhibition","h":"","p":215},{"i":218,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix Caffeine-containing liquids (tea, coffee)","s":"Requirements","u":"/experiments/caffeine-inhibition","h":"#requirements","p":215},{"i":221,"t":"Yeasts are versatile eukaryotes that have biological systems synonymous to those found in humans. Substances that affect us are likely to affect yeast as well, so yeasts are commonly used in research to study certain behaviours. Let's take a look at yeast reactions to caffeine, and model these behaviours using our Pioreactor! Caffeine is the most common stimulant in the world, and is found in many consumed items such as coffees, teas, chocolates, and even within certain medication. Ponder this: what do you expect to happen when caffeine is added to yeast cultures? We know that we feel more awake and focused after consumption, but have your students think about why this happens. Think about both the positives and negatives of consuming coffee and form a hypothesis on how yeast cultures will react to caffeine addition. Also consider the other components of black tea","s":"Introduction","u":"/experiments/caffeine-inhibition","h":"#introduction","p":215},{"i":223,"t":"We used two Pioreactors and two vials containing 15 mL of YPD media. We added 1 mL DI water to one vial and 1 mL steeped black tea to another. For the steeped black tea, a teabag was steeped in 250 mL hot water for 5 minutes before inoculation. Finally, we inoculated with 100 uL yeast slurry using a micropipette.","s":"Experiment","u":"/experiments/caffeine-inhibition","h":"#experiment","p":215},{"i":225,"t":"The growth rate chart clearly demonstrates an inhibition of growth occuring in the sample containing tea:","s":"Results","u":"/experiments/caffeine-inhibition","h":"#results","p":215},{"i":227,"t":"We recommend trying different amounts of tea, coffee, or other caffeine containing liquids to evaluate effects of caffeine concentrations. For example, how does adding one drop of black coffee compare to one drop of black tea? For a larger study, also consider giving your students a collection of common substances (vinegar, teas, salt, sugars) and see how these can boost or reduce growth rates.","s":"Recommendations","u":"/experiments/caffeine-inhibition","h":"#recommendations","p":215},{"i":229,"t":"Prepare identical sterile stocks in vials with your media of choice. Add some amount (a few drops to 1 mL) of a liquid containing caffeine to a vial. Add the same amount of DI water to another vial. If the media appears different before inoculation, we recommend you blank your vials before adding your culture. Inoculate each vial with a very small amount of your microorganism, using best practices to avoid other contamination. In our example, a yeast stock solution can be made by diluting a small amount of yeast in 15mL of YPD stock media, then a drop of this stock solution can be added to your vials. Wipe the vials and place them in the Pioreactors. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start Stirring activity, Temperature automation activity (set to an optimal temperature; ex. 30°C) and OD reading activity. Confirm that everything looks normal (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/caffeine-inhibition","h":"#detailed-procedure","p":215},{"i":231,"t":"Since the behaviour of the Pioreactor is controlled by Python objects, you can write Python scripts that use those objects. Here's a simple example of starting the stirring by creating the Stirrer object: from pioreactor.background_jobs.stirring import Stirrer, RpmFromFrequency from pioreactor.whoami import get_unit_name from pioreactor.whoami import get_latest_experiment_name unit = get_unit_name() experiment = get_latest_experiment_name() st = Stirrer( target_rpm=300, unit=unit, experiment=experiment, rpm_calculator=RpmFromFrequency() ) st.start_stirring() st.block_until_disconnected() # pauses the execution, but stirring continues Save this code to a local file on your Pioreactor's Raspberry Pi called stirring_script.py. Then, running python stirring_scripy.py, you should see that stirring on the Pioreactor starts. With the script running, you should also updates on the Pioreactor UI (ex: see pioreactor.local/pioreactors page). Typing ctrl-c will exit the script. info What is get_unit_name and get_latest_experiment_name? These are helper functions that get the current name of the Pioreactor, and the current experiment name, respectively. Using the current experiment name will ensure that your data shows up in the UI, and is correctly stored in the database. Automations​ Using automations requires you to invoke them with a Controller. For example, below we start a chemostat with some specific parameters, and set the target temperature to 30C. from pioreactor.background_jobs.dosing_control import DosingController from pioreactor.background_jobs.temperature_control import TemperatureController from pioreactor.whoami import get_latest_experiment_name unit = get_unit_name() experiment = get_latest_experiment_name() dc = DosingController( \"chemostat\", # automation name duration=1, # every minute, volume=1, # dose 1mL unit=unit, experiment=experiment, ) tc = TemperatureController( \"thermostat\", target_temperature=30, unit=unit, experiment=experiment ) dc.block_until_disconnected()","s":"Writing scripts","u":"/developer-guide/writing-scripts","h":"","p":230},{"i":233,"t":"On the command line, you can run your script with python your_script.py If you want to run the script in the background (so you can close terminal and the job continues in the background), use python your_script.py >/dev/null 2>&1 & disown You can also use the Pioreactor's plugin architecture to control the start and stop of the script.","s":"Starting a long-running script","u":"/developer-guide/writing-scripts","h":"#starting-a-long-running-script","p":230},{"i":235,"t":"RepeatedTimer: this class allows you to scheduale a function to run every N seconds in a non-blocking manner.","s":"Useful utility objects","u":"/developer-guide/writing-scripts","h":"#useful-utility-objects","p":230},{"i":237,"t":"Success Goal Conduct a simple control test to evaluate results between Pioreactors, using the same media composition, culture, and activities.","s":"Control testing","u":"/experiments/control-testing","h":"","p":236},{"i":239,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix","s":"Requirements","u":"/experiments/control-testing","h":"#requirements","p":236},{"i":242,"t":"Like any biotechnology, sources of error exist due to slight differences between Pioreactors. This can include bulb intensity variations, minute differences in the Pioreactor plastics, and even slight differences between vials! We can minimize how these differences affect our experiment through calibrations (check out available calibrations) and test these differences by conducting control tests. Control tests for the Pioreactor, unlike typical experiments, look at two or more instruments under the same conditions to determine any variances. This is an important statistical consideration when comparing data between several Pioreactors for research purposes. Ideally, we'd expect Pioreactors run under the same conditions to have very similar results. If results are dissimilar, we can begin to investigate sources of error by manipulating internal factors (such as configurations).","s":"Introduction","u":"/experiments/control-testing","h":"#introduction","p":236},{"i":244,"t":"The experiment is simple: place identical sterile vials into your Pioreactors, inoculated with the same amount of culture. Set stirring at the same RPM, temperature, and turn on OD reading and growth rate. With all factors the same, you should see similar normalized OD and growth rate graphs being generated.","s":"Experiment","u":"/experiments/control-testing","h":"#experiment","p":236},{"i":246,"t":"Here are graphs we generated though our A/A test: These kinds of tests make it easy to identify any unusual activity occuring in a specific Pioreactor (i.e, if it is missing an LED, temperature malfunctions, etc). In our case, though, both ran almost identically! Thus, we conclude that reliable comparisons can be drawn between these Pioreactors.","s":"Results","u":"/experiments/control-testing","h":"#results","p":236},{"i":248,"t":"Prepare identical sterile stocks in vials with your media of choice. Inoculate each vial with a very small amount of your microorganism, using best practices to avoid other contamination. In our example, a yeast stock solution can be made by diluting a small amount of yeast in 15mL of YPD stock media, then a drop of this stock solution can be added to your vials. Wipe the vials and place them in the Pioreactors. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start Stirring activity, Temperature automation activity (set to an optimal temperature; ex. 30°C) and OD reading activity. Confirm that everything looks normal (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/control-testing","h":"#detailed-procedure","p":236},{"i":251,"t":"For this introductory example, we'll create a background job that controls an LED in channel A on the Pioreactor HAT. When the job ends (either by us exiting, or via a MQTT signal), the LED will turn off. We start with some imports, and a class definition: from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" We've given the class the simple name of IntroJob. Our background job must inherit from BackgroundJob. All jobs require a job_name: the job_name is usually the snake-case of the class name. Next we'll define some initial attributes: from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" We declare that the intensity attribute is to be published and controllable over MQTT. We'll see this in action later. We also set intensity to be 0 initially, and use channel A to control. Next we add the __init__, which should always accept at least unit and experiment (as strings). unit refers to the name of the Pioreactor (the hostname), and experiment is the experiment the job is associated to. from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" def __init__(self, unit, experiment): super().__init__(unit=unit, experiment=experiment) We call super to initialize the super class, BackgroundJob, with the unit, and experiment. Next, we define a function, set_intensity that will be called whenever intensity is changed remotely (we'll do this later). The set_intensity function updates intensity and will change the onboard LED power for channel A. Remember, whenever the attribute intensity changes, it's published to MQTT. from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" def __init__(self, unit, experiment): super().__init__(unit=unit, experiment=experiment) def set_intensity(self, intensity): self.intensity = intensity led_intensity(channels=self.LED_channel, intensities=self.intensity) Next, we create the \"on exit\" behaviour (turn off LED) by overwriting the on_disconnected function. from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" def __init__(self, unit, experiment): super().__init__(unit=unit, experiment=experiment) def set_intensity(self, intensity): self.intensity = intensity led_intensity(channels=self.LED_channel, intensities=self.intensity) def on_disconnected(self): self.set_intensity(0) Finally, we add a small script at the bottom to run our new job when the Python file is invoked: from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" def __init__(self, unit, experiment): super().__init__(unit=unit, experiment=experiment) def set_intensity(self, intensity): self.intensity = intensity led_intensity(channels=self.LED_channel, intensities=self.intensity) def on_disconnected(self): self.set_intensity(0) if __name__ == \"__main__\": from pioreactor.whoami import get_unit_name from pioreactor.whoami import get_latest_experiment_name job = IntroJob(unit=get_unit_name(), experiment=get_latest_experiment_name()) job.block_until_disconnected() If you save this code in a file called intro_job.py, we can run it from the command line: python3 intro_job.py. In another terminal window, try the following: pio mqtt -t \"pioreactor/+/+/intro_job/#\" You should see some metadata about this job ($state is ready, some info about intensity), but also you should see the current value of intensity, namely 0. You can cancel the job with ctrl-c in the original terminal window. Adding an additional line in intro_job.py: if __name__ == \"__main__\": from pioreactor.whoami import get_unit_name from pioreactor.whoami import get_latest_experiment_name job = IntroJob(unit=get_unit_name(), experiment=get_latest_experiment_name()) job.set_intensity(10) job.block_until_disconnected() And rerunning the job, you should see MQTT have updated intensity data.","s":"Introductory example","u":"/developer-guide/writing-background-jobs","h":"#introductory-example","p":249},{"i":253,"t":"We'll explain how a more advanced background job is written using the example application of a job that controls an external motor (the load). This motor may control a larger stirrer, or shaker, or air-pump, but is regulated by the amount of voltage applied - that is, the more voltage applied, the more output from the motor. The Pioreactor HAT has four available pulse-width modulation (PWM) outputs, with programmable frequency and duty cycle (DC). For this example, we'll set a frequency that works for the motor. We also wish to increase the DC in proportion to the normalized optical density (this may represent needing to add more air, or shaking, as the culture's oxygen requirements increase). Let's start with the some imports and the class' __init__: from pioreactor.background_jobs.base import BackgroundJob class MotorDriver(BackgroundJob): job_name=\"motor_driver\" def __init__(self, hz, initial_duty_cycle, unit, experiment, **kwargs): super().__init__(unit=unit, experiment=experiment) self.hz = hz self._initial_duty_cycle = initial_duty_cycle self.duty_cycle = initial_duty_cycle ... We see that the __init__ requires the two parameters for PWM: hz and an inital_duty_cycle. One rarely changes the hertz of PWM, so its fixed - but we do often change the duty cycle, so we create a variable self.duty_cycle and assign it the initial_duty_cycle. We also need to supply the unit name (the hostname), and the experiment name. We'll populate these at run time later. Finally, we need a job_name to pass to the super class, BackgroundJob. This should be unique from other jobs that may run. Often we use the \"snake_case\" of the class name as the job name. We give it the job name motor_driver. We next initialize the PWM code (this is still in the __init__) that controls the PWM outputs on the HAT, and add more imports: from pioreactor.hardware_mappings import PWM_TO_PIN from pioreactor.utils.pwm import PWM from pioreactor.config import config ... def __init__(...) ... pwm_pin = PWM_TO_PIN[config[\"PWM_reverse\", \"motor_driver\"]] self.pwm = PWM(pwm_pin, self.hz) self.pwm.lock() ... The PWM_TO_PIN is lookup that maps settings in your config.ini to the Raspberry Pi's GPIO pins (which we use for the output PWM). Which means we also need update the [PWM] section in your config.ini: [PWM] 1=motor_driver 2=media 3=alt_media 4=waste 5=heater In the above code, we next initialize the PWM class. This is an abstraction to make working with the PWM hardware easier. For example, the next line, self.pwm.lock(), will put a lock on that Raspberry Pi GPIO pin, making it difficult for other processes to use it by mistake. We haven't started the PWM yet, we'll do that later. Next, we want to include the behavior to update the duty cycle when we get new normalized OD readings. This is typically done with a callback when a new MQTT message is received. See code below: def __init__(...) ... ... self.start_passive_listeners() ... def start_passive_listeners(self): self.logger.debug(\"Listening for od_filtered topics\") self.subscribe_and_callback( self.update_duty_cycle_by_normalized_od, f\"pioreactor/{self.unit}/{self.experiment}/growth_rate_calculating/od_filtered\", ) Note the self.logger.debug(...) line. Each background job has a Python logger that will log to four places: MQTT, the SQLite3 database, the terminal, and the log file on disk. See Python's logging module for more. The callback, update_duty_cycle_by_normalized_od, needs to be written: import json ... def update_duty_cycle_by_normalized_od(self, message): payload = json.loads(message.payload) if self.state == self.READY: self.set_duty_cycle(payload[\"od_filtered\"] * self._initial_duty_cycle) def set_duty_cycle(self, new_duty_cycle): self.duty_cycle = clamp(0, float(new_duty_cycle), 100) self.pwm.change_duty_cycle(self.duty_cycle) self.logger.debug(f\"new dc: {self.duty_cycle}\") In the callback, update_duty_cycle_by_normalized_od, we accept the message object. The message has two important properties: topic and payload. We only care about the payload, which is a string of json. We de-serialize the json to a dict. We only want to update the duty cycle if the job is in state READY (read about states here). If this is true, we call set_duty_cycle to update our duty cycle. This method handles the logic of clamping the value to be between 0 and 100, and we've stuck a debug in there so we can watch it change. What is the relationship between normalized OD and duty cycle. We do something naive, and just multiple the initial duty cycle by the normalized OD. So if the initial_duty_cycle is 10%, and the culture has 3.5x, then our new duty cycle is 35%. It is very naive. Finally, we need to think about changing states. What should our job do when the user pauses the job? How do we safely disconnect from the PWM? We use the state callback methods to handle these changes: def on_init_to_ready(self): self.pwm.start(self.duty_cycle) def on_ready_to_sleeping(self): self._previous_duty_cycle = self.duty_cycle self.set_duty_cycle(0) def on_sleeping_to_ready(self): self.set_duty_cycle(self._previous_duty_cycle) def on_disconnected(self): self.pwm.clean_up() After the job moves from init to ready (implicitly done after the __init__ finishes), the function on_init_to_ready is called. This starts the PWM, which starts the motor. When we sleep (pause), we record the last duty_cycle value, and use that to populate the duty_cycle when we re-start the job. Let's recap what we have so far, and save this to a file called motor_driver.py (ideally we save it in /home/pioreactor/.pioreactor/plugins/: # -*- coding: utf-8 -*- import json from pioreactor.config import config from pioreactor.background_jobs.base import BackgroundJob from pioreactor.hardware_mappings import PWM_TO_PIN from pioreactor.utils.pwm import PWM from pioreactor.utils import clamp class MotorDriver(BackgroundJob): job_name=\"motor_driver\" published_settings = { \"duty_cycle\": {\"datatype\": \"float\", \"settable\": False, \"unit\": \"%\"}, } _previous_duty_cycle: None def __init__(self, hz, initial_duty_cycle, unit, experiment, **kwargs): super().__init__(unit=unit, experiment=experiment) self.hz = hz self._initial_duty_cycle = initial_duty_cycle self.duty_cycle = initial_duty_cycle self.pwm_pin = PWM_TO_PIN[config[\"PWM_reverse\", \"motor_driver\"]] self.pwm = PWM(self.pwm_pin, self.hz) self.pwm.lock() self.start_passive_listeners() def update_duty_cycle_by_normalized_od(self, message): payload = json.loads(message.payload) if self.state == self.READY: self.set_duty_cycle(payload[\"od_filtered\"] * self._initial_duty_cycle) def set_duty_cycle(self, new_duty_cycle): self.duty_cycle = clamp(0, float(new_duty_cycle), 100) self.pwm.change_duty_cycle(self.duty_cycle) self.logger.debug(f\"new dc: {self.duty_cycle}\") def start_passive_listeners(self): self.logger.debug(\"Listening for od_filtered topics\") self.subscribe_and_callback( self.update_duty_cycle_by_normalized_od, f\"pioreactor/{self.unit}/{self.experiment}/growth_rate_calculating/od_filtered\", ) def on_init_to_ready(self): self.pwm.start(self.duty_cycle) def on_ready_to_sleeping(self): self._previous_duty_cycle = self.duty_cycle self.set_duty_cycle(0) def on_sleeping_to_ready(self): self.set_duty_cycle(self._previous_duty_cycle) def on_disconnected(self): self.logger.debug(\"disconnecting... will clean up PWM\") self.pwm.clean_up() This class works as is, but we also want to develop a command line interface for it so we can run it like pio run motor_driver. At the bottom of the file, we add: import click @click.command(name=\"motor_driver\") @click.option( \"--initial-dc\", default=config.getfloat(\"motor_driver\", \"initial_duty_cycle\"), show_default=True, type=click.FloatRange(0, 100, clamp=True), ) @click.option( \"--hz\", default=config.getfloat(\"motor_driver\", \"hz\"), show_default=True, type=click.FloatRange(1, 10_000, clamp=True), ) def click_motor_driver(initial_dc, hz): \"\"\" Start the external motor \"\"\" from pioreactor.whoami import get_unit_name, get_latest_experiment_name job = MotorDriver( hz=hz, initial_duty_cycle=initial_dc, unit=get_unit_name(), experiment=get_latest_experiment_name(), ) job.block_until_disconnected() Note the helper functions get_unit_name and get_latest_experiment_name to get the metadata for the class. The method block_until_disconnected will halt the program at that line (and only continue when a keyboard interrupt is detected). If you save it in the plugins folder, you can now execute: pio run motor_driver --initial-dc 10 and it should just work! You can exit with ctrl-c, and note that the on_disconnect is called when you do this. Adding published_settings​ Suppose we wish to monitor, or log, or just otherwise publish the duty_cycle from the MotorDriver class. We can \"register\" the attribute duty_cycle in the published_settings: class MotorDriver(BackgroundJob): ... published_settings = { \"duty_cycle\": {\"datatype\": \"float\", \"settable\": False, \"unit\": \"%\"}, } def __init__(...) If you open up the MQTT stream using pio mqtt, you should see duty_cycle appear under the topic pioreactor/<unit>/<experiment>/motor_driver/duty_cycle.","s":"More advanced example","u":"/developer-guide/writing-background-jobs","h":"#more-advanced-example","p":249},{"i":255,"t":"Success goal Use a turbidostat system with selective pressures to study evolutionary principles.","s":"Directed evolution of salt-tolerant yeast","u":"/experiments/directed-evolution-salt-tolerance","h":"","p":254},{"i":257,"t":"# Two available Pioreactors Dry baker's yeast Table salt YPD media Scale (accurate to 0.1) Two peristaltic pumps: One media pump One waste pump Two liquid containers: One labelled \"media\" One labelled \"waste\"","s":"Requirements","u":"/experiments/directed-evolution-salt-tolerance","h":"#requirements","p":254},{"i":260,"t":"Let's consider how we can combine our Pioreactor abilities to explore more complex ideas: Our turbidostat allows us to perform long-term experiments without the concern of limiting nutrients or space. By itself, there are no selective pressures to stop our cultures from reaching their maximum specific growth rate. We can introduce a selective pressure (like salt) that would reduce the growth rate. Over time, we will see our cultures adapt to the new salt conditions.","s":"Introduction","u":"/experiments/directed-evolution-salt-tolerance","h":"#introduction","p":254},{"i":262,"t":"Turbidostats remove and add media periodically to keep our culture size low and nutrient availability high. We inoculated some drops of baker's yeast into a vial, then set the turbidostat pumps to add and remove 1 mL of media to achieve our target OD of 2 AU. Once your culture has acclimated, inoculate new vials to compare the newly-grown salt-tolerant strain to the wild type strain.","s":"Experiment","u":"/experiments/directed-evolution-salt-tolerance","h":"#experiment","p":254},{"i":264,"t":"The following normalized OD graph resulted from our turbidostat using salted media: A maximum growth rate of 0.6 h⁻¹ was reached. In contrast, when you look back at our secondary level salt experiment, the 4.5% w/v salt vial only reached 0.29 h⁻¹ before the stationary phase occured. This is because our previous experiment selected for salt tolerant yeast, but the culture reached stationary phase before any long term adaptation could be observed. Using the turbidostat system to supply new nutrients and keep the population low, we were able to double the maximum growth rate! Our yeast culture exhibited an adaptation to grow in high salt, indicating our turbidostat yeast culture has gained a higher fitness in 4% w/v salted media. We then grew batch cultures of our new, salt-tolerant yeast, alongside our original (wildtype) yeast culture in 2 Pioreactors using 4% w/v salt media. Here's our result: You can see just how effective our turbidostat system was in creating an environment that pushed yeast into becoming more salt tolerant.","s":"Results","u":"/experiments/directed-evolution-salt-tolerance","h":"#results","p":254},{"i":266,"t":"Part 1: Growing your turbidostat culture​ Prepare one liquid container of 5% w/v YPD broth with 4% w/v salt. Sterilize by autoclaving, along with your sample vial. Sterilize and setup your pumps. Once cooled, fill your sample vial with the autoclaved media by setting the Add media value to 14 mL. Inoculate the sample vial with baker's yeast. Visit pioreactor.local and start a new experiment. Click Manage and Start the Dosing automation. Change the automation type to Turbidostat. Set your Volume and Target OD. End the experiment once the maximum specific growth rate has increased suffienctly. This may take a day or more. note The maximum specific growth rate will increase over time, as faster-growing yeast outcompete slow-growing yeast. Part 2: Comparing batch cultures​ Inoculate one vial of sterile salted YPD media with the new, salt-tolerant yeast. Inoculate a second vial of sterile salted YPD media with the wild type yeast. Determine their growth rates using two Pioreactors. You should be able to observe that the yeast from the turbidostat are quicker to grow in the salt heavy media.","s":"Detailed procedure","u":"/experiments/directed-evolution-salt-tolerance","h":"#detailed-procedure","p":254},{"i":268,"t":"Now that you've set up your Pioreactor, you can start a brand new experiment. Explore the sidebar for experiments you can perform with your Pioreactor. We encourage you to expand on the sample protocols we provided using your own cultures and media. info If you haven't already, please reference the Experiment basics page for information on media preparation, sterilization, and using the Pioreactor UI.","s":"Biology experiments and protocols","u":"/experiments/introduction","h":"","p":267},{"i":270,"t":"This entire site is open-source, and any suggestions or comments can be added to our Issue Tracker. If you're up for it, feel free to send a pull request, too!","s":"Have edits, corrections, or suggestions?","u":"/experiments/introduction","h":"#have-edits-corrections-or-suggestions","p":267},{"i":272,"t":"Success Goal Conduct a simple comparison of yeast growth between a low percent and high percent YPD media.","s":"Comparing concentrations of media","u":"/experiments/low-vs-high-conc-media","h":"","p":271},{"i":274,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix","s":"Requirements","u":"/experiments/low-vs-high-conc-media","h":"#requirements","p":271},{"i":277,"t":"The most accessible introductory experiment you can conduct with basic supplies is comparing concentrations of media. In this particular example, we will use YPD media and grow yeast cultures, but any media/culture you have readily available will work! YPD is a common complete media used to propagate yeast cultures, containing peptone and sugars nexcessary for yeast growth. Now consider creating two YPD media compositions: one with 1% YPD w/v, and one with 5% YPD w/v. We can easily infer that a culture grown in 5% YPD will flourish more than one grown in 1% &#151 but let's expore our hypothesis further! Discuss with your students the following ideas: How would both cultures start off? Will one have a faster rate than another? Why? Will one reach a higher growth rate? Why or why not? How long will it take for the culture in 5% YPD to slow in growth? Compared to the culture in 1% YPD?","s":"Introduction","u":"/experiments/low-vs-high-conc-media","h":"#introduction","p":271},{"i":279,"t":"We created 1% YPD by adding 0.15 grams of YPD broth powder to 15 mL: \\text \\{w/v \\%\\}= \\frac \\{\\text\\{mass\\}\\}\\{\\text \\{volume\\}\\} {mass}={0.01}×{15 {mL}}\\text \\{mass\\} = \\{0.01\\} \\times \\{15 \\:\\text \\{mL\\}\\}{mass}={0.01}×{15{mL}}{mass}=0.15 {grams}\\text \\{mass\\} = 0.15 \\:\\text \\{grams\\}{mass}=0.15{grams} Using the same logic, 5% YPD was created by adding 0.75 grams to 15 mL. We inoculated both with 100 uL of a yeast slurry using a micropipette. If this is unavailable, a dropped will work as well!","s":"Experiment","u":"/experiments/low-vs-high-conc-media","h":"#experiment","p":271},{"i":281,"t":"As expected, growth diminished earlier for the culture inoculated in 1% YPD:","s":"Results","u":"/experiments/low-vs-high-conc-media","h":"#results","p":271},{"i":283,"t":"Consider lower or higher bounds for your media compositions. How much sooner will yeast stop growing in 0.5% YPD? Can we test when yeast growth is halted by YPD concentration versus reaching a peak turbidity?","s":"Recommendations","u":"/experiments/low-vs-high-conc-media","h":"#recommendations","p":271},{"i":285,"t":"Prepare a sterile stock of two different concentrations of your media of choice. If the media appears different before inoculation, we recommend you blank your vials before adding your culture. Inoculate each vial with a very small amount of your microorganism, using best practices to avoid other contamination. In our example, a yeast stock solution can be made by diluting a small amount of yeast in 15mL of YPD stock media, then a drop of this stock solution can be added to your vials. Wipe the vials and place them in the Pioreactors. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Calibrate for each Pioreactor and under the Blanks tab, click Start. Select Manage all Pioreactors, and start Stirring activity, Temperature automation activity (set to an optimal temperature; ex. 30°C) and OD reading activity. Confirm that everything looks normal (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Optional: you can change the names of the Pioreactor in the UI to display the percent of media. Students can watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/low-vs-high-conc-media","h":"#detailed-procedure","p":271},{"i":287,"t":"Success Goal Demonstrate the effect of temperature on yeast growth. tip Requirements​ # At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix Introduction​ Students may have a prior belief that temperature effects are linear. For example: a culture at 10℃ will grow at half the rate compared to a culture at 20℃, and a third the rate at 30℃. In reality, cells have a range of temperatures it will do well at, and temperatures too cold or too hot will lead to slower growth rates. This experiment would show the non-linear effect of temperature on growth (and relate it to how refrigerators halt spoilage for so long!). Students and the teacher can pick temperatures to test beforehand. info The Pioreactor doesn't cool samples, so it can't achieve temperatures below your ambient temperature. If you want to test low temperatures, you can place the Pioreactor in a fridge, or in a cooler with ice packs (making sure the electronics won't get wet).","s":"Yeast growth at varying temperatures","u":"/experiments/yeast-growth-by-temperature","h":"","p":286},{"i":289,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix","s":"Requirements","u":"/experiments/yeast-growth-by-temperature","h":"#requirements","p":286},{"i":292,"t":"Students may have a prior belief that temperature effects are linear. For example: a culture at 10℃ will grow at half the rate compared to a culture at 20℃, and a third the rate at 30℃. In reality, cells have a range of temperatures it will do well at, and temperatures too cold or too hot will lead to slower growth rates. This experiment would show the non-linear effect of temperature on growth (and relate it to how refrigerators halt spoilage for so long!). Students and the teacher can pick temperatures to test beforehand. info The Pioreactor doesn't cool samples, so it can't achieve temperatures below your ambient temperature. If you want to test low temperatures, you can place the Pioreactor in a fridge, or in a cooler with ice packs (making sure the electronics won't get wet).","s":"Introduction","u":"/experiments/yeast-growth-by-temperature","h":"#introduction","p":286},{"i":294,"t":"The following experiment was performed using four Pioreactors. Four vials containing 15 mL of the sterile YPD stock were inoculated with 1 drop of rehydrated active yeast (0.500 g of dry yeast in a 15mL YPD broth vial). They were grown at temperatures of 28°C, 32°C, 36°C and 40°C.","s":"Experiment","u":"/experiments/yeast-growth-by-temperature","h":"#experiment","p":286},{"i":296,"t":"Over the course of 12 hours, the following graphs were recorded: Though subtle, non-linear patterns of growth rate are observed between the temperatures. Key data points are summarized in the following table: Temperature Peak growth rate (h⁻¹) Time to reach stationary phase 28°C 0.65 9 hours 32°C 0.73 8.5 hours 36°C 0.76 7.5 hours 40°C 0.59 9.5 hours Rather than increasing as temperature increases, the highest growth rates form a bell curve, with the highest overall growth rate of 0.76 h⁻¹ occurring at 36°C. It decreases at 40°C since this temperature lies outside of the ideal temperature range for yeast. The time it takes for each culture to reach the stationary phase is also related to the peak growth rates. Cultures that peaked higher did so in a quicker time frame, thus reaching the stationary phase sooner! Consider the extremes in this case: what would happen if we drop the temperature? Increased it to 50°C? How does this relate to cooking and food storage?","s":"Results","u":"/experiments/yeast-growth-by-temperature","h":"#results","p":286},{"i":298,"t":"We chose a relatively small temperature range that mostly aligned with optimal temperatures for yeast growth. We encourage you to explore temperatures outside of this range, whether by cooling the Pioreactor externally (using ice/a cooler) or increasing the temperature (the maximum that can be reached is room temperature plus 20°C). Keep in mind to not get the electronics of your Pioreactor wet! Elevate your Pioreactor to protect it from any spills.","s":"Recommendations","u":"/experiments/yeast-growth-by-temperature","h":"#recommendations","p":286},{"i":300,"t":"Prepare a stock of 50g YPD / 1L distilled water. Aim for 20ml × the number of Pioreactors you are using, as each Pioreactor will require about 15mL of media. Divide this stock into small vials, then sterilize by autoclaving. Allow stock to cool. Dilute a small amount of yeast in 15mL of YPD stock media. Sterily add 3-4 drops of this yeast solution to your vials. Wipe the vials and place them in the Pioreactor. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start: Stirring activity OD reading activity Select Manage on an individual Pioreactor. Turn on the Temperature automation activity on Thermostat, selecting your temperature of interest. Confirm that everything looks normal on the Overview page (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. Optional: you can change the names of the Pioreactor in the UI to display the target temperature. Students can watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/yeast-growth-by-temperature","h":"#detailed-procedure","p":286},{"i":302,"t":"Success goal Determine the maximum specific growth rate of your culture using turbidostat strategies and pump extentions of the Pioreactor.","s":"Continuous cultures using a turbidostat","u":"/experiments/continuous-cultures-using-turbidostat","h":"","p":301},{"i":304,"t":"# One available Pioreactor Two peristaltic pumps: One media pump One waste pump Two liquid containers: One labelled \"media\" One labelled \"waste\" Scale to calibrate, if needed","s":"Requirements","u":"/experiments/continuous-cultures-using-turbidostat","h":"#requirements","p":301},{"i":307,"t":"Your Pioreactor can be transformed into a turbidostat, where pumps are used to replenish media around a target OD, creating a continuous culture. Due to the abundance of resources and lack of rate-limiting nutrients, the specific growth rate of a species is maximized. Learn more about the differences in bioreactor strategies here! This setup is a powerful tool that tests the limits of population growth. Students can investigate the specific maximum growth rate of a species and evaluate what innate biological processes are limiting growth.","s":"Introduction","u":"/experiments/continuous-cultures-using-turbidostat","h":"#introduction","p":301},{"i":309,"t":"In our turbidostat system, we studied a small vial of YPD media inoculated with 4 drops of a yeast slurry. We set our volume to be exchanged to be 1 mL when the target OD was reached. This means at our target OD, 1 mL of media in the vial would be removed, and 1 mL of fresh media is added. We initially set our turbidostat target OD to 2 AU. To demonstrate how quickly our system can adapt, we changed our target OD to 3.5 AU after 6 hours. A higher target OD allows the culture to become more turbid.","s":"Experiment","u":"/experiments/continuous-cultures-using-turbidostat","h":"#experiment","p":301},{"i":311,"t":"After 16 hours, the following results are recorded: FYI: Why does normalized OD look like that? After the time period set by you (the Time between dosing), the system assesses the normalized OD. As the normalized OD approaches the target OD, an automated amount of new media is added and waste is removed. The next time the system \"wakes up\", the OD will equals/be close to the set target OD. Over time, we expect faster growing yeast to out-compete slower growing yeast, resulting in an increase in maximum growth rate. As seen above, the growth rate improves from 0.30 h⁻¹ to 0.41 h⁻¹ in the span of 15 hours.","s":"Results","u":"/experiments/continuous-cultures-using-turbidostat","h":"#results","p":301},{"i":313,"t":"There is a myriad of further applications for turbidostats, such as characterization of species, directed evolution, responses to stimuli (gene-regulating metabolites) and so much more. We encourage you to choose species and media compositions to suit your interests. Have fun!","s":"Recommendations","u":"/experiments/continuous-cultures-using-turbidostat","h":"#recommendations","p":301},{"i":315,"t":"Add media into your media container. Sterilize by autoclaving. Adjust the tube lengths on the cap of your small sterile vial such that one just touches the media, while another sits above the media. Inoculate your small sterile vial with drops of your culture. Wipe vial and place in the Pioreactor. For your media pump: Attach the source tube to your media container. Attach the sink tube to the vial cap tube that sits above the media. For your waste pump: Attach the source tube to the vial cap tube that touches the media. Attach the sink tube to your waste container. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Select Manage, start Stirring activity and OD reading activity. Confirm everything looks correct, then start the Growth rate activity. Start the Dosing automation. Change automation to Turbidostat. Set your Volume and Target OD. You can change the parameters of the turbidostat automation in the Settings tab. Changes will take effect immediately.","s":"Detailed procedure","u":"/experiments/continuous-cultures-using-turbidostat","h":"#detailed-procedure","p":301},{"i":317,"t":"Success Goal Apply turbidostat functions with temperature cycling to study yeast behaviour in a more natural temperature environment.","s":"Temperature cycling of continuous cultures","u":"/experiments/temp-cycle","h":"","p":316},{"i":319,"t":"Two available Pioreactors Four peristaltic pumps: Two media pumps Two waste pumps Two liquid containers: One labelled \"media\" One labelled \"waste\" Scale to calibrate, if needed Culture of choice (ex. Baker's Yeast) Media of choice (ex. YPD)","s":"Requirements","u":"/experiments/temp-cycle","h":"#requirements","p":316},{"i":321,"t":"Observations of cultures in lab settings are often disconnected from real world behaviours. In nature, cultures are subjected to many cyclic changes tied to the day and night cycle. We can mimic these cycled environments using plugins on our Pioreactor. We created a plugin that cycles the temperature between 30°C and 40°C sinusoidally over a 24 hour period. Together with turbidostat media cycling, the maximum specific growth rate can be characterized between a culture held at a static temperature versus a culture undergoing temperature cycling. This experiment explores concepts described in Knutson et al., (2018).","s":"Introduction","u":"/experiments/temp-cycle","h":"#introduction","p":316},{"i":323,"t":"Check out our blog post for an in-depth evaluation of our experiment!","s":"Experiment","u":"/experiments/temp-cycle","h":"#experiment","p":316},{"i":325,"t":"Once we exported our data, we charted our yeast growth rate against the temperature readings to generate the following graph:","s":"Results","u":"/experiments/temp-cycle","h":"#results","p":316},{"i":328,"t":"Add media into your media container. Sterilize by autoclaving. Adjust the tube lengths on the cap of your small sterile vial such that one just touches the media, while another sits above the media. Inoculate your small sterile vial with drops of your culture. Wipe vial and place in the Pioreactor. For your media pump: Attach the source tube to your media container. Attach the sink tube to the vial cap tube that sits above the media. For your waste pump: Attach the source tube to the vial cap tube that touches the media. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Select Manage, start Stirring activity and OD reading activity. Install the cycle_temp plugin from the Plugins tab. This will give you a new option in your Temperature automation activity. Under Manage > Activities > Temperature automation, select Cycle Temp from the drop down menu. Click Start. Confirm everything looks correct, then start the Growth rate activity. Start the Dosing automation. Change automation to Turbidostat. Set your Volume and Target OD. You can change the parameters of the turbidostat automation in the Settings tab. Changes will take effect immediately.","s":"Detailed procedure","u":"/experiments/temp-cycle","h":"#detailed-procedure","p":316},{"i":330,"t":"Knutson, C. M., McLaughlin, E. M., & Barney, B. M. (2018). Effect of temperature control on green algae grown under continuous culture. Algal research, 35, 301-308. https://doi.org/10.1016/j.algal.2018.08.020","s":"References","u":"/experiments/temp-cycle","h":"#references","p":316},{"i":333,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix Table salt Scale (accurate to 0.1)","s":"Requirements","u":"/experiments/salt-stress-on-yeast","h":"#requirements","p":331},{"i":336,"t":"In early biology classes, students learn the core concepts of osmolarity across a cell's membrane. The cell's environment can contain different concentrations of impermeable molecules, creating osmotic pressure and resulting in water entering or leaving the cell. You can quantitatively measure this effect on growth rate using your Pioreactor! The inside and outside of a cell are separated by the cell's semi-permeable membrane. Only water and certain molecules can pass through via active or passive transport (diffusion). All other molecules are impermeable and cannot pass through the membrane. We'll refer to these as solutes. Through the process of osmosis, water (our solvent) is drawn across a cell's membrane towards higher concentrations of solutes, until an equilibrium is reached. If the concentration of solutes inside and outside a cell is the same, then the cell is in an isotonic solution. Less external solutes or more solutes create hypotonic and hypertonic solutions, respectively. Increasing salt content to create a hypertonic solution will slow the yeast's fermentation or reproductive activities, leading to slower growth. As salt is added in excess, yeast cells will fail to grow; yeast needs water and their cell volume eventually becomes too small for growth.","s":"Introduction","u":"/experiments/salt-stress-on-yeast","h":"#introduction","p":331},{"i":338,"t":"We performed this experiment using five Pioreactors and vials containing 15 mL of sterile YPD stock and salt concentrations of 0%, 1.5%, 3%, 4.5%, and 6% w/v. A sample calculation is as follows: \\text \\{w/v \\%\\}= \\frac \\{\\text\\{mass\\}\\}\\{\\text \\{volume\\}\\} To create a salt concentration of 3% w/v for 15 mL of media: 0.03 = \\frac \\{\\text\\{mass\\}\\}\\{15 mL\\}{mass}=0.45g\\text \\{mass\\} = 0.45 g{mass}=0.45g Therefore, 0.45 grams of table salt is needed for 3% w/v of salt. To each vial, 0g, 0.225g, 0.45g, 0.675g and 0.9g of table salt were added, repectively. They were then innoculated with one drop of rehydrated active yeast (0.500 g of dry yeast in a 15 mL YPD broth vial). The Temperature automation was set on Thermostat at 32.5°C.","s":"Experiment","u":"/experiments/salt-stress-on-yeast","h":"#experiment","p":331},{"i":340,"t":"After approximately 26 hours, the following growth rates were recorded: We can summarize our results in the following table to highlight our data: Salt percent (w/v) Peak growth rate (h⁻¹) Time to reach stationary phase 0% (control) 0.78 8 hours 1.5% 0.67 8.3 hours 3% 0.49 11.5 hours 4.5% 0.29 17 hours 6% 0.22 24 hours The highest growth was recorded in the vial at 0% salt w/v (no salt stress), at approximately 0.78 h⁻¹. The phases of growth (lag, log phase) occured quickly and the stationary phase was reached in the smallest time frame of about 8 hours. As the salt percentage increased, the peak growth rate decreased and the time to reach the stationary phase was extended. These time increases are non-linear; between 0% and 1.5% salt, the stationary phase was reached within an increment of half an hour &#151 however 4.5% and 6% salt had a large increment of 7 hours (from 17 to 24 hours).","s":"Results","u":"/experiments/salt-stress-on-yeast","h":"#results","p":331},{"i":342,"t":"The flexibility of the Pioreactor means you can do much more with this simple concept! Here are some recommendations: performing the experiment over a longer period of time, or with higher salt percentages; papers commonly go up to 10%. exploring pretreated cells (by growing one culture in a saltier environment, then comparing a non-treated culture to the treated culture under the same conditions). See our experiment on directed evolution. considering different species and how they react to the same salt conditions.","s":"Recommendations","u":"/experiments/salt-stress-on-yeast","h":"#recommendations","p":331},{"i":344,"t":"Prepare a stock of 50g YPD / 1L distilled water. Aim for 20ml × the number of Pioreactors you are using, as each Pioreactor will require about 15mL of media. Divide this stock into small vials, then sterilize by autoclaving. Allow stock to cool. Weigh table salt to add to your media. This amount can be calculated as per the example above. Divide the stock into the sterilized vials and add salt. Mix the salt with gentle shaking or by using the Stirring function on the Pioreactor. Dilute a small amount of yeast in 15mL of YPD stock media. This can be stored in a fridge for future use. Using sterile techniqes, add 3-4 drops of this yeast solution to your vials. Wipe the vials and place them in the Pioreactor. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start: Stirring activity OD reading activity Temperature automation activity Confirm that everything looks normal on the Overview page (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. Watch the growth progress on the Overview page!","s":"Detailed procedure","u":"/experiments/salt-stress-on-yeast","h":"#detailed-procedure","p":331},{"i":346,"t":"Success goal Explore the ethanol fermentation process and practice dilution calculations for media preparation.","s":"Yeast growth in ethanol","u":"/experiments/yeast-in-ethanol","h":"","p":345},{"i":348,"t":"At least two available Pioreactors Dry baker's yeast Ethanol (95% rubbing alcohol) Distilled water","s":"Requirements","u":"/experiments/yeast-in-ethanol","h":"#requirements","p":345},{"i":350,"t":"To get their energy, yeast species are fermentors; they take sugars and oxygen and metabolize them into ethanol and carbon dioxide. We've used these products to create many goods in the food industry, such as breads and beers! While we have found many applications for yeast products, yeasts themselves see these as waste products. These waste products can accumulate, leading to what's called the \"staling effect\" where yeasts can't grow because of an over-accumulation of their own waste. We know that most yeasts can tolerate an alcohol concentration of 10-15% before dying. Now, let's choose some alcohol concentrations and explore this inhibition using our Pioreactor! We've included two methods to calculate ethanol precentages; teachers can prepare this beforehand or allow their students to calculate it themselves.","s":"Introduction","u":"/experiments/yeast-in-ethanol","h":"#introduction","p":345},{"i":352,"t":"We conducted an experiment using 4 Pioreactors and vials with ethanol concentrations of 0%, 4%, and 6%. After adding 15 mL YPD stock into each vial, we calculated the amount of ethanol to use per vial using Method 1 below. Method 2 can be done instead to simplify the procedure.","s":"Experiment","u":"/experiments/yeast-in-ethanol","h":"#experiment","p":345},{"i":354,"t":"The first concentration of 0% ethanol is easy &#151 we just add 1 mL of distilled water. For the rest, the following calculations were done to determine the volume of ethanol to add to each vial: {[{ethanol}]}{{media volume+ethanol volume}}={ethanol%}\\frac\\{[\\text\\{ethanol\\}]\\}\\{\\text\\{media\\thickspace volume + ethanol\\thickspace volume\\}\\}=\\text\\{ethanol \\%\\}[{​{ethanol}]}{{mediavolume+ethanolvolume}}={ethanol%} In our case, we have 15 mL of YPD broth per vial, and want to add 1 mL of diluted ethanol; we want to determine our final concentration of ethanol in 1 mL to get an overall 2% concentration in our complete, 16 mL of media. For 2%: {[{ethanol}]}{{15mL+1mL}}={2%}\\frac\\{[\\text\\{ethanol\\}]\\}\\{\\text\\{15 mL + 1 mL\\}\\}=\\text\\{2\\%\\}[{​{ethanol}]}{{15mL+1mL}}={2%}[{ethanol}]=32%[\\text\\{ethanol\\}]=32\\%[{ethanol}]=32% Now, we know we want our 1 mL of dilute ethanol concentration to equal 32%. Since we're starting with an initial concentration of 95%, we can apply the following dilution equation to figure out the concentration of 95% ethanol to use: Initial volume (Vi)= ? Initial concentration (Ci)= 95% Final volume (Vf)= 1 mL Final concentration (Cf)= 32% Now we substitute our variables into the equation Ci Vi = Cf Vf: Vi={(32%)({1mL})}{95%}V_i = \\frac\\{(32\\%)(\\text\\{1 mL\\})\\}\\{95\\%\\}Vi​=({​32%)({1mL})}{95%}Vi={0.34mL}V_i = \\text\\{0.34 mL\\}Vi​={0.34mL} So the composition to create 2% ethanol media is: 15 mL YPD stock 0.34 mL of 95% ethanol 0.66 mL distilled water (1 mL - 0.34 mL) tip If you don't have a small enough resolution on your measuring tools, you can increase the total amount of ethanol dilution. For example, instead of making 1 mL diluted ethanol, we used 3.4 mL of 95% ethanol and 6.6 mL of distilled water measured in a graduated cylindar to create a total 10 mL diluted ethanol. From that, we mixed well and added 1 mL into our vial. We repeated this for 4% and 6% ethanol concentrations.","s":"Method 1","u":"/experiments/yeast-in-ethanol","h":"#method-1","p":345},{"i":356,"t":"Instead of finding the exact ethanol amounts to add to create a specific ethanol percentage, we can keep halving the ethanol solution and calculate the ethanol percentage afterwards. For example: Vial 1: 1 mL of 95% ethanol Vial 2: 0.5 mL of 95% ethanol; 0.5 mL distilled water Vial 3: 0.25 mL of 95% ethanol; 0.75 mL distilled water Vial 4: 1 mL distilled water To calculate the resulting ethanol percentage: {[{ethanol}]}{{media volume+ethanol volume}}={ethanol%}\\frac\\{[\\text\\{ethanol\\}]\\}\\{\\text\\{media\\thickspace volume + ethanol\\thickspace volume\\}\\}=\\text\\{ethanol \\%\\}[{​{ethanol}]}{{mediavolume+ethanolvolume}}={ethanol%} Substitute the [ethanol] value for half of 95% (or 47.5%): {47.5%}{{15mL+1mL}}={ethanol%}\\frac\\{47.5\\%\\}\\{\\text\\{15 mL + 1 mL\\}\\} = \\text\\{ethanol \\%\\}4{​7.5%}{{15mL+1mL}}={ethanol%}{ethanol%}≈3%\\text\\{ethanol \\%\\} \\approx 3\\%{ethanol%}≈3% This technique produces halving ethanol percentages of 0%, 1.5%, 3%, and 6% to be studied on a cluster of 4 Pioreactors.","s":"Method 2","u":"/experiments/yeast-in-ethanol","h":"#method-2","p":345},{"i":358,"t":"After approximately 18 hours, the following implied growth rates were recorded: We can summarize our results in the following table: Alcohol percent Peak growth rate (h⁻¹) Percent of control Time to reach stationary phase 0% 0.75 100% 7 hours 4% 0.46 61% 9 hours 6% 0.27 36% 14 hours As expected, just the smallest addition of ethanol really cut down on our yeasts' ability to grow. At a 4% alcohol concentration, the maximum growth rate decreased by almost 40%!","s":"Results","u":"/experiments/yeast-in-ethanol","h":"#results","p":345},{"i":360,"t":"We encourage you to select alcohol concentrations outside of the expected range. At what point does yeast show no growth? Can you see anything interesting when your culture reaches the stationary phase? Hint: you may be able to observe a diauxic shift! Plenty of yeast strains are available at your local breweries. You can do the same experiment on different strains to see which yeasts are more tolerant than others. What concentrations of beers can they make?","s":"Recommendations","u":"/experiments/yeast-in-ethanol","h":"#recommendations","p":345},{"i":362,"t":"Prepare a sterile stock of 50g YPD / 1L distilled water. Aim to make 20 mL × the number of Pioreactors you are using, as each Pioreactor will require about 15 mL of media. Prepare 1 mL of each ethanol concentration you would like to use. Detailed calculations are found in the example above. Aim for an end ethanol concentration between 0-10%. Evenly divide the YPD stock into the vials you’d like to use (ie. 15 mL in each vial). Add the mililitre of ethanol solution into the respective vial. Mix with gentle shaking. Inoculate the stock with a very small amount of baker's yeast using best practices to avoid other contamination. Wait for the yeast granules to dissolve, aided by gentle rocking or stirring. Alternatively, a yeast stock solution can be made by diluting a small amount of yeast in 15 mL of YPD stock, then 1 drop of this stock solution can be added to your vials. Wipe the vials and place them in the Pioreactors. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start Stirring activity and OD reading activity. Optional: you can turn on the Temperature automation activity and set it on Thermostat at an optimal temperature (ex. 30C). Confirm that everything looks normal (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Optional: you can change the names of the Pioreactor in the UI to display the target temperature. Students can watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/yeast-in-ethanol","h":"#detailed-procedure","p":345},{"i":364,"t":"Alba-Lois, L., & Segal-Kischinevzky, C. (2010). Yeast fermentation and the making of beer and wine. Nature Education, 3(9), 17. Gray, W. D. (1941). Studies on the alcohol tolerance of yeasts. Journal of Bacteriology, 42(5), 561-574.","s":"References","u":"/experiments/yeast-in-ethanol","h":"#references","p":345},{"i":376,"t":"Info You can expect the assembly to take approximately 20-30 minutes.","s":"Before you begin assembly","u":"/user-guide/20ml-v11-hardware-setup-intro","h":"","p":375},{"i":382,"t":"For more customization and control of your Pioreactor, you can access the Raspberry Pi's command line. From the command line, you can view more logs, control individual Pioreactors, and more.","s":"Accessing the Raspberry Pi","u":"/user-guide/accessing-raspberry-pi","h":"","p":381},{"i":384,"t":"There are two simple ways to access the Raspberry Pi from a Windows desktop.","s":"Access from Windows","u":"/user-guide/accessing-raspberry-pi","h":"#access-from-windows","p":381},{"i":386,"t":"Open the command prompt. Type ssh pioreactor@<insert unit name>.local. For example, to access on our Pioreactor named worker3, we typed ssh pioreactor@worker3.local. The default password is raspberry (see \"info\" below). If asked \"The authenticity of host...\", enter \"yes\". info When typing in the password, characters may not show up as you type - that's normal. This is a security feature. If successful, try entering pio blink - your Pioreactor's blue LED should starting blinking. See more commands here.","s":"1. Using the Command Prompt","u":"/user-guide/accessing-raspberry-pi","h":"#1-using-the-command-prompt","p":381},{"i":388,"t":"Start by installing the program PuTTY. Once downloaded, open PuTTY. Enter your Pioreactor's name as the hostname (if working with a cluster, enter your leader's hostname). Click \"Open\". If this is the first time to connect to the Raspberry Pi, you will have to accept its SSH certificate. On the next screen, use the username / password: pioreactor / raspberry. If successful, try entering pio blink - your Pioreactor's blue LED should starting blinking. See more commands here.","s":"2. Using PuTTY","u":"/user-guide/accessing-raspberry-pi","h":"#2-using-putty","p":381},{"i":390,"t":"Open the Terminal application. From the command line, enter ssh pioreactor@<name of pioreactor>.local. If this is the first time to connect to the Raspberry Pi, you will have to accept its SSH certificate. When prompted, enter the password raspberry. info When typing in the password, it may not show up as you type (this is a security feature) If successful, try entering pio blink - your Pioreactor's blue LED should starting blinking. See more commands here.","s":"Access from a Mac","u":"/user-guide/accessing-raspberry-pi","h":"#access-from-a-mac","p":381},{"i":392,"t":"You don't need my help. Try entering pio blink - your Pioreactor's blue LED should starting blinking. See more commands here.","s":"Access from Linux","u":"/user-guide/accessing-raspberry-pi","h":"#access-from-linux","p":381},{"i":394,"t":"If the above steps aren't working for your system, try the following: Instead if using the <unit name>.local, try using the IP address (if available). Example, ssh pioreactor@192.168.1.30 for a Raspberry Pi at IP address 192.168.1.30. Try power-cycling the Pioreactor.","s":"Troubleshooting","u":"/user-guide/accessing-raspberry-pi","h":"#troubleshooting","p":381},{"i":403,"t":"Below is a list of activities that come available with the Pioreactor. Additionally, you can add activities using plugins. Read more about using plugins. Stirring: this starts the stirring in the Pioreactor. After starting to stir, you can change the stirring speed in the Settings tab. You can modify the default stirring speed in the configuration settings. We recommend keeping the stirring range of 150 RPM to 600 RPM. Optical density: this turns on the system that measures culture density. Readings will start to populate the Experiment Overview page. It's useful to inspect the first few minutes of readings to ensure the readings are as expected (e.g., the readings aren't erratic, and the stirring speed is appropriate, etc.). Growth Rate: this activity requires that stirring and optical density be running as well. This starts the calculation of a normalized optical density, and the implied growth rate. Both calculations will populate the Experiment Overview page. Temperature automation: turning on a temperature automation will start collecting temperature readings. For example, the Thermostat automation will use a feedback loop to stabilize the Pioreactor to a set temperature. Pausing an automation will cease both any active heating and temperature data collection. Stopping an automation will stop the heating and temperature collection. To change a running temperature automation, use the \"Change Temperature Automation\" button. Read more about specific temperature automations. Dosing automation: turning on a dosing automation to start listening periodically for dosing triggers. A dosing automation requires at least 1 pump to be available and calibrated. More about using pumps. Pausing a dosing automation will stop any currently, and future, dosing occurring until the automation is unpaused. Read more about the different types of dosing automations. LED automation: turning on a LED automation to start listening periodically for LED change triggers. Read more about LED automations.","s":"Activities","u":"/user-guide/activities","h":"","p":402},{"i":405,"t":"The PWM output default to 5V (specifically, it's tied to the power supply, so it may be 5.1V, 5.2V etc. See your power supply). You are able to use 12V pumps successfully even at 5V output. However, you can also use the AUX power connection to change the PWM output. Note that the inner tubing on pumps is often different from the outer tubing. For example, for the peristaltic pumps that we supply: Interior tubing dimensions: 3.3mm OD, 1mm ID Exterior tubing dimensions: 1/8\" OD, 1/16\" ID Pumps that we have used and we like: note These pumps require some assembly to work with the Pioreactor Adafruit","s":"More on peristaltic pumps","u":"/user-guide/addition-hardware-pumps","h":"","p":404},{"i":407,"t":"Plugins offer a powerful way to extend your Pioreactor. Below is a list of our favourite plugins. Visit the guide on how to install plugins into your Pioreactor.","s":"List of available plugins","u":"/user-guide/available-plugins","h":"","p":406},{"i":410,"t":"Depending on the purposes of your research, you may want to calibrate your Pioreactor against known samples and OD600 values. We've given you the option to do this through the command line, similar to how pump calibrations currently work. Calibrations using the UI are coming soon! OD600 calibrations are straightforward, and only require one vial, your sample of interest, and an accurate way to measure liquids. We recommend a micropipette of volume range 100 to 1000 uL. The calibration works by reading a dilution series. You will start with 10mL of your sample of interest cultivated in your media, at the highest density you expect to observe. During the calibration, you will specify and add an amount of your media to dilute your sample. To avoid overflowing, the program will prompt you to reduce the volume in your vial to 10mL at set intervals. Calibrations should be specific to your experiment setup. Any changes to your media, culture, or optical setup (i.e. changing IR intensity, replacing pieces, or changing the angle) will require a new calibration. If everything remains consistent, then we recommend running calibrations every 6 months, or whatever suits your purposes.","s":"Calibrating your OD600 readings","u":"/user-guide/calibrate-od600","h":"#calibrating-your-od600-readings","p":408},{"i":412,"t":"Connect to your Pioreactor by typing ssh pioreactor@<insert unit name>.local. For example, to calibrate on our Pioreactor named worker3, we typed ssh pioreactor@worker3.local. The default password is raspberry. To begin calibrations, type pio run od_calibration. Start off by inputting some metadata of your calibration. Provide a descriptive and unique name to make it easier to find your calibration again, if needed. Follow the rest of the questions. info One of your photodiodes will be located in the 45°, 90°, or 135° pocket on the vial holder. You will be prompted to confirm the angle of your PD cable. If this is incorrect, go to the Configuration tab on the Pioreactor UI and under od_config.photodiode_channel, change to your angle of choice, then restart your OD calibration. Following the questions, stirring and optical density reading will begin. A graph is generated as you calibrate so you can see your progress. Depending on your number of measurements, you may be prompted to reduce your vial volume to 10 mL. OPTIONAL: At this point, you may take the OD600 reading of your vial on a different instrument and input this OD600 value for the current measurement. Once you complete all your measurements, a calibration curve will appear over your graph. If you are satisfied with this, save your calibration. info By default, we fit the calibration curve with a polynomial. You can choose the degree of the polynomial if you wish, but we found that degree 4 works well for wide OD600 calibrations, and degree 1 (a linear model) works will for narrow calibrations near 0.","s":"Running the calibration","u":"/user-guide/calibrate-od600","h":"#running-the-calibration","p":408},{"i":414,"t":"Calibrations are applied automatically. That is, after performing a calibration, your future experiments that use optical density readings will use the post-calibration values and be displayed in the UI and saved to the database. If you wish to stop using calibrations, you can switch if off in the config.ini by setting adding use_calibations=0 under the [od_config] section.","s":"Using calibrations in your experiments","u":"/user-guide/calibrate-od600","h":"#using-calibrations-in-your-experiments","p":408},{"i":416,"t":"On the command line, you can display your current calibrations using pio run od_calibration display_current). This will display the calibration graphs and metadata for each angle (45°, 90°, and 135°). Setting a new calibration would replace the information shown here, and be applied to new experiments that use the given angle. To see a full list of all previous calibrations, use pio run od_calibration list.","s":"Viewing your previous calibrations","u":"/user-guide/calibrate-od600","h":"#viewing-your-previous-calibrations","p":408},{"i":418,"t":"If you wish to change your calibration to a previous version, use pio run od_calibrations change_current <name> where <name> is some previous calibration you've run (i.e from pio run od_calibration list).","s":"Changing a calibration","u":"/user-guide/calibrate-od600","h":"#changing-a-calibration","p":408},{"i":420,"t":"For those interested, you can use the command line to interact with the Pioreactors. This is called the command line interface (CLI). Log onto either the leader or worker and you can execute the following commands. Full options and up-to-date documentation are available with pio <command> --help.","s":"Command line interface","u":"/user-guide/cli","h":"","p":419},{"i":422,"t":"Interacting with the Pioreactor on the command line are through the pio tool. Available arguments are: pio logs will produce a stream of recent logs events. Logs are stored in /var/log/pioreactor.log. pio kill --name <job> --experiment <exp> or pio kill --all-jobs to end jobs. pio run <job> <options> will run the <job>. Each job may have specific command line arguments. pio version print the version of the PioreactorApp software. pio update app will update the software to the latest app version. pio plugins install <plugin name> will install a plugin pio plugins uninstall <plugin name> will uninstall a plugin pio plugins list will list the currently installed plugins pio blink will blink the Pioreactor's onboard LED. pio log -m <message> will log a message pio view-cache <cache> will print out the contents of the specified cache. pio clear-cache <cache> <key> will remove <key> from cache <cache>.","s":"Worker commands","u":"/user-guide/cli","h":"#worker-commands","p":419},{"i":424,"t":"The leader also has their own unique set of pio commands (these commands do not interact with the workers): pio db: open the sqlite3 CLI of the Pioreactor database. pio mqtt: tail the MQTT broker. pio update ui will update the UI software to the latest version and adding --app will upgrade the Pioreactor Python app (repo: pioreactor/pioreactor). pio update app will update the software to the latest version. pio cluster-status will report to the user each Pioreactor in the cluster, and metadata like status, IP, and state. pio workers has many subcommands for manager your cluster. For example: pio workers add <hostname>: add a Pioreactor to your cluster, with given (unique) name. Need a worker Pioreactor on the network first. See instructions here. pio workers discover will return a list of workers on the network (may be a superset of the current cluster.) Leader-only commands to control workers​ The leader computer interacts with the worker computers using the pios command. Unless otherwise noted, the pios will target all worker computers. Available pios commands on the leader computer are the following: pios kill --name <job> terminate the job <job> on the workers. Ex: pios kill --name dosing_control. pios run <job> on each worker, run the job <job> in the background. Job specific arguments can be specified after. Ex: pios run add_media --ml 1. Use -y to skip confirmation. pios update install the latest PioreactorApp code on each worker. pios sync-configs deploy the config.ini files to workers. pios install-plugin <plugin name> will install the plugin on each worker and the leader. pios reboot will reboot all workers, by default, in the cluster. See --units arg below. pios shutdown will shut down all workers, by default, in the cluster. See --units arg below. pios cp <filepath> will copy (and overwrite) filepath on the leader to all the workers. pios rm <filepath> will remove filepath on all the workers. tip In each of the above commands, specific workers can be invoked with --units (which can be used multiple times. Ex: pios run stirring --units pio1 --units pio2. tip -y will skip user confirmation of the command to run.","s":"Leader-only commands","u":"/user-guide/cli","h":"#leader-only-commands","p":419},{"i":426,"t":"The following provides solutions to: using a different pumping system for the Pioreactor instead of our peristaltic pumps adding additional pumps to the Pioreactor (i.e., more than media and alt-media). These additional pumps may be provided via another system, for example an Arduino.","s":"Custom & additional pumps for dosing automations","u":"/developer-guide/writing-pump-software","h":"","p":425},{"i":428,"t":"The first thing to do is to add a hook to your custom pump into Pioreactor's software. To do this, we attach new functions to a dosing automation that are invoked when execute_io_action is called. These functions will call your logic that runs the external pump. Specifically, if we wish to overwrite the media pump, we create a function called add_media_to_bioreactor, with signature (cls, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client: pioreactor.pubsub.Client) -> float) To see this in an example: from pioreactor.automations.dosing.base import DosingAutomationJob class CustomPumper(DosingAutomationJob): automation_name = \"custom_pumper\" def __init__(self, **kwargs): super().__init__(**kwargs) def add_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # overrides the built in add_media_to_bioreactor # add your custom logic here. Example could be interfacing with i2c, serial, PWM, etc. ... pwm = PWM(...) self.logger.info(f\"pumping {ml}\") return ml def execute(self): self.execute_io_action(media_ml=1.0, waste_ml=1.0) Whenever execute_io_action is called upon to add media, the custom function add_media_to_bioreactor is invoked. Similar logic applies to alt_media. Overriding waste uses a different name, as the next example shows: class CustomPumper(DosingAutomationJob): automation_name = \"custom_pumper\" def add_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # overrides the built in add_media_to_bioreactor ... return ml def add_alt_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # overrides the built in remove_waste_from_bioreactor ... return ml def remove_waste_from_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # overrides the built in remove_waste_from_bioreactor ... return ml def __init__(self, **kwargs): super().__init__(**kwargs) def execute(self): self.execute_io_action(media_ml=1.0, alt_media_ml=1.0, waste_ml=2.0)","s":"Using external pumps with a custom automation","u":"/developer-guide/writing-pump-software","h":"#using-external-pumps-with-a-custom-automation","p":425},{"i":430,"t":"In general, we can use this same pattern to add even more pumps to the Pioreactor software, beyond media and alt-media. Let's say we have a third pump, salty-media, that we wish to also use along with media and alt-media. We define the function add_salty_media_to_bioreactor with the same signature above: class ThreePumps(DosingAutomationJob): automation_name = \"three_pumps\" def add_salty_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # call an external pump, via i2c, serial, GPIO, etc., # or pumping_functions.add_salt_media ... return ml def __init__(self, **kwargs): super().__init__(**kwargs) With this function defined, we can invoke execute_io_action with an additional kwarg, salty_media_ml: def execute(self): results = self.execute_io_action(waste_ml=3.0, media_ml=1.0, alt_media_ml=1.0, salty_media_ml=1.0) Notice the salty_media_ml=1.0 kwarg: this represents how much salty-media volume to add (your pump is responsible to dosing the correct volume). (Note in the above example, media and alt-media are not overwritten, so would use the \"traditional\" peristaltic pump system provided.) info In general, execute_io_action will try to call a function called add_<name>_to_bioreactor if provided with a kwarg <name>_ml.","s":"Adding additional pumps beyond media and alt-media","u":"/developer-guide/writing-pump-software","h":"#adding-additional-pumps-beyond-media-and-alt-media","p":425},{"i":433,"t":"Configuration of the Pioreactors is through configuration files, prefixed by .ini. There are two types of .ini files: a shared config.ini, which is the same across all units, and a unit-specific unit_config.ini file, which can have settings that overwrite those found in the shared config.ini. For example (and see image below), each unit will use the shared config.ini setting of target_rpm=500, unless an alternative setting is present in their specific unit_config.ini files (like target_rpm=400 found in unit1_config.ini) . This overriding lets you customize specific behavior per Pioreactor, without having to duplicate lots of configuration over and over again. Last-occurrence wins​ The config.ini can have duplicate entries (though it's not recommended), but only the last occurrence in the file will be used.","s":"How configuration works across Pioreactors","u":"/user-guide/configuration","h":"#how-configuration-works-across-pioreactors","p":431},{"i":435,"t":"At pioreactor.local, navigate to the Configuration page in the sidebar. Select the configuration file you wish to edit from the dropdown: Clicking [Save] will save the new configuration and will deploy the new configuration to the proper Pioreactor unit(s). Pioreactor also stores a history of changes to each configuration file. You can view previous versions of configuration files in the dropdown. Clicking [Revert] will save the displayed configuration file.","s":"Editing the configuration files from the web interface","u":"/user-guide/configuration","h":"#editing-the-configuration-files-from-the-web-interface","p":431},{"i":437,"t":"All the .ini files come from the leader unit. They are stored in /home/pioreactor/.pioreactor - one config.ini and a config_<unitName>.ini for each Pioreactor unit. The command pios sync-configs will deploy the .ini files to their correct unit. Editing the .ini files on the leader is correct workflow, as any edits on the worker units will be overwritten on the next pios sync-configs. One can programmatically, or by hand, edit the config_<unitName>.ini files to create varying parameters in an experiment. Running pios sync-configs will deploy the config files.","s":"Editing the configuration files from the command line","u":"/user-guide/configuration","h":"#editing-the-configuration-files-from-the-command-line","p":431},{"i":439,"t":"Sometimes it's desirable to make changes to the config.ini without having to boot the Pioreactor first. You can do this by plugging the microSD card into your computer, and adding a config.ini to the boot/ folder on it. This config.ini doesn't need to have all the fields, only the fields you wish to change. At start up, the Pioreactor will merge /boot/config.ini into the Pioreactor's config.ini, and then delete /boot/config.ini.","s":"Editing the config.ini before booting","u":"/user-guide/configuration","h":"#editing-the-configini-before-booting","p":431},{"i":441,"t":"If you need a reference config.ini, or to replace parts of yours, here's our default one that ships with the Raspberry Pi image. To use it, you'll need to make some changes, specifically to `cluster.leader` and `inventory`.","s":"Example config.ini","u":"/user-guide/configuration","h":"#example-configini","p":431},{"i":443,"t":"Pioreactor operation Optical density and LEDs Heating and Temperature control Mixing and stirring in the Pioreactor Raspberry Pi Hardware Dosing Data storage, access and recovery Networking","s":"Common questions","u":"/user-guide/common-questions","h":"","p":442},{"i":445,"t":"How can I restart my Pioreactor? Is pulling the power plug out safe?​ We suggest using the UI to reboot a Pioreactor: Pulling the plug is usually fine, but try to avoid doing it as much as possible. Can I still use the Pioreactor software without the hardware?​ Yes - the Pioreactor UI and software will still work. We provide a \"leader-only\" image that is designed to only host a cluster, and not be an active worker. The leader-only image, pioreactor_leader.zip , are available here. Why does the onboard blue LED keep flashing?​ There may be a problem. You can diagnose the problem by counting the number of flashes observed. What does the onboard button do?​ The button on the Pioreactor HAT sends a signal to the web UI to display a \"hello\" message. This is useful to know which Pioreactor in a cluster you are interacting with. The button also will republish the state of the Pioreactor. The button can be reprogrammed, too. How do I change the date or time on the Pioreactor?​ SSH into your Pioreactor, and run: sudo date --set \"Thu Nov 2 09:46:50 EDT 2023\"","s":"Pioreactor operation","u":"/user-guide/common-questions","h":"#pioreactor-operation","p":442},{"i":447,"t":"How does optical density work on the Pioreactor?​ The Pioreactor uses turbidity to measure optical density (other systems, like spectrophotometers, use attenuation). Specifically, the Pioreactor uses scattering of light. The system will shine infrared light into the culture, and measure the amount of light that is scattered off cells. The scattering has a good linear range (see below for more), and higher saturation point than attenuation for cultures of 20ml volume. If you have an instrument that measures OD600 or some other measurement of optical density, and you wish to calibrate to that, the Pioreactor has a routine to perform a calibration and record in the instruments units. See docs here. What are the units of Pioreactor's optical density​ The uncalibrated optical densities reported the UI and recorded in the database are have an arbitrary unit, and are per Pioreactor (so they can't be compared to each other). However, the normalized optical density, generated after starting the activity Growth rate in the UI, is comparable, which is why we suggest using it for inferences (especially if you haven't calibrated to some OD600 machine). Read more about our optical density measurements here. How can I change the frequency (rate) of optical density measurements?​ In the configuration, you can edit the parameter samples_per_second to adjust the how often the Pioreactor takes an optical density snapshot. Note that this parameter is the inverse of \"duration between readings\". For example, if you wish to record a measurement every 60 seconds, then samples_per_second=0.01666667 (which is 1/60). Why does the intensity for LED A turn on & off during an experiment?​ You may have noticed that the LED labelled A turns on & off every 5 seconds or so. This is (normally) the channel for the infrared (IR) LED, which is used in the optical density measurements. We only take reading every 5 seconds (the default), we don't need the IR LED on all the time. The Pioreactor will only turn on LED when needed. This preserves the strength of the LED over longer periods of time. For more advanced use cases, it also allows other optical measurements to take place without the IR LED interfering with them. Why does my optical density flatten, or even decrease? What is a saturation point?​ For some experiments, especially when using a scatter angle of 135°, you may notice that the optical density starts to flatten, and even decrease, when you know the culture should still be growing. This is not a property of the culture, but occurs because the culture is getting too dense, and light is now being interrupted before it reaches the photodiodes. Prior to this point, called the saturation point, the relationship between culture density and optical density is nearly linear. But after this point, there is a flattening, even negative, relationship between culture density and optical density. For all analysis, we recommend only studying when the culture is in the linear regime. You can mitigate the problem by choosing a smaller scatter angle (like 90° or 45°), diluting the culture using an automation like the turbidostat, or using a lower concentration of nutrient(s) in the media. Read more about Pioreactor's optical system here. What does the effect of the scatter angle have on optical density?​ The scatter angle is the angle between the IR LED and a photodiode. This angle can be 45°, 90°, or 135° (although 180° is possible, we don't consider it here). What is there to consider when choosing an angle. In general, the trend is shorter angles => less sensitive at low densities, but higher saturation point. By default, we suggest 45° as a good trade off between sensitivity and saturation. You can mix angles, and the Pioreactor's internal algorithm will still combine them into a single growth rate. Read more about Pioreactor's optical system here. Can I use my own 5mm LEDs and photodiodes for optical density?​ Of course! The only two requirements are that the spectrum of the LED overlaps with the spectrum of the photodiode, and that the LED light won't be absorbed by media/culture, nor damage the media/culture. Thus, the often-used 600nm light source works in the Pioreactor. None of our internal algorithms or analytics are dependent on the wavelength of light chosen. When you are using additional LEDs outside of the optical density LED & photodiode pair, you may worry that your additional LEDs will interfere with the optical density measurement. This won't happen, as we turn off all non-optical density LEDs before taking an optical density measurement. Is optical density the same as turbidity?​ Turbidity is a measure of optical density, like how decibels are a measurement of sound intensity. Likewise, absorbance is a measure of optical density.","s":"Optical density and LEDs","u":"/user-guide/common-questions","h":"#optical-density-and-leds","p":442},{"i":449,"t":"Why does the Pioreactor only provide a temperature reading every few minutes?​ We made a design choice early on to make preparation as error-free as possible. This involved thinking about sensors being in situ (in place), versus the sensors being on the outside of the vial. The temperature sensor in the Pioreactor is outside the vial, which means less chance of contamination, but there's a tradeoff (as you could guess): we have to rely on an estimation algorithm that requires a gew minutes to gather data on. We think this is a fair trade-off, as high frequency temperature readings are not that important in an experiment that lasts 12 hours or more. Why does the Pioreactor's heating keep shutting off?​ If you find that the Pioreactor's heating is shutting off, typically with an accompanying error and flashing blue light, then likely the temperature is becoming too high for safe handling. We restrict the onboard PCB's temperature to be no higher than 63℃. Temperature's higher than this can deform the plastic, and possibly cause burns. If the Pioreactor detects a temperature near or above this value, the software will shut off the heating, and possible the entire Raspberry Pi in extreme cases. To avoid this occurring, we suggest not setting the target temperature too high - not more than 20℃ above ambient temperature. Also, reducing the Kd parameter in [temperature_automation.stable] section in the config.ini would help. How does heating work on the Pioreactor?​ The Pioreactor has an onboard PCB, called the heating PCB, that sits below the glass vial. On the PCB are resistors that convert current from PWM outputs into heat. By varying the duty cycle of the PWM, we vary the amount of heat converted.","s":"Heating and Temperature control","u":"/user-guide/common-questions","h":"#heating-and-temperature-control","p":442},{"i":451,"t":"How is mixing / stirring performed in the Pioreactor?​ Stirring is performed with a micro stir bar inside the vial, controlled by a pair of magnets spinning below the vial. The rotation speed, RPM, of the stir bar can be controlled using the Pioreactor software. This stirring is also how aeration is done. Can I use my own stir bar?​ Of course! The maximum length of a stir bar is 20mm. Keep the height low as to not interfere with the optics. (The provided stir bar is 3mm high). Try using other stir bar shapes / designs! The magnets rubs against the plastic screws above them, causing the stirring performance to be degraded / stop. How do I fix this?​ Dis-attach the top faceplate. Under the faceplate, slightly unscrew each of the four metal screws. This will add more space between the magnets and the plastic screws. How can I increase the strength of the magnetic force applied to the stirbar?​ For Pioreactor 20ml v1.0: Try to reduce the distance between the stirring magnets and the stir bar by carefully raising the stirring fan a small amount. Going even further, you can remove the 4mm screws in the bottom of the vial holder (but find another way to secure the PCB), thereby be able to bring the magnets even closer. How can I improve mixing and aeration?​ If the standard mixing and aeration with the stir bar is not enough for your application, you can do a few things, (in increasing order of complication, not necessarily effectiveness): If the tubes in the cap are submerged during operation, this is reduce the transfer of air. Pull them up from the top of the cap to keep them out of the liquid. Even more effective: shorten them with scissors. Increase the RPM of the stirring. This will increase the surface area exposed to the air. Be warned though: too high of an RPM will cause either a large enough vortex to interfere with the optical systems, or will causing the stir bar to fall out of sync. Add a baffle to the vial cap. A simple cylinder that rests into the liquid causes disturbance in the rotating liquid that both mixing and aeration are significantly improved. A tube can be removed from the cap, and a autoclavable rod can be inserted such that it enters the media, but won't interfere with the optics. Adding external aeration to your Pioreactor. In the simplest case, using an air pump.","s":"Mixing and stirring in the Pioreactor","u":"/user-guide/common-questions","h":"#mixing-and-stirring-in-the-pioreactor","p":442},{"i":453,"t":"What Raspberry Pi hardware can I use? I see Raspberry Pi 1, 2, 3, 4, 5, A, B, +, Zero - it's confusing!​ We've designed the hardware and software to be compatible with any Raspberry Pi that has onboard Wifi and a 40 pin header. That includes (at the time of writing): Raspberry Pi 3 Model B & B+ Raspberry Pi 3 Model A+ Raspberry Pi 4 Model B ³ Raspberry Pi 5 Model B Raspberry Pi Zero W (with header) ¹ Raspberry Pi Zero 2 W (with header) Raspberry Pi 400 ² Although you can use any above, we like the Raspberry Pi 3 Model A+, and Raspberry Pi Zero 2 W because of their low power consumption, slim build, and low price. Both have the necessary CPU power and memory for the Pioreactor workload, and are generally easy to source. However, they don't have ethernet connections! So talk to your team about if you need to use ethernet or wifi. If you need ethernet, we like the model 3B. ¹ Raspberry Pi Zero W is on the list above, and is very low cost compared to the others. They can absolutely be used for Pioreactors as workers - we don't recommend them to be your leader (note sure what these terms mean? Here's an introduction to leader and workers). As workers, Raspberry Pi Zero W perform just fine, but will respond slower to commands. Note that this does not include the Raspberry Pi Zero 2 W model, which is fine for all roles. ² The Raspberry Pi 400 has its 40 pin header exposed in a different orientation, so your Pioreactor won't be able to sit on top like for other RPi versions. Take a look at this forum post to see how another user used the Raspberry Pi 400 with their Pioreactor. ³ Note that you don't need a lot of RAM for the Pioreactor, so we recommend getting the lower RAM option RPi 4s (1GB or 2GB) to save some money. However, 4GB and 8GB are fine, too. What microSD cards do you recommend?​ At least 16GB. We like 16GB or 32GB SanDisk Edge or Samsung microSD cards for their longevity, but any good quality, class 10 SD card will do. What power supply unit (PSU) do I need?​ If you look at the power rating, it should be about 5 V and at least 2.25 A, or above 12 W. We really like the official Raspberry Pi PSUs, available at most places you can purchase Raspberry Pis. Do I need any cooling for the Raspberry Pi?​ Nope, you shouldn't, unless you are connecting an external monitor. However, extra heat sinks are never a bad idea! Could a Raspberry Pi-compatible board work, like Rock Pi 4?​ Maybe? We haven't tested them, but so long as i) the GPIO pins are identical, and ii) Raspberry Pi OS can be installed, it should work. Why are the Raspberry Pi LEDs/USB/etc. turned off?​ We turn off the \"activity\" LED (usually the green one) to save some power for the Pioreactor's peripherals. You can turn these back on by editing the /boot/config.txt file on the RPi. What is the username/password for the Raspberry Pi?​ When setting up your Raspberry Pi with the Pioreactor software, you would have chosen a password. Try the recommended username: pioreactor, and password: raspberry. Can I use the desktop interface (with a display) with the Pioreactor?​ Not currently. Our software is based of the \"headless\" operating-system, which doesn't have display output.","s":"Raspberry Pi Hardware","u":"/user-guide/common-questions","h":"#raspberry-pi-hardware","p":442},{"i":455,"t":"Why does the Media card in the UI not update when I run a dosing command?​ The Media card will only update when an Dosing Automation is active (even the Silent automation). Why is it done this way? Often, you don't want volumes to be recorded there: during cleaning, during testing, etc. Often you only want volumes associated with the experiment to be there. note All dosing events ares recorded to the database however, and with a record of when the event occurred, and source of action. This data is available in the \"Export data\" web page, under Dosing event log.","s":"Dosing","u":"/user-guide/common-questions","h":"#dosing","p":442},{"i":457,"t":"💡 For any important project, we suggest manually exporting or backing up critical data multiple different places. This doesn't just apply to using the Pioreactor, but is good advice in general. Where are logs stored?​ For the logs that you see in the Log Table in the Experiment Overview page, these can be download on the Download experiment data page in the Pioreactor web interface. Other logs are also available, including dosing event and algorithm change-logs. More granular logs per Pioreactor are available in /var/log/pioreactor.log on the Raspberry Pis. How do I access raw experiment data?​ The Download experiment data page in the Pioreactor web interface provides CSV exports of common datasets from a pre-selected experiment. All data eventually lands in a SQLite3 database on the leader Pioreactor, by default located in /home/pioreactor/.pioreactor/storage/pioreactor.sqlite. This can be download using a tool like scp. To access the SQLite3 database from the command line, try pio db. My microSD card is corrupted - what can I do?​ Unfortunately, the microSD card becoming corrupted or damaged is an infrequent but possible risk with using Raspberry Pis. If the microSD card was inside a non-leader Pioreactor, it's best to try to reformat the microSD card and start fresh (i.e. reinstall the Pioreactor software and reintroduce it to the cluster). This is usually okay as no critical data is stored locally in workers, only log files and hardware calibrations will be lost. If the microSD was inside the leader Raspberry Pi, this is a bigger problem. Likely any running experiment will have to be restarted. Fortunately, if you have more than one Pioreactor in your cluster, then the leader's SQLite database has been periodically backing itself up to other Pioreactors in the cluster every few days. Using the command line, check other Pioreactors' /home/pioreactor/.pioreactor/storage directory for the latest backup named pioreactor.sqlite.backup (should be from within the past few days hours). You can use this database to restart a new leader.","s":"Data storage, access and recovery","u":"/user-guide/common-questions","h":"#data-storage-access-and-recovery","p":442},{"i":459,"t":"How do I change/edit the network the Pioreactor on?​ With modern Raspberry Pis, Can I use Ethernet cable connections instead of Wifi connections?​ Yes, so long as the Raspberry Pi's are connected to the same network and discoverable, this should work. Even mixing Ethernet and Wifi is fine. How can I determine the Pioreactor's IP address? Or the MAC address?​ Depending on your access to the Pioreactor, there are a few ways: In the UI's Inventory page. If you can't access the Pioreactor's UI or SSH in: the software will write the IP address to the /boot directory on the SD card. After the Pioreactor's blue LED has blinked, you can unplug the Pioreactor, remove the SD card, and place the SD card in another computer. Navigate to the card, and in the directory you should see a file called ip. Open this file, and the IP address should be there. Place the SD card back into the Pioreactor and plug it back in. I'm using a local access point, but I'd like to install plugins, update software, etc.​ To install a plugin​ On a computer that is connected to the internet, download the .whl file from the plugins webpage on PyPI. Then, connect that computer to your Pioreactor's local access point's network. To each Pioreactor you wish to install the plugin on, transfer the .whl file to the Pioreactor (using SFTP or FTP). Then, run pio plugins install <plugin-name> <path/to/local/.whl> To upgrade the Pioreactor software​ See steps here. If I have multiple Pioreactor leaders on my network, what leader does http://pioreactor.local point to?​ If there are multiple leaders on the same network, then each will override the other's pioreactor.local alias, and the alias will be unreliable. You can either access the leaders by their hostnames: http://<leader hostname>.local, or you can change the alias in the config.ini, too, by editing domain_alias under section [ui] (changing this requires a restart of the machine).","s":"Networking","u":"/user-guide/common-questions","h":"#networking","p":442},{"i":461,"t":"When pairing the Pioreactor with dosing pumps, there are new capabilities and experiments you can run. The Pioreactor is pre-programmed with the following dosing automations. In the below automations, values highlighted like so are configurable. Silent Chemostat Turbidostat PID Morbidostat Fed batch","s":"Dosing automations","u":"/user-guide/dosing-automations","h":"","p":460},{"i":463,"t":"Requires: None The silent automation is the simplest automation: doing nothing. The automation will still \"wake up\" every duration minutes, but does nothing.","s":"Silent","u":"/user-guide/dosing-automations","h":"#silent","p":460},{"i":465,"t":"Requires: 2 peristaltic pumps: one media pump one waste pump 2 liquid containers with luer attachments one labelled \"waste\" one labelled \"media\" The chemostat automation is the second simplest dosing automation. Every duration minutes, the media and waste pumps run and exchange volume (mL) of liquid inside the Pioreactor. Initially, the culture is growing and consuming nutrients and energy. Eventually, a nutrient will become scarce and will stall growing. Upon a pump refresh, this growth-limiting nutrient becomes abundant once again, and the culture can grow, up until consuming all of it again and stalling growth. Thus, the bioreactor enters into a nutrient near-equilibrium (hence the term \"chemostat\", for \"chemical-static\"). However, more long-term, because the culture is under an evolutionary pressure to grow, adaptions will occur that will improve the acquisition or utilization of the growth-limiting nutrient.","s":"Chemostat","u":"/user-guide/dosing-automations","h":"#chemostat","p":460},{"i":467,"t":"Requires: 2 peristaltic pumps: one media pump one waste pump 2 liquid containers with luer attachments one labelled \"waste\" one labelled \"media\" A turbidostat (\"turbidity-static\") tries to keep the turbidity (the optical density, or OD), constant over time. This is usually accomplished by taking frequent measurements of the turbidity (every 30 seconds), and performing a set media/waste pump cycle if the optical density (or normalized optical density) exceeds a target OD (or target nOD). The amount exchanged is the volume parameter (mL). For very fast growing cultures, we recommend a volume between 1.0 ml and 2.0 ml. This automation will always dose the volume parameter, even if it's not enough for the OD to drop below the target OD. If that happens, then OD > target OD, and so the automation will trigger after the next check (30 seconds).","s":"Turbidostat","u":"/user-guide/dosing-automations","h":"#turbidostat","p":460},{"i":469,"t":"Requires: 3 peristaltic pumps: one media pump one waste pump one alt media pump 3 liquid containers with luer attachments one labelled \"waste\" one labelled \"media\" one labelled \"alt media\" By introducing another pump (labelled \"alt media\"), another dimension of experiments opens up. We can exploit the short-time scale of adaption in microbes to evolve the culture from thriving in the original media to thriving in the alternative media, or some point in between the two. Think of it as slowly shifting the environment between the two media stocks so that the microbes are under constant evolutionary pressure. This is where the name morbidostat is from: \"morbid-static\". In the Pioreactor software, the transition between environments is controlled by observing the growth rate, and artificially keeping it suppressed (set to be target growth rate) by dynamically adjusting the ratio between the original media and the alternative media when a pump cycle is run. A pump cycle is run every duration minutes. Another parameter is the target OD, which should be low to keep the culture in a state of nutrient abundance (so that the primary evolutionary pressure is the alternative media adaptation).","s":"PID Morbidostat","u":"/user-guide/dosing-automations","h":"#pid-morbidostat","p":460},{"i":471,"t":"Requires: 1 peristaltic pump A source and sink, with the pump in-between. This automation moves a preset amount of volume every duration minutes using a pump. You choose the start and end points of the tube! info How does the vial maintain a constant volume throughout operation? When liquid is added, say 1ml, the volume rises an additional 1ml. Then 1ml of liquid is removed via efflux, but then the efflux pump runs again for an additional few seconds. The efflux pump is run for an additional few seconds to eliminate any volume deltas (for example, if the volume added is greater than the volume removed due to pumping errors). Otherwise, the deltas accumulate and the vial can overflow. This additional step helps guarantee that that volume of liquid never exceeds the end of the efflux tube.","s":"Fed batch","u":"/user-guide/dosing-automations","h":"#fed-batch","p":460},{"i":474,"t":"Experiment profiles are another way to automatically control your Pioreactor(s). Think of them as \"scripts\" (in the \"movie script\" sense) that you can write, and the Pioreactor will perform. For example, you can use experiment profiles to automatically start stirring and start temperature control when an experiment begins, and then automatically turn off stirring and temperature control hours later. They can be used to update activity settings, without you needing to be around. We think of them as \"clicking in the UI, but headless\".","s":"What are experiment profiles?","u":"/user-guide/experiment-profiles","h":"#what-are-experiment-profiles","p":472},{"i":476,"t":"In your UI, visit Profiles page on the left-hand sidebar. Here, you can choose an experiment profile to run, start it, stop it (if running), and edit an existing or create a new profile. There's also a \"dry-run\" option, which won't actually execute any actions, but instead will log the action that would have occurred. This is useful to testing a profile first.","s":"How do I use experiment profiles?","u":"/user-guide/experiment-profiles","h":"#how-do-i-use-experiment-profiles","p":472},{"i":478,"t":"Experiment profiles are written as a YAML file (rhymes with \"camel\"). A YAML file is a structured way to describe data, and we use that to define our experiments. You can browse experiment profile examples below.","s":"What do they look like?","u":"/user-guide/experiment-profiles","h":"#what-do-they-look-like","p":472},{"i":480,"t":"See examples of experiment profiles here.","s":"Examples","u":"/user-guide/experiment-profiles","h":"#examples","p":472},{"i":487,"t":"When a Pioreactor successfully boots, the onboard blue LED will flash quickly for 2 seconds, and then stop. However, there are times when the Pioreactor encounters an error, and will use the LED to alert to you that something is wrong. By counting the number of short flashes (per cycle), you can diagnose what might be wrong. Number of flashes Error 1 Can't connect to network 2 Can't connect to leader 3 SD card is almost full 4 Stirring RPM is 0 5 ADC input is very high 6 Heating PCB is above 60 ℃ 7 Voltage problem 8 Webserver offline","s":"Blue LED flashing & error codes","u":"/user-guide/error-codes","h":"","p":486},{"i":489,"t":"If your blue LED is constantly on, it suggests either an hardware error, or that your Pioreactor is missing it's config.ini. Try a reboot, and if it persists, SSH in and check for the file ~/.pioreactor/config.ini. If that file is missing, it's either a worker that hasn't been connected to a cluster, or some part of the installation has gone wrong.","s":"The blue LED is constantly on?","u":"/user-guide/error-codes","h":"#the-blue-led-is-constantly-on","p":486},{"i":491,"t":"Experiment data can be exported using the Export data tab on the Pioreactor site. You can retrieve datasets from any previous experiments, including from all experiments simultaneously using the <All experiments> option at the bottom of the list. Select your experiment from the drop down menu. Select the datasets you would like to download. Click the Export button to download the raw data as .csv files. Each dataset on the list will export as its own .csv file. note Is a dataset not available in the list? Is there a specific data point you'd like but can't find? Feel free to ask about it on our forums.","s":"Exporting data","u":"/user-guide/export-data","h":"","p":490},{"i":493,"t":"When exporting datasets, most csv files will include a single metric against a time series. If you'd like to compare many datasets using a single time series, we recommend export of the Pioreactor Unit Activity dataset. This dataset summarizes all activities from one Pioreactor against a single time series to make working with data easier. The dataset will follow a running timeseries (column A) and include metrics for OD, temperature, stirring, LED updates and dosing. Consider this example where we turned on temperature and stirring: Temperature and stirring datasets are exported on separate .csv files and follow their unique time series. In comparison, the Pioreactor Unit dataset compiles both against the same time series, making it much more accessible:","s":"Pioreactor Unit Activity Data","u":"/user-guide/export-data","h":"#pioreactor-unit-activity-data","p":490},{"i":496,"t":"Experiment profiles can be managed in the UI at http://pioreactor.local/experiment-profiles. See video below for a demonstration.","s":"Using the UI","u":"/user-guide/create-edit-experiment-profiles","h":"#using-the-ui","p":494},{"i":498,"t":"All profiles are stored on the leader's disk under ~/.pioreactor/experiment_profiles/. You can create and edit profiles in this directory, as well.","s":"On the command line","u":"/user-guide/create-edit-experiment-profiles","h":"#on-the-command-line","p":494},{"i":501,"t":"When writing a profile, note that the hours_elapsed field refers to when the experiment profile started, and not when the experiment started.","s":"hours_elapsed refers to the profile start time","u":"/user-guide/create-edit-experiment-profiles","h":"#hours_elapsed-refers-to-the-profile-start-time","p":494},{"i":503,"t":"The if directive can be included in any action to conditionally execute it or not. The if statement is evaluated when the action is to be executed (i.e., when elapsed_hours has passed). The if directive is a general boolean expression, and to common operators can be used: and or not True and False ( and ) Also included are numbers (floats), and strings (examples later). The comparison operators are: == >= and <= > and < The operators addition +, subtraction -, multiplication *, and division / are allowed on floats, as well. The power of if comes when you combine it with expressions, see below:","s":"How the if directive works","u":"/user-guide/create-edit-experiment-profiles","h":"#how-the-if-directive-works","p":494},{"i":505,"t":"Expressions are the method used to get is dynamic data, provided from jobs, during execution of profiles. For example, the following: pio1::stirring::target_rpm will fetch the target_rpm from pio1's stirring job at the time the action is to be executed. To use this in an example: stirring: ... - type: update hours_elapsed: 6.0 if: pio1::stirring::target_rpm >= 500 options: target_rpm: 400 will check, after 6 hours, if the target_rpm is above 500, and if true, will update the target RPM to 400. You can also compare against strings. For example, to stop a job if the temperature automation running is equal to thermostat, use: temperature_control: ... - type: stop hours_elapsed: 6.0 if: pio1::temperature_control::automation_name == thermostat Where do these dynamic values come from? Each job has published_settings that can be referenced (refer to the job's source code to all published_settings for a job, or they are published in MQTT). Some published settings have are actually nested json blobs, but we need either numbers or strings to compare in our boolean expression. You can index these json blobs in the boolean expression using ., for example: temperature_automation: ... - type: update hours_elapsed: 6.0 if: pio1::temperature_control::temperature.temperature <= 30 options: target_temperature: 32 We use temperature.temperature because the temperature published setting is a json blob that looks like the following, and we wish to reference the \"temperature\" field in the blob: { \"temperature\": <float>, \"timestamp\": <ISO 8601 timestamp> }","s":"How expressions work","u":"/user-guide/create-edit-experiment-profiles","h":"#how-expressions-work","p":494},{"i":507,"t":"Similar to an if directive using dynamic data, options can also have dynamic data (see notes above for syntax, too). However, to distinguish between a string and an expression, an expression must be wrapped in ${{ ... }}. For example, consider the following update action: pioreactors: worker1: jobs: stirring: actions: - type: start hours_elapsed: 0 options: target_rpm: 500 - type: update hours_elapsed: 12 options: target_rpm: ${{ worker1:stirring:target_rpm + 50 }} This will update the value of target_rpm to whatever its current value is (after 1 hour), and add 50 to it. You can use the any pioreactor and any job in an expression - you aren't limited to the job your editing. For example, the update below will dynamically set the target_rpm to a function of optical density. pioreactors: worker1: jobs: stirring: actions: - type: start hours_elapsed: 0 options: target_rpm: 500 - type: update hours_elapsed: 12 options: target_rpm: ${{ worker1:stirring:target_rpm + worker1:od_reading:od1.od * 10 }}","s":"Expressions in options","u":"/user-guide/create-edit-experiment-profiles","h":"#expressions-in-options","p":494},{"i":509,"t":"Expressions can reference individual Pioreactors, for example worker1:stirring:target_rpm, but what if you want to specify all Pioreactors in an expression? This is useful for using expressions in the common block. The syntax for this is to use the following ::<job_name>:setting For example, to conditionally change the stirring RPM in all Pioreactors, and to update it: common: jobs: stirring: actions: - type: update hours_elapsed: 6 if: ${{ ::stirring:target_rpm <= 500 }} options: target_rpm: 500 You can also use this syntax in options: common: jobs: stirring: actions: - type: update hours_elapsed: 6 if: ${{ ::stirring:target_rpm <= 500 }} options: target_rpm: ${{ ::stirring:target_rpm + 10 * ::od_reading:od1.od }}","s":"Expressions in the common block","u":"/user-guide/create-edit-experiment-profiles","h":"#expressions-in-the-common-block","p":494},{"i":511,"t":"The repeat directive is the most powerful action, as it allows you loop actions over and over again to check for a condition change, update based on state, etc. The repeat action requires two new necessary fields: actions: a list of actions (start, stop, update, etc.) that you want to repeat. The field hours_elapsed refers to the start of the loop, not when the profile starts. repeat_every_hours: this is a float describing how long, in hours, the loop should last for. For example, repeat an action every 2 hours, or generally: repeat a sequence of actions every X hours. Your repeat action should look like, for example: - type: repeat hours_elapsed: 6.0 # when to start the looping, 6 hours repeat_every_hours: 0.5 # perform the actions every 30 minutes actions: - type: update hours_elapsed: 0.0 ... - type: update hours_elapsed: 0.1 ... Finally, there is more control using the other optional fields: max_hours: this controls how long the loop should run for. For example, if repeat_every_hours is 0.5 (or 30 minutes), and max_hours is 6, then the loop will repeat 12 times before exiting. while: this is an expression, like if, that runs at the start of each loop, including the first. For example, the following profile will run media until the OD is less than 3.0. We also remove waste so we don't overflow the vial. This is a really coarse turbidostat, and is just for demonstration - don't use this: You can also use the if directive to skip running the entire repeat action, too. add_media: actions: - type: repeat hours_elapsed: 6.0 repeat_every_hours: 0.0025 # every 9 seconds while: ${{ worker1:od_reading:od1.od > 3.0 }} actions: - type: start options: volume: 1 remove_waste: actions: - type: repeat hours_elapsed: 6.0 repeat_every_hours: 0.0025 # every 9 seconds while: ${{ worker1:od_reading:od1.od > 3.0 }} actions: - type: start options: volume: 1.5","s":"The repeat action","u":"/user-guide/create-edit-experiment-profiles","h":"#the-repeat-action","p":494},{"i":513,"t":"A common task is to start the thermostat, and you may want to do something like: # wrong, this won't work ❌ common: jobs: thermostat: actions: - type: start hours_elapsed: 0.0 options: target_temperature: 30 However, to start (and stop) automations (which the thermostat is), you actually need to use the controllers: # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat target_temperature: 30 Likewise, to stop a automation, you need to stop the controller: # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat target_temperature: 30 - type: stop hours_elapsed: 12.0 How do you update target_temperature, see below.","s":"Start/stop controllers instead of automations","u":"/user-guide/create-edit-experiment-profiles","h":"#startstop-controllers-instead-of-automations","p":494},{"i":515,"t":"A setting like target_temperature or volume is attached to the automation, not a controller, so you need to update the automation: # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat target_temperature: 30 - type: stop hours_elapsed: 12.0 temperature_automation: # this is thermostat - type: update hours_elapsed: 1.0 options: target_temperature: 32 - type: update hours_elapsed: 2.0 options: target_temperature: 34","s":"Update automations instead of controllers","u":"/user-guide/create-edit-experiment-profiles","h":"#update-automations-instead-of-controllers","p":494},{"i":517,"t":"Check your YAML syntax with a tool like: https://www.yamllint.com/ Note that indentation matters! For example, these mean different things, and only the second one is correct: # wrong ❌ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat # this should be indented to align with options target_temperature: 30 # this should be indented to align with options # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat # lined up! target_temperature: 30","s":"YAML syntax check, and indentation problems","u":"/user-guide/create-edit-experiment-profiles","h":"#yaml-syntax-check-and-indentation-problems","p":494},{"i":519,"t":"This is likely because you are using - where you shouldn't: # wrong ❌ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: - automation_name: thermostat # don't put - here - target_temperature: 30 # don't put - here # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat # don't put - here target_temperature: 30 # don't put - here","s":"Expected `object`, got `array` - at ` ... .options`","u":"/user-guide/create-edit-experiment-profiles","h":"#expected-object-got-array---at---options","p":494},{"i":522,"t":"tip We're here to help: we can offer email or live support, just email us at hello@pioreactor.com. Here's how we suggest your workflow be. Starting with your leader Pioreactor, make note of the name of it. The next steps will turn off all data collection, so do this outside of any running experiments. SSH into the leader, and create a new file with: nano ~/export_data.sh Paste the code linked here into the editor. crtl-x to exit the editor. Run this export script with bash export_data.sh. This creates an export file with all your experiment data, config files, Python plugins, profiles, etc. Exporting will take time proportional to how large your database is. Once the export file is finished being created, make note of the filename of the export. Locally, on the command line (or with FileZilla), download the file. You can do: # this is run on your local computer, i.e. the one you SSH from. scp pioreactor@<leader name>.local:/home/pioreactor/<filename of export> . Optional: do this for each Pioreactor worker in your cluster. Exporting workers will save data like calibrations, but we suggest you re-calibrate after anyways. Almost all important data, like historical experiments and logs, are stored on the leader, so you may be okay with just transferring leader data and wiping workers. It's up to you. Happy to chat further at hello@pioreactor.com. With the export file(s) local, you may now proceed with re-imaging your Pioreactors, by following the same steps here. Important: choose the same Pioreactor hostnames!","s":"Export your data","u":"/user-guide/export-import-existing-data","h":"#export-your-data","p":520},{"i":524,"t":"Once your new Pioreactor leader is running (check that you can access the UI at http://pioreactor.local), we'll upload the export with: # this is run on your local computer scp <filename of export> pioreactor@<leader name>.local:/home/pioreactor/ You may receive an error: host key verification failed. Open the known_hosts file in your .ssh folder and delete the line containing your <leader name>. When prompted, Are you sure you want to continue connecting? enter yes. Enter password raspberry and continue. SSH into the leader, and create a new file with: nano ~/import_data.sh Paste the code linked here into the editor. crtl-x to exit the editor. Run this export script with bash import_data.sh <filename of export>. The Pioreactor will update itself, and then perform a restart. Once the Pioreactor is back online, you should see your old experiments in the UI. Optional: If you exported your worker data, you can do the same thing. You're done!","s":"Import your data to a new, fresh, Pioreactor","u":"/user-guide/export-import-existing-data","h":"#import-your-data-to-a-new-fresh-pioreactor","p":520},{"i":526,"t":"Some applications require more power to your Pioreactor if it is using lots of peripherals. This may include using more powerful pumps, more powerful external LEDs, etc. Or, if you see warning messages that reference under voltage or throttling, you probably are asking the Pioreactor to do too much given its default 5V power supply. You can supply a higher voltage / amp power to the peripherals using the barrel jack connection. The barrel jack connection allows for power supply units of up to 18V to the PWM channels 1 through 4 (PWM channel 5, used for onboard heating, is not effected, and always tied to the 5V rail). Please make sure your barrel jack connector is positive center. Look for a symbol like the following, or confirm in some other manner Finally, to enable the PWM channels to use the new auxiliary power supply, you need to move the shunt connector to the position closest to the LED outputs. (If the shunt connector is not present, the PWM rail is powered by the RPi's power supply, minus a diode drop. It's recommend to replace the shunt, however.) note When changing the default power supply, any stirring calibration and pump calibrations will need to be updated. Also, the initial_duty_cycle under stirring in the configuration may need to change. caution Be mindful that the default stirring motor provided with the Pioreactor has a maximum voltage rating of 12V.","s":"Supplying more power to the PWM channels","u":"/user-guide/external-power","h":"","p":525},{"i":528,"t":"When using multiple of Pioreactor's peristaltic pumps, we recommend a 12V power supply, with at least 1 amp (this is the same as a 12W power supply). Our pumps use maximum 0.4A, and the stirring motor uses 0.1A.","s":"Power supply for using Pioreactor peristaltic pumps","u":"/user-guide/external-power","h":"#power-supply-for-using-pioreactor-peristaltic-pumps","p":525},{"i":530,"t":"positive center barrel size: 2.1mm I.D. x 5.5mm O.D. Maximum voltage: 18V","s":"More details on power supply","u":"/user-guide/external-power","h":"#more-details-on-power-supply","p":525},{"i":532,"t":"Hardware calibrations serve as a method to get accurate performance from your Pioreactor.","s":"Hardware calibrations","u":"/user-guide/hardware-calibrations","h":"","p":531},{"i":534,"t":"info You'll need the following: Pioreactor HAT Pioreactor sleeve Vial and stirbar Internally, the Pioreactor will vary the amount of voltage to apply to the stirring motor to reach the desired RPM, however, this can take a few minutes. We can significantly improve this by asking the Pioreactor to create a \"map\" between voltage and RPM beforehand. Then the Pioreactor only needs to perform a lookup in the map to hit the desired RPM. note This is optional, but can really help stirring performance. Creating a stirring calibration is also very easy, so we recommend it. Calibrating the stirring in the UI # Start by filling a Pioreactor vial about 3/4th with water, and place the stirbar inside. Close with lid. Place into the Pioreactor. From the web interface, in Pioreactors, find the Pioreactor you wish to calibrate. Click Calibrate. Click stirring. Click Start. The Pioreactor will increment the voltage applied to the motor, and record the RPM. After it's done, it will collect this data into a calibration curve, and store it locally. You're done! Your stirring RPM should be much more responsive now.","s":"Stirring calibration (optional)","u":"/user-guide/hardware-calibrations","h":"#stirring-calibration-optional","p":531},{"i":537,"t":"Calibrating a pump, like a low-volume peristaltic pump, is very important to accurately dispense or remove a target volume. There is no liquid feedback loop in the Pioreactor (unlike in the stirring & RPM relationship), so this calibration curve is important. There are three pumps on the Pioreactor: media, alt-media, and waste. You don't need to have all three available, and can calibrate them one at a time. For calibration, you'll need the following: A pump, with power connection to Pioreactor's PWM outputs An accurate weighing scale, with accuracy of 0.1g or better. Container of water tip Supplying external power? Make sure to plug in your external power before pump calibration! Calibrating the pumps # We'll perform this routine through your computer's command line. Need help accessing it? Enter ssh pioreactor@<insert unit name>.local. For example, to calibrate on our Pioreactor named worker3, we typed ssh pioreactor@worker3.local. The default password is raspberry. Enter pio run pump_calibration. Follow the prompts to calibrate your media, waste, and/or alternate media pumps. Calibrations can be performed depending on the frequency of your Pioreactor use.","s":"Pump calibration","u":"/user-guide/hardware-calibrations","h":"#pump-calibration","p":531},{"i":540,"t":"Starting in software version 23.12.11, you can edit your calibration, too. At the end of the calibration, your data is listed (or use pio run pump_calibration display to see the data again). Copy the json data (between { and }) into new json file on the Raspberry Pi, say ~/pump_data.json for example. Make any edits you wish to the data. Then you can \"rerun\" the calibration with data from that file: pio run pump_calbration -f ~/pump_data.json","s":"Made a mistake, or want to change some data?","u":"/user-guide/hardware-calibrations","h":"#made-a-mistake-or-want-to-change-some-data","p":531},{"i":542,"t":"Normally, the external hardware will have two terminals, corresponding to positive and ground. The positive terminal may be marked by a dot, or \"+\" symbol, or be colored red. Make note of this terminal. The PWM outputs on the Pioreactor are 0.100\" (2.54mm) pitch connectors, with the positive pin closer to the onboard button (also marked on the edge on the underneath of the HAT circuit board). Simple Dupont female square head fit just fine in them (example). The only problem with using these connectors is that they are not locked in-place, and can slip out of the connection. The nice connectors we use for LEDs, the stirring motor and our pumps are TE Connectivity AMP connectors 487526-1. These also require a specific socket connector.","s":"Hardware connection assembly","u":"/user-guide/hardware-connection-assembly","h":"","p":541},{"i":544,"t":"Below is a schema for experiment profiles. We also do a run-time check # Main structure of the experiment profile experiment_profile_name: <string> # Name of the experiment profile # Metadata section (optional) metadata: author: <string> # Author of the experiment profile description: <string> # Description of the experiment profile # Plugins section (optional) plugins: - name: <string> # Name of the plugin min_version: <string> # Minimum required version of the plugin # Common jobs section (optional) # Jobs that are common for all Pioreactors common: jobs: <job_name>: actions: - type: <string> # Type of action: \"start\", \"pause\", \"resume\", \"stop\", \"update\", or \"log\" hours_elapsed: <float> # Time when the action is scheduled (in hours after experiment start) # Options for the action (optional) # If type is 'log', a 'message' parameter is required here options: <option_name>: <value> # Arguments for the action (optional) arguments: <list> # Pioreactors section (optional) # Jobs that are specific to some Pioreactors pioreactors: <pioreactor_unit_name>: # Optional label for the Pioreactor label: <string> jobs: <job_name>: actions: - type: <string> # Type of action: \"start\", \"pause\", \"resume\", \"stop\", or \"update\" hours_elapsed: <float> # Time when the action is scheduled (in hours after experiment start) # Optional 'if' directive for conditional execution of actions if: <string> # Can be an expression # Options for the action (optional) # Values can be expressions, denoted with ${{ }} options: <option_name>: <value>","s":"Experiment profiles schema","u":"/user-guide/experiment-profiles-schema","h":"","p":543},{"i":546,"t":"See examples of experiment profiles here.","s":"Examples","u":"/user-guide/experiment-profiles-schema","h":"#examples","p":543},{"i":548,"t":"Info You can expect the assembly to take approximately 20-30 minutes.","s":"Before you begin assembly","u":"/user-guide/hardware-setup-intro","h":"","p":547},{"i":554,"t":"The Pioreactor is an mostly open source, affordable, and extensible bioreactor platform. The goal is to enable biologists, educators, DIYers, biohackers, and enthusiasts to be able to reliably control and study the growth of microorganisms.","s":"Pioreactor user guide","u":"/user-guide/introduction","h":"","p":553},{"i":556,"t":"To start assembling your Pioreactor, check out our Getting Started guides.","s":"Need to assemble your Pioreactor?","u":"/user-guide/introduction","h":"#need-to-assemble-your-pioreactor","p":553},{"i":558,"t":"See the basic steps to operating your Pioreactor, or check out our repository of biology experiments.","s":"Help with your first experiment?","u":"/user-guide/introduction","h":"#help-with-your-first-experiment","p":553},{"i":560,"t":"If you are interested in the software internals, take a look at our developer guide.","s":"Developers","u":"/user-guide/introduction","h":"#developers","p":553},{"i":562,"t":"Check out the documentation (you're on it right now)! Ask a question on our community forums Contact us at support@pioreactor.com","s":"Looking for further help?","u":"/user-guide/introduction","h":"#looking-for-further-help","p":553},{"i":564,"t":"LED automations are ways to automatically control the 4 available LEDs in the Pioreactor. These LEDs can be used as a light source for photosynthetic microbes, influence the environment of the microbes, as additional sensors, or improve existing sensors.","s":"LED automations","u":"/user-guide/led-automations","h":"","p":563},{"i":566,"t":"Requires: None The silent automation is the simplest automation: doing nothing. The automation will still \"wake up\" every duration minutes, but does nothing.","s":"Silent","u":"/user-guide/led-automations","h":"#silent","p":563},{"i":568,"t":"Requires: up to 2 LEDs, in channels C and D. This automation will turn the LEDs in channels C & D on and off on a predetermined scheduale, specified by light_duration_minutes and dark_duration_minutes. The intensity of the LED is given by light_intensity. The LEDs start ON. Note: duration is permanently set to be 1 minute. The LEDs should go in pockets X2 and X3 on the Pioreactor.","s":"Light/Dark cycle","u":"/user-guide/led-automations","h":"#lightdark-cycle","p":563},{"i":570,"t":"Choose from the guides below:","s":"Getting started guides","u":"/user-guide/getting-started","h":"","p":569},{"i":572,"t":"✨New Pioreactor 20ml v1.1 Pioreactor 20ml v1.0","s":"Pioreactor 20ml assembly","u":"/user-guide/getting-started","h":"","p":569},{"i":576,"t":"✨New Pioreactor 20ml v1.0 → v1.1 upgrade kit Temperature Expansion Kit Adding peristaltic pumps Adding more LEDs","s":"Upgrade kits and accessories","u":"/user-guide/getting-started","h":"","p":569},{"i":582,"t":"Software installation","s":"Software guides","u":"/user-guide/getting-started","h":"","p":569},{"i":585,"t":"note This article isn't intended as a crash course in Python, or Pioreactor software, but some helpful ways to write small scripts for your Pioreactor. If interested in learning more, check out the developer docs for detailed information. For some testing and playing purposes, it's really easy to get started writing scripts to automate parts of your Pioreactor. For this tutorial, you'll need to be able to SSH into your Raspberry Pi.","s":"Writing Pioreactor scripts with Python","u":"/user-guide/intro-python-scripting","h":"","p":584},{"i":587,"t":"SSHing means to connect to a computer remotely, and interact with its command line. In our case, we wish to interact with the Raspberry Pi remotely. SSH software depends on your operating system: Windows users: use the Command Prompt, or install PuTTY, or install the Secure Shell App for Google Chrome. macOS users: open up the terminal app: command+space, search for \"terminal\". linux users: y'all don't need my help :) We need to connect to the Raspberry Pi: hostname: your Pioreactor's name (see web interface) also-known-as your Raspberry Pi's hostname. user: pioreactor password: the one you used when you installed the Pioreactor, by default it's raspberry. One your online, you can have some fun and type pio blink to have your Pioreactor blink!","s":"1. SSHing into your Raspberry Pi","u":"/user-guide/intro-python-scripting","h":"#1-sshing-into-your-raspberry-pi","p":584},{"i":589,"t":"We'll start with something simple: writing a script to turn on the Pioreactor's stirring. To create a file called script_test.py and edit it on the Raspberry Pi command line, type nano script_test.py. You'll be shown an editor. Let's enter the following Python code: import time from pioreactor.background_jobs.stirring import start_stirring stirrer = start_stirring(target_rpm=400) time.sleep(10) Hit crtl-x, and then Y to save our file.","s":"2. Writing our first script.","u":"/user-guide/intro-python-scripting","h":"#2-writing-our-first-script","p":584},{"i":591,"t":"To run our script, type python3 script_test.py in the command line. If everything works correctly, your Pioreactor's stirring will start, and then finish after 10 seconds. You're a hacker now :) To make stirring run forever, let's edit the file again: nano script_test.py, and replace time.sleep(10) with: import time from pioreactor.background_jobs.stirring import start_stirring stirrer = start_stirring(target_rpm=400) stirrer.block_until_disconnected() Save the file with crtl-x, and then Y, and run the script again. Now, the job will run until you log off, or exit the program with ctrl-c. This is because block_until_disconnected will block to program at that line.","s":"3. Running our Python script","u":"/user-guide/intro-python-scripting","h":"#3-running-our-python-script","p":584},{"i":593,"t":"Let's add some more to our script. Let's say we also want to: turn on an LED in channel B, turn on optical density reading (with 90° photodiode in channel 1 and reference in channel 2). After 10 seconds, slow down the stirring RPM import time from pioreactor.background_jobs.stirring import start_stirring from pioreactor.background_jobs.od_reading import start_od_reading from pioreactor.actions.led_intensity import led_intensity led_intensity({'B': 50}) stirrer = start_stirring(target_rpm=400) od_reader = start_od_reading(\"90\", \"REF\") time.sleep(10) stirrer.set_target_rpm(300) stirrer.block_until_disconnected() You should see data coming into to your experiment overview in the web interface!","s":"4. Extending our script: more jobs, changing RPM, and adding lights.","u":"/user-guide/intro-python-scripting","h":"#4-extending-our-script-more-jobs-changing-rpm-and-adding-lights","p":584},{"i":595,"t":"Next, we'd like to start heating and keep our vial at a constant temperature. Recall that all temperature tasks are actually temperature automations. In this case, we require the thermostat temperature automation, invoked from a temperature controller: import time from pioreactor.background_jobs.stirring import start_stirring from pioreactor.background_jobs.od_reading import start_od_reading from pioreactor.actions.led_intensity import led_intensity from pioreactor.background_jobs.temperature_control import start_temperature_control led_intensity({'B': 50}) stirrer = start_stirring(target_rpm=400) od_reader = start_od_reading(\"90\", \"REF\") temp_controller = start_temperature_control(\"thermostat\", target_temperature=32) time.sleep(10) stirrer.set_target_rpm(300) stirrer.block_until_disconnected()","s":"5. Adding an automation","u":"/user-guide/intro-python-scripting","h":"#5-adding-an-automation","p":584},{"i":597,"t":"This is just a small example of scripts you can make. If you need to learn more, we suggest checking out the developer guide.","s":"Conclusion","u":"/user-guide/intro-python-scripting","h":"#conclusion","p":584},{"i":599,"t":"info Previously, Raspberry Pis used a file called wpa_supplicant.conf to handle wifi network connections. This is not longer the case. Modern Raspberry Pi software, including the Pioreactor, doesn't use wpa_supplicant.conf at all. Instead, the tool nmcli replaces it. Don't follow tutorials that use wpa_supplicant.conf.","s":"Networking","u":"/user-guide/networking","h":"","p":598},{"i":601,"t":"The main \"entry point\" for networking on the Pioreactor (and Raspberry Pi's in general) is the tool nmcli. This controls discovering networks, connecting to them, and editing connections. For example, running nmcli con will diplay a list of possible networking connections, and connected ones in green.","s":"General networking tools","u":"/user-guide/networking","h":"#general-networking-tools","p":598},{"i":603,"t":"You can first discover all the visible networks with: sudo nmcli d wifi list If you see your network on the list, then run: sudo nmcli device wifi connect <ssid name> password <ssid password> ifname wlan0 (If you get a \"Can't find\" error, try running the above list command again.)","s":"Connecting to a wifi network using nmcli","u":"/user-guide/networking","h":"#connecting-to-a-wifi-network-using-nmcli","p":598},{"i":605,"t":"First, some terminology and understanding for us: a computer, like a Pi, has networking interfaces. For example, the onboard wifi on RPi’s is one such interface. The larger, model Bs, have an ethernet connector, which is another interface. Each interface can connect to 0 or 1 networks. In order to connect to multiple networks, you need a Raspberry Pi with multiple interfaces. You can add interfaces with devices like a USB wifi device. To see what your current interfaces are doing, use: nmcli device The right hand side shows your connected interfaces. For example, if have a ethernet connection to a router, you'll see an eth0 connection active. If you have an additional wifi hardware device attached to your Pi, you'll see wlan1. To connect to another wifi network using wlan1, use: sudo nmcli device wifi connect <ssid name> password <ssid password> ifname wlan1 If your leader is connected to multiple networks A and B, and you access the UI over network A, but your workers access over network B, the leader is in the position called a \"gateway\". You'll need to make some configuration changes to your cluster. Since the leader is attached to networks A and B, it has two IPs (use hostname -I to see all the ips), let's call them ipA and ipB respectively. Access the configuration in the UI. In the shared config.ini, edit the [mqtt] broker field to be equal to ipA. Also edit the leader_address to be ipB. In each of the workers (including the leader's config.ini, if it's a worker), add the following: [mqtt] broker=ipB You may need to restart your cluster for these to take full effect.","s":"Connecting to multiple networks","u":"/user-guide/networking","h":"#connecting-to-multiple-networks","p":598},{"i":607,"t":"Note that you can only have 1 network connection for each network interface. So if you have only 1 wifi device (by default, RPi's only have 1 wifi device on them -> only 1 wifi interface), the following will replace any existing wifi connection. sudo nmcli con up PioreactorAP Setting leader_address and MQTT broker in your config.ini​","s":"Starting the Pioreactor local access point using nmcli","u":"/user-guide/networking","h":"#starting-the-pioreactor-local-access-point-using-nmcli","p":598},{"i":609,"t":"To change the web UI port from the default of 80, following these instructions: SSH into your leader Pioreactor. We'll edit the lighttpd configuration first: sudo nano /etc/lighttpd/lighttpd.conf and find the line starting with server.port. Change this to something else (preferably not a value below 1024). Save and exit. Restart lighttpd with: sudo systemctl restart lighttpd.service You should be able to access the web UI only on http://leader name:new port, for example: http://leader.local:8080 In your configuration, under the [ui] section, change the port option from 80 to your new port value. Save. You may need to restart your cluster for this new port to propagate to all machines correctly.","s":"Changing web UI port from 80 to something else","u":"/user-guide/networking","h":"#changing-web-ui-port-from-80-to-something-else","p":598},{"i":611,"t":"This is a work-in-progress, but here's one example.","s":"Connecting to eduroam","u":"/user-guide/networking","h":"#connecting-to-eduroam","p":598},{"i":613,"t":"Pioreactors are able to be used as individual units, or in concert with other Pioreactors. In either case, a Pioreactor needs to be assigned as a leader. The leader unit controls other Pioreactors (and that may include itself), stores the database, hosts the web interface, and is the interface between users and the hardware. A leader will communicate and control all the workers (non-leader Pioreactors) in the inventory. info When you set up your first Pioreactor using our software installation guide, your Pioreactor was set up to be a leader already. You only need one leader in a Pioreactor cluster.","s":"Creating a Pioreactor cluster","u":"/user-guide/create-cluster","h":"","p":612},{"i":615,"t":"After installing the worker image onto your additional Pioreactor (see the instructions here), visit the Inventory page. On the Inventory page, you can search for and add worker Pioreactors to your cluster. Click \"Add new Pioreactor\" at the top right corner of this tab. In the popup, add the name of your worker and click \"Add Pioreactor\". Once a new Pioreactor is added, you may need to refresh the page to see the new worker in the cluster. This Inventory tab will display metadata pertaining to each of your Pioreactors. You can use this page to identify a Pioreactor (causes the blue LED on the HAT to blink), unassign a Pioreactor from any experiment, reboot a Pioreactor, or remove it from your cluster. This page also provides a summary of which Pioreactors are assigned to which experiment, as highlighted in yellow in the image below.","s":"Adding Pioreactors to your cluster","u":"/user-guide/create-cluster","h":"#adding-pioreactors-to-your-cluster","p":612},{"i":617,"t":"Workers can be active (available for running activities and cultures), or inactive. Inactive Pioreactors can still be assigned to experiments, but won't response to commands to run activities or participate in experiment profiles. Turning a worker to inactive will halt all it's activities.","s":"Active and inactive","u":"/user-guide/create-cluster","h":"#active-and-inactive","p":612},{"i":619,"t":"A cluster can be made up of a single Pioreactor, or can be scaled to as many Pioreactors as you have. This gives us a few different possible topologies of what your cluster of Pioreactor(s) might look like. Single Pioreactor​ The simplest topology is when you have a single Pioreactor, and so by default the Pioreactor is both the leader and the only worker. Cluster, and leader is a worker​ When you have multiple Pioreactors, you can nominate one to be the leader, and retain it as a worker, too: Cluster, and leader is not a worker​ You can also choose not to have the leader be a worker. This is useful if you have a spare Raspberry Pi without the Pioreactor hardware, or the number of Pioreactors grows large and you wish to keep one out of the inventory to focus on being a leader only.","s":"Possible cluster topologies","u":"/user-guide/create-cluster","h":"#possible-cluster-topologies","p":612},{"i":621,"t":"Can I change the name of a worker?​ Yes, so long as that worker isn't the leader. Note: this doesn't change historical data. Remove the worker from your cluster using the Inventory page. SSH into the worker (it should still be on your network, even if not part of the cluster). Run sudo hostnamectl set-hostname <new-worker-name> && sudo reboot After a moment, the worker will turn back on with the new name. You can then use the Inventory page to add the worker again.","s":"Common questions","u":"/user-guide/create-cluster","h":"#common-questions","p":612},{"i":623,"t":"So far, we have worked with basic activities that you can directly set as a one time thing, typically at the beginning of your experiment (starting stirring, OD readings, etc.). For more advanced experiments, we introduce automations. Automations are preset functions that are automated, or performed by the Pioreactor without the need of your intervention. This is great for when you want to change the environment of your experiment in some way, whether periodically or at a given time — and you don't want to change your settings each time! Some examples: Every 15 minutes, you want to introduce new media and remove old media using pumps. When working with phototrophs (such as algae), you want to create “day/night” cycles by turning on/off your LEDs. Setting automations can be done so that the Pioreactor performs these tasks automatically. These automations can be found under Activities, when you Manage your Pioreactor.","s":"Introduction to automations","u":"/user-guide/intro-to-automations","h":"","p":622},{"i":625,"t":"When starting an automation, like a chemostat, it is ambiguous whether to start dosing (or checking whether to dose) immediately, or wait N minutes to start. Checking Skip first run will choose the latter: wait N minutes, and then begin.","s":"Skip first run?","u":"/user-guide/intro-to-automations","h":"#skip-first-run","p":622},{"i":628,"t":"You can run the pumps from the Pioreactor UI. These are NOT automations, but rather simple actions to use to set up an experiment, perform cleaning, or intervene in an experiment. Cycling​ Under the Dosing tab, you run the media pump or the alt-media pump and concurrently the waste pump. This is called cycling. By running the waste pump simultaneously, the vial will avoid overflow. You can cycle for a set duration of time. Cycling is good for cleaning pumps, priming tubes with media, or filling your vial with media. Specific control of pumps​ Under the Dosing tab, you can also run specific pumps (media, waste, and alt-media) for a specific duration, volumes (if calibrated), or continuously. The latter will run until the Stop button is pressed. caution Careful not to overflow your vial! The vial can hold 20ml, but stay well below this. Adjustments from manual changes​ Sometimes you may want to add or remove liquid from the vial manually. These changes can be recorded by using the Manual adjustments form under the Dosing tab. These do not run the pumps, but will log the adjustments. This is useful for recording adjustments into the database, and keeping metrics accurate.","s":"Dosing","u":"/user-guide/manual-dosing-leds","h":"#dosing","p":626},{"i":630,"t":"Under the LED tab, you can update specific intensities of the LEDs.","s":"LEDs","u":"/user-guide/manual-dosing-leds","h":"#leds","p":626},{"i":632,"t":"For some use cases, you may want to create a local WiFi network just for your Pioreactors (this is called a local access point, or a hotspot). Why might you want to do this? If you want to get started right away, without dealing with exiting WiFi networks. If your usual WiFi network is restrictive (ex: doesn't allow Raspberry Pis, or requires IT support to host them). If you want to take the Pioreactor, or cluster of Pioreactors, out into the field where there is no network. The Pioreactor comes with the ability to create its own local access point, which other Pioreactors can connect to. See image below: info The built-in local access point is meant for small clusters of Pioreactors, and it's range and stability is limited. If you want a proper local access point, we suggest purchasing an inexpensive wifi router and using that (the router does not need to be connected to the internet - it will still create a wifi network you can connect Pioreactors to regardless).","s":"Local access points","u":"/user-guide/local-access-point","h":"","p":631},{"i":634,"t":"The Pioreactor has the necessary software and hardware to create the local access point. To start the access point: If starting with a new Pioreactor, during software set up: Leave the \"Configure wireless LAN\" unchecked. Continue with the instructions at Setting up your Raspberry Pi. After the SD card has been written to, remove the SD card from your computer, and immediately insert it back in. A boot (or bootfs) device should be present now that is your SD card. If asked to reformat the SD card, select NO. Select your country: -- Select --AfghanistanAland IslandsAlbaniaAlgeriaAmerican SamoaAndorraAngolaAnguillaAntarcticaAntigua And BarbudaArgentinaArmeniaArubaAustraliaAustriaAzerbaijanBahamasBahrainBangladeshBarbadosBelarusBelgiumBelizeBeninBermudaBhutanBoliviaBosnia And HerzegovinaBotswanaBouvet IslandBrazilBritish Indian Ocean TerritoryBrunei DarussalamBulgariaBurkina FasoBurundiCambodiaCameroonCanadaCape VerdeCayman IslandsCentral African RepublicChadChileChinaChristmas IslandCocos (Keeling) IslandsColombiaComorosCongoCongo, Democratic RepublicCook IslandsCosta RicaCote D'IvoireCroatiaCubaCyprusCzech RepublicDenmarkDjiboutiDominicaDominican RepublicEcuadorEgyptEl SalvadorEquatorial GuineaEritreaEstoniaEthiopiaFalkland Islands (Malvinas)Faroe IslandsFijiFinlandFranceFrench GuianaFrench PolynesiaFrench Southern TerritoriesGabonGambiaGeorgiaGermanyGhanaGibraltarGreeceGreenlandGrenadaGuadeloupeGuamGuatemalaGuernseyGuineaGuinea-BissauGuyanaHaitiHeard Island & Mcdonald IslandsHoly See (Vatican City State)HondurasHong KongHungaryIcelandIndiaIndonesiaIran}, Islamic Republic OfIraqIrelandIsle Of ManIsraelItalyJamaicaJapanJerseyJordanKazakhstanKenyaKiribatiKoreaKuwaitKyrgyzstanLao People's Democratic RepublicLatviaLebanonLesothoLiberiaLibyan Arab JamahiriyaLiechtensteinLithuaniaLuxembourgMacaoMacedoniaMadagascarMalawiMalaysiaMaldivesMaliMaltaMarshall IslandsMartiniqueMauritaniaMauritiusMayotteMexicoMicronesia}, Federated States OfMoldovaMonacoMongoliaMontenegroMontserratMoroccoMozambiqueMyanmarNamibiaNauruNepalNetherlandsNetherlands AntillesNew CaledoniaNew ZealandNicaraguaNigerNigeriaNiueNorfolk IslandNorthern Mariana IslandsNorwayOmanPakistanPalauPalestinian Territory}, OccupiedPanamaPapua New GuineaParaguayPeruPhilippinesPitcairnPolandPortugalPuerto RicoQatarReunionRomaniaRussian FederationRwandaSaint BarthelemySaint HelenaSaint Kitts And NevisSaint LuciaSaint MartinSaint Pierre And MiquelonSaint Vincent And GrenadinesSamoaSan MarinoSao Tome And PrincipeSaudi ArabiaSenegalSerbiaSeychellesSierra LeoneSingaporeSlovakiaSloveniaSolomon IslandsSomaliaSouth AfricaSouth Georgia And Sandwich Isl.SpainSri LankaSudanSurinameSvalbard And Jan MayenSwazilandSwedenSwitzerlandSyrian Arab RepublicTaiwanTajikistanTanzaniaThailandTimor-LesteTogoTokelauTongaTrinidad And TobagoTunisiaTurkeyTurkmenistanTurks And Caicos IslandsTuvaluUgandaUkraineUnited Arab EmiratesUnited KingdomUnited StatesUnited States Outlying IslandsUruguayUzbekistanVanuatuVenezuelaVietnamVirgin Islands}, BritishVirgin Islands}, U.S.Wallis And FutunaWestern SaharaYemenZambiaZimbabwe and download the specific local_acccess_point file: Download Drag/move the downloaded local_access_point file to the SD card directory. Eject the SD card safely, and continue with instructions at Setting up your Raspberry Pi. If starting from an existing Pioreactor: with the power off remove the SD card from the Pioreactor and insert it into a computer. Select your country: -- Select --AfghanistanAland IslandsAlbaniaAlgeriaAmerican SamoaAndorraAngolaAnguillaAntarcticaAntigua And BarbudaArgentinaArmeniaArubaAustraliaAustriaAzerbaijanBahamasBahrainBangladeshBarbadosBelarusBelgiumBelizeBeninBermudaBhutanBoliviaBosnia And HerzegovinaBotswanaBouvet IslandBrazilBritish Indian Ocean TerritoryBrunei DarussalamBulgariaBurkina FasoBurundiCambodiaCameroonCanadaCape VerdeCayman IslandsCentral African RepublicChadChileChinaChristmas IslandCocos (Keeling) IslandsColombiaComorosCongoCongo, Democratic RepublicCook IslandsCosta RicaCote D'IvoireCroatiaCubaCyprusCzech RepublicDenmarkDjiboutiDominicaDominican RepublicEcuadorEgyptEl SalvadorEquatorial GuineaEritreaEstoniaEthiopiaFalkland Islands (Malvinas)Faroe IslandsFijiFinlandFranceFrench GuianaFrench PolynesiaFrench Southern TerritoriesGabonGambiaGeorgiaGermanyGhanaGibraltarGreeceGreenlandGrenadaGuadeloupeGuamGuatemalaGuernseyGuineaGuinea-BissauGuyanaHaitiHeard Island & Mcdonald IslandsHoly See (Vatican City State)HondurasHong KongHungaryIcelandIndiaIndonesiaIran}, Islamic Republic OfIraqIrelandIsle Of ManIsraelItalyJamaicaJapanJerseyJordanKazakhstanKenyaKiribatiKoreaKuwaitKyrgyzstanLao People's Democratic RepublicLatviaLebanonLesothoLiberiaLibyan Arab JamahiriyaLiechtensteinLithuaniaLuxembourgMacaoMacedoniaMadagascarMalawiMalaysiaMaldivesMaliMaltaMarshall IslandsMartiniqueMauritaniaMauritiusMayotteMexicoMicronesia}, Federated States OfMoldovaMonacoMongoliaMontenegroMontserratMoroccoMozambiqueMyanmarNamibiaNauruNepalNetherlandsNetherlands AntillesNew CaledoniaNew ZealandNicaraguaNigerNigeriaNiueNorfolk IslandNorthern Mariana IslandsNorwayOmanPakistanPalauPalestinian Territory}, OccupiedPanamaPapua New GuineaParaguayPeruPhilippinesPitcairnPolandPortugalPuerto RicoQatarReunionRomaniaRussian FederationRwandaSaint BarthelemySaint HelenaSaint Kitts And NevisSaint LuciaSaint MartinSaint Pierre And MiquelonSaint Vincent And GrenadinesSamoaSan MarinoSao Tome And PrincipeSaudi ArabiaSenegalSerbiaSeychellesSierra LeoneSingaporeSlovakiaSloveniaSolomon IslandsSomaliaSouth AfricaSouth Georgia And Sandwich Isl.SpainSri LankaSudanSurinameSvalbard And Jan MayenSwazilandSwedenSwitzerlandSyrian Arab RepublicTaiwanTajikistanTanzaniaThailandTimor-LesteTogoTokelauTongaTrinidad And TobagoTunisiaTurkeyTurkmenistanTurks And Caicos IslandsTuvaluUgandaUkraineUnited Arab EmiratesUnited KingdomUnited StatesUnited States Outlying IslandsUruguayUzbekistanVanuatuVenezuelaVietnamVirgin Islands}, BritishVirgin Islands}, U.S.Wallis And FutunaWestern SaharaYemenZambiaZimbabwe and download the specific local_acccess_point file: Download Drag/move the downloaded local_access_point file to your SD card (called boot or bootfs). Eject the SD card safely, and put back into the Pioreactor.","s":"Starting a local access point","u":"/user-guide/local-access-point","h":"#starting-a-local-access-point","p":631},{"i":636,"t":"After plugging in the Pioreactor, the local access point will start and you should see a new network called pioreactor, with password raspberry. You should be able to connect to this new access point with any computer, phone, tablet, etc. Once connected, the usual urls should work: http://pioreactor.local will bring up the Pioreactor interface (having trouble? Not working? Try our troubleshooting steps below. info Without access to the internet, the Pioreactor will have the wrong internal time. You can change this using this method","s":"Access the local access point","u":"/user-guide/local-access-point","h":"#access-the-local-access-point","p":631},{"i":638,"t":"info Raspberry Pi 3B and Raspberry Pi Zero W have trouble connecting to these local access points. Follow instructions here. Other Pioreactors will need to be reconfigured to connect to this new access point. During set up in the Raspberry Pi Imager, using the ssid / wifi credentials: pioreactor and password raspberry in the wireless LAN section. Don't add the local_access_point file to these other Pioreactors - you only need to do that once. The maximum number of machines (Pioreactors and computers) that can be connected to a local access point on a Pioreactor is ~4-8. There is a possibility to add more, see issue here. This network may not be connected to the internet, so you won't be able to upgrade any software on the Pioreactors. See section below on how to add internet.","s":"Connecting more Pioreactors to your local access point","u":"/user-guide/local-access-point","h":"#connecting-more-pioreactors-to-your-local-access-point","p":631},{"i":640,"t":"If you are hosting the local access point on a Raspberry Pi that has an ethernet port (B models), you can plug this into a router that has access to the internet to provide internet to your entire cluster.","s":"Adding internet access to your local access point","u":"/user-guide/local-access-point","h":"#adding-internet-access-to-your-local-access-point","p":631},{"i":642,"t":"After SSH-ing into your Pioreactor, simply delete the local_access_point file in the /boot/firmware/ directory, and reboot.","s":"Turning off a local access point","u":"/user-guide/local-access-point","h":"#turning-off-a-local-access-point","p":631},{"i":644,"t":"In the config.ini, the SSID and password are editable under the section local_access_point. This requires a power-cycle to take effect.","s":"Changing SSID name or password for your local access point","u":"/user-guide/local-access-point","h":"#changing-ssid-name-or-password-for-your-local-access-point","p":631},{"i":647,"t":"Do you see the pioreactor network in the list of available wifi networks?​ If presented, use the option \"Use security key to connect\" (this is an alias for the password). Try power-cycling your Pioreactor The maximum number of machines (Pioreactors and computers) that can be connected to a local access point on a Pioreactor is ~4-8. There is a possibility to add more, see issue here. Alternatively, do you not see the pioreactor network in the list of available wifi networks?​ Try power-cycling the Raspberry Pi If you unplug the Pioreactor, and place the SD card back into your computer, do you see the local_access_point file? If not, try adding the file again, inserting the SD card in the Pioreactor, and restarting the Pioreactor.","s":"My computer can't connect to the local-access-point","u":"/user-guide/local-access-point","h":"#my-computer-cant-connect-to-the-local-access-point","p":631},{"i":649,"t":"Try http://<your_leaders_hostname>.local. Still not working? Try http://10.42.0.1)","s":"I'm on the network, but can't load the Pioreactor UI at http://pioreactor.local","u":"/user-guide/local-access-point","h":"#im-on-the-network-but-cant-load-the-pioreactor-ui-at-httppioreactorlocal","p":631},{"i":651,"t":"confirm that you are using the right wifi name and password in the Imager (default pioreactor and raspberry) The maximum number of access point clients (Pioreactors and computers) that can be connected to a local access point on a Pioreactor is ~4-8. There is a possibility to add more, see issue here.","s":"I can't connect a worker to my local access point","u":"/user-guide/local-access-point","h":"#i-cant-connect-a-worker-to-my-local-access-point","p":631},{"i":653,"t":"You can purchase an inexpensive wifi router and use that as the access point. Note that you don't need to connect this router to the internet - it will operate a network regardless. You can purchase a WIFI USB stick to improve the clients and range of your Pioreactor. For example, the Alfa AWUS036AC (take note to confirm your Raspberry Pi can has the correct USB connection).","s":"I'm pretty sure I'm at the limit of ~4-8 clients on my access point - what can I do?","u":"/user-guide/local-access-point","h":"#im-pretty-sure-im-at-the-limit-of-4-8-clients-on-my-access-point---what-can-i-do","p":631},{"i":655,"t":"Navigate to the Overview page on the Pioreactor web interface. Here you can view live charts for growth rate, OD, normalized OD, and temperature. These overview graphs are used to monitor collected data during the experiment runtime.","s":"Monitoring your experiment","u":"/user-guide/monitor-experiment","h":"","p":654},{"i":657,"t":"Recent event logs are found along the right side of the main Overview page. These logs document any errors, processes, or updates for each Pioreactor.","s":"Event logs","u":"/user-guide/monitor-experiment","h":"#event-logs","p":654},{"i":659,"t":"To change the settings of activities after starting, navigate to the Pioreactors tab. Under Manage for a single Pioreactor or Manage all Pioreactors, click the Settings tab. Here you can change the settings of your activities (such as temperature, RPM, and dosing volume) without pausing or stopping the activity.","s":"Changing settings","u":"/user-guide/monitor-experiment","h":"#changing-settings","p":654},{"i":661,"t":"To locate a Pioreactor, click Identify for the corresponding Pioreactor on the Pioreactors page. This will cause the Pioreactor's onboard LED to blink a blue light. Conversely, you can also find a Pioreactor's name by pressing the white button on the Pioreactor. This causes a tag to come up on the interface for as long as you are holding the button down:","s":"Identifying Pioreactors in your cluster","u":"/user-guide/monitor-experiment","h":"#identifying-pioreactors-in-your-cluster","p":654},{"i":663,"t":"Keep an eye on the optical density graph in the Overview page. Initially, you can expect the the OD to be relatively stable. The following are some common issues:","s":"Troubleshooting","u":"/user-guide/monitor-experiment","h":"#troubleshooting","p":654},{"i":665,"t":"This type of noise is typically caused by bubbling in the media due to metabolism. Noise gradually gets worse as the culture grows, where more metabolism leads to more CO2 bubbles. Thus, you would notice noise build up gradually as the culture becomes larger. To reduce the noise made by bubbles, we recommend allowing more airflow by raising the tubing enough so they aren't submerged in your media.","s":"Gradual increase in noise in OD","u":"/user-guide/monitor-experiment","h":"#gradual-increase-in-noise-in-od","p":654},{"i":667,"t":"note Optical density can decrease early => growth rates can dip negative early on & this is an artifact of turbidity measurements! For variations in OD at the beginning, make sure that your stirbar is in the vial! This is a common mistake we experienced after several experiments.","s":"Initial noise in OD","u":"/user-guide/monitor-experiment","h":"#initial-noise-in-od","p":654},{"i":669,"t":"Random, large spikes in OD readings are indicative of solid debris in your vial. Remove the vial and inspect the media for any debris. You may need to remake your vials and start over. Be sure to thoroughly wash and autoclave your vials and rinse any pumps (if being used). If clumps are to be expected (and unavoidable), you can increase your stirring RPM if allowed in your experiment protocol. This will cause larger clumps to aggregate in the center of the vial, due to a mini \"vortex\" formed by stirring.","s":"Random spikes in OD","u":"/user-guide/monitor-experiment","h":"#random-spikes-in-od","p":654},{"i":671,"t":"If your target temperature is close to room temperature, it can be subject to fluctuations based on changes in room temperature. For example, we set our target to 26 degrees C, and worked in a room with no AC: Each Pioreactor had an increase in temperature since the target fell below ambient. Note that the leader unit Pioreactor in the cluster was more sensitive to increases in ambient temperature since it requires more processing power.","s":"Temperature fluctuations","u":"/user-guide/monitor-experiment","h":"#temperature-fluctuations","p":654},{"i":673,"t":"If none of these issues apply to your data, feel free to contact us at support@pioreactor.com or post to our forums for further assistance.","s":"Looking for further help?","u":"/user-guide/monitor-experiment","h":"#looking-for-further-help","p":654},{"i":681,"t":"If you would like to expose the Pioreactor UI to view remotely, you can use a service like Ngrok to do so. caution This exposes your Pioreactor UI and therefore your Raspberry Pi over the internet. You should have a strong password on your Raspberry Pi leader, and use a strong password for basic-auth (below). We make our best security effort in our products, however we are not responsible for any damages as a result of exposing your Raspberry Pi online. The following are the steps to take: Sign up for Ngrok - the free plan is all we need. Make sure to confirm your account through your email. Download the app onto the Raspberry Pi: wget -O ngrok.tgz https://bin.equinox.io/c/bNyj1mQVY4c/ngrok-v3-stable-linux-arm.tgz Unzip: tar zxvf ngrok.tgz Make a new folder for the program: sudo mkdir /opt/ngrok Move ngrok file there: sudo mv ngrok /opt/ngrok Make a config folder: mkdir ~/.ngrok Fill in the following: nano ~/.ngrok/ngrok.yml. We advise changing the basic auth credentials below to something more secure authtoken: <add your ngrok auth token here, find in nrgok dashboard> tunnels: ui: proto: http addr: 80 inspect: false basic_auth: [\"pioreactor:vogue-awesome-brag\"] #change this schemes: - http ws: proto: http addr: 9001 inspect: false schemes: - http version: \"2\" region: us Run in background: nohup /opt/ngrok/ngrok start ui ws --config ~/.ngrok/ngrok.yml & Alternatively, if you wish to set this up as a service that will launch on start up, the following sudo systemctl enable ngrok At dashboard.ngrok.com, you'll see two urls. One of the unique urls should link to your Pioreactor dashboard (when asked for a name and password, use the user name and the password used in the config above). However, the UI will crash - this is expected. Continue on. The other url is added to your config.ini. While SSH'd into your leader, open the config.ini: nano ~/.pioreactor/config.ini And edit the following section (but put in your unique url) [mqtt] ... # this should not have any https:// infront: ws_url=<your url>.ngrok-free.app ws_protocol=wss ... Deploy your config with pios sync-configs, and refresh your UI that previously crashed. You're all done! You can now access the Pioreactor UI anywhere. The username and password are the same you added to your yaml file above.","s":"Ngrok","u":"/user-guide/ngrok-remote-access","h":"","p":680},{"i":684,"t":"The interaction of light within samples of suspended microorganisms will differ from light passing through concentrated solutions. Instead of being absorbed, light is scattered by the cells in suspension. This scattered light is measured as optical density (OD). As turbidity increases, more scattering occurs, resulting in a higher OD reading. tip Looking to calibrate for OD600 readings? Visit this page.","s":"Background on optical density","u":"/user-guide/od-normal-growth-rate","h":"#background-on-optical-density","p":682},{"i":686,"t":"Due to manufacturing variables such as differences in LED strength and sensitivity, the raw OD readings can't be compared against each other. Instead, we use the normalization technique described below: A series of initial OD readings are averaged to produce a reference value (denominator). New OD readings after the reference value are normalized using the following simple equation: latest ODreference OD=normalized OD\\frac{\\normalsize \\text{latest\\thickspace OD}}{\\normalsize \\text{reference\\thickspace OD}}=\\text{normalized\\thickspace OD}referenceODlatestOD​=normalizedOD For example: Pioreactor name Reference OD Latest OD Pioreactor1 0.030 0.033 Pioreactor2 0.010 0.015 It's difficult to compare raw OD readings since the starting values are different. However, if we normalize using the above equation: Pioreactor1​ 0.0330.030=1.1\\frac{\\small 0.033}{\\small 0.030}=1.10.0300.033​=1.1 Culture growth by 1.1x. Pioreactor2​ 0.0150.010=1.5\\frac{\\small 0.015}{\\small 0.010}=1.50.0100.015​=1.5 Culture growth by 1.5x. We can more accurately compare culture growth using these ratios as opposed to using the raw OD values. tip Because of the way we defined normalized optical density, it has the following easy interpretation: its the multiplicative amount the culture has changed by. So if the normalized OD is 2.0, the culture has doubled its initial concentration, i.e. doubled the population since the volume is fixed. This also works for traditional OD600 measurements: if your initial sample has OD600 equal to 0.45, then a normalized OD of 2.0 is the same as an OD600 of twice that, or 0.90. (Generally...).","s":"Normalization","u":"/user-guide/od-normal-growth-rate","h":"#normalization","p":682},{"i":688,"t":"While basic normalization accounts for initial OD differences, it does not consider the optical density of the media itself. For a more accurate growth rate calculation, you can blank your sample. Blanking your vials is recommended for experiments that begin with low OD readings (ex. inoculating small amounts of yeast). By blanking, you are able to observe the OD of only the microorganism of interest. As an example, let's consider the same data as above, but this time we have information on the blank ODs: Pioreactor name Blank OD (media) Reference OD (media with culture) Difference (reference - blank) Latest OD Pioreactor1 0.025 0.030 0.005 0.033 Pioreactor2 0.005 0.010 0.005 0.015 We can now subtract the blank values from the latest OD and reference OD values: latest OD−blank ODreference OD−blank OD=blanked normalized OD\\frac{\\normalsize \\text{latest\\thickspace OD}-\\text{blank\\thickspace OD}}{\\normalsize \\text{reference\\thickspace OD}-\\text{blank\\thickspace OD}}=\\text{blanked\\thickspace normalized\\thickspace OD}referenceOD−blankODlatestOD−blankOD​=blankednormalizedOD Pioreactor1​ 0.033−0.0250.030−0.025=1.6x\\frac{\\small 0.033-0.025}{\\small 0.030-0.025}=1.6x0.030−0.0250.033−0.025​=1.6x Culture growth by 1.6x. Pioreactor2​ 0.015−0.0050.010−0.005=2x\\frac{\\small 0.015-0.005}{\\small 0.010-0.005}=2x0.010−0.0050.015−0.005​=2x Culture growth by 2x. By accounting for the OD of the blank media, we are able to calculate a more accurate growth rate.","s":"Blanking","u":"/user-guide/od-normal-growth-rate","h":"#blanking","p":682},{"i":690,"t":"We inoculated two vials with a drop of re-hydrated yeast, and tracked their growth at temperatures 27°C and 35°C. The following normalized optical density chart was generated by the Pioreactor: From the normalized optical density, an implied growth rate graph is generated. The relationship between the implied growth rate, gr\\text{gr}gr and the normalized optical density, nOD\\text{nOD}nOD is exponential, defined by the following equation: nOD(t)=exp⁡(∫0tgr(s)ds)\\text{nOD}(t) = \\exp{ \\left( \\int_0^t \\text{gr}(s)ds \\right)}nOD(t)=exp(∫0t​gr(s)ds) We can rewrite this equation in terms of the growth rate: gr(t)=nOD′(t)nOD(t)\\text{gr}(t)= \\frac{ \\text{nOD}'(t)} {\\text{nOD}(t)}gr(t)=nOD(t)nOD′(t)​ which plainly states that the growth rate is the rate of change of the size of the culture, normalized by the size of the culture. This rate can give insight on the state of your culture under different external conditions. These graphs can be interpreted in 4 phases: The lag phase: No observed growth, but high cell activity. In this stage, cells are in a nutrient rich environment and are preparing for growth by synthesizing proteins and other necessary molecules. Exponential (or log) phase: Cells are now dividing and doubling in numbers after each generation time. Generation times are dependent on the species you are using for your experiment. Stationary phase: Eventually the growth of cells reaches a plateau as nutrients are used up and waste products accumulate. At this point, the number of dividing cells will equal the number of dying cells. Decline (or death) phase: As nutrients are depleted, cell growth slows while cell death increases. Here's how these phases would apply to our graphs, focusing on the 35°C vial: Some things to note: The lag phase can be detected easily in the growth rate graph, as the rate is stable and doesn't begin increasing until a bit after 6 PM. This is not easily determined in the nOD graph, since at this point the overall turbidity of the culture is low. The exponential phase occurs when the growth rate is high/increasing. When the culture reaches the stationary phase, growth rate drops to 0 since the culture is no longer growing in size. The turbidity is constant. The decline phase is not represented in the graphs above, as yeast remain in the stationary phase over many days.","s":"Growth rate","u":"/user-guide/od-normal-growth-rate","h":"#growth-rate","p":682},{"i":692,"t":"Pinch valves are useful for controlling gas into the Pioreactor by \"pinching\" a gas line closed (or keeping it open). This could used be for injecting gas periodically into the headspace, or acting as a bubbler by putting the injection tube directly into the culture. Below is a diagram of using a pinch valve to periodically provide CO₂ into the head space of the Pioreactor's vial: The pinch valve opens and closes, controlled by the Pioreactor, to allow gas from the CO₂ source into the headspace. The Pioreactor controls the pinch valve via the PWM channels and software (plugins). warning Keeping a pinch valve powered continuously for a long time can reach temperatures above 60℃!","s":"Pinch valves","u":"/user-guide/pinch-valves","h":"","p":691},{"i":694,"t":"Some options for pinch valves that will be useful for your application: Normally closed (NC) / normally open (NO). When no power is provided to the pinch valve, a normally closed pinch valve will force the tube to be closed. Conversely, a normally open pinch valve will keep the tube open when no power is provided. tip We suggest a normally closed valve most of the time, since if the Pioreactor loses power, or an experiment ends and power is turned off, we would like the tube to be closed to avoid losing gas. PWM: safest option is \"continuously\" (or \"continuous\"). This means that we can power the pinch valve continuously without it overheating, however it still may be hot to touch. Voltage: The Pioreactor normally operates at 5V, and there are pinch valves that work at this voltage. More common though are pinch valves that work at 12V. To use a 12V pinch valve, you'll need to supply 12V to the auxiliary power input on your Pioreactor. Tube size: this is dependent on your system.","s":"Pinch valve options","u":"/user-guide/pinch-valves","h":"#pinch-valve-options","p":691},{"i":696,"t":"To control the pinch valve, we suggest using the pioreactor relay plugin. This plugin will turn the PWM channel for the pinch valve (specified in your config.ini) on and off at your control. By default, it won't operating when OD readings are taken. You can install this plugin from the Pioreactor UI.","s":"Software","u":"/user-guide/pinch-valves","h":"#software","p":691},{"i":698,"t":"Takasago Fluidics have a quality product with lots of options. However, the distribution is from Japan, and is quite expensive though, and they require buying through a sales person. We've also designed a simple housing to attach it to our Pioreactor dosing platform.","s":"Recommended pinch valves","u":"/user-guide/pinch-valves","h":"#recommended-pinch-valves","p":691},{"i":701,"t":"Cleaning the vial​ It's recommend to clean your vial before every use. The vial and cap can be cleaned with soapy water. A useful accessory for cleaning is a small bottle brush / test tube brush. Rinse the vial to remove any soap residue. Choosing a volume for your culture​ We suggest using between 8ml to 16ml volume of liquid in the vial. tip Some things to consider when selecting a volume: a lower volume will provide more aeration per mL since the liquid-air interface is fixed. A lower volume will also be more responsive to changes in temperature, and be able to achieve a higher maximum temperature. But too low and the vortex caused by stirring may start interfering with the Pioreactor's optical system (a lower RPM can fix this though). Position of tubes in cap​ Keep at least 1 cap tube out of the liquid and well away from potential bubbles / foam that may occur. This will prevent gas pressure from building up. Something also to keep in mind: more tubes out of the liquid means more gas transfer with the ambient atmosphere. If using pumps with your Pioreactor, see the note below.","s":"1. Preparing the vial","u":"/user-guide/prepare-vial-for-cultures","h":"#1-preparing-the-vial","p":699},{"i":703,"t":"Prepare your media as your protocol suggests. For example: in the our experiments, we typically showcase yeast grown in YPD broth. To create YPD broth, mix YPD and water at a ratio of 50 grams YPD powder to 1 liter distilled water.","s":"2. Preparing media","u":"/user-guide/prepare-vial-for-cultures","h":"#2-preparing-media","p":699},{"i":705,"t":"Using heat​ Divide the mixture into the vials to the correct volume, and add the stir bar in the vial. The glassware vial, stir bar and vial cap that come with your Pioreactor are all fully autoclavable, and heat resistant up to 125℃. The luer lock ends can be covered with tin foil, or attached to air filters, or neither. Since the volume in the vial is so little, the autoclave only needs to be at its maximum temperature for a very short duration. tip Don't have an autoclave? A kitchen pressure cooker works just as well. Still don't have that? You can use a stove top or hotplate: heat on a medium-low heat until boiling, and let boil for a few minutes. However, an autoclave or a pressure cooker is a more effective sterilizer. tip \"Flick\" away any trapped liquid in the cap's tubes. Using sterile filtration​ Filtered media can be directly added to a sterilized glass vial, or via the (sterilized) male luer lock ports.","s":"3. Sterilization","u":"/user-guide/prepare-vial-for-cultures","h":"#3-sterilization","p":699},{"i":707,"t":"Ideally in a sterile environment, the vial's lid can be removed and the inoculant can be added. Alternatively, for additional sterility, a needle can be sent down a tube, without removing the cap at all. How much inoculant should you add? That depends on the concentration of your inoculant. From our experience, we create a dense culture/stock culture by adding some amount of culture to sterile media or water, and then inoculate our vials from this stock. For example, we add 0.5 grams of dried Baker's yeast to 15 mL of YPD broth, then store it in a fridge for further use. We recommend measuring with a micropipette. If you are using a dropper, hold it vertically for more accurate, consistent drops.","s":"4. Inoculation","u":"/user-guide/prepare-vial-for-cultures","h":"#4-inoculation","p":699},{"i":709,"t":"Keep the bottoms of the tubes in the cap from being submerged in your media to avoid creating a pressured environment. Adjust each luer lock end until the other end of the tube is above liquid level.","s":"5. Adjusting tube lengths (Optional)","u":"/user-guide/prepare-vial-for-cultures","h":"#5-adjusting-tube-lengths-optional","p":699},{"i":711,"t":"We recommend handling the vial with gloves, or handling only the cap. Minimize touching the glass as much as possible to avoid getting oils and fingerprints on the glass. Before placing in the Pioreactor sleeve, wiping the surface of the glass with a kimwipe is a great idea!","s":"6. Handling the glass","u":"/user-guide/prepare-vial-for-cultures","h":"#6-handling-the-glass","p":699},{"i":713,"t":"danger The outside of the glassware vial should be dry. If the vial is wet, even with single droplet, it can damage the electronics underneath. Place the glassware vial into the Pioreactor sleeve. Ensure that the vial is pressed all the way down and is touching the bottom of the vial holder. This ensures correct temperature regulation of the culture. Next, you can start your experiment in the browser.","s":"7. Positioning glassware in the Pioreactor sleeve","u":"/user-guide/prepare-vial-for-cultures","h":"#7-positioning-glassware-in-the-pioreactor-sleeve","p":699},{"i":715,"t":"Using pumps: influx and efflux.​ When using the Pioreactor with pumps, you'll be using the four luer lock tubes as influx and efflux. The tubes, which are identical lengths, can be moved up and down, and we suggest using this as a way to \"label\" tubes, and to control the maximum volume in the vial. This can be done before sterilization. Here's how: One tube can be pulled high up, so that about a millimeter is showing on the underside of the cap. This will be our air influx and efflux (recall that when liquid is added or removed, air needs to be removed or added respectively to not create a pressure difference). Two tubes can be pulled such they are aligned with the bottom rim of the cap. These two tubes will be the liquid influx tubes. For some operations, like a chemostat, you'll only be using one of these tubes, but some operations require more than one influx. The final tube is the liquid efflux tube. It will be positioned such that it controls the final amount of volume in the vial. Fill your vial to the desired final volume using water. Pull the final tube down such that its end just touches the top of the water when the cap is fully screwed on. It may take some minor adjustments to achieve this. info How does this maintain a constant volume throughout operation? When liquid is added, say 1ml, the volume rises an additional 1ml. Then 1ml of liquid is removed via efflux, but then the efflux pump runs again for an additional few seconds. The efflux pump is run for an additional few seconds to eliminate any volume differences or deltas (for example, if the volume added is greater than the volume removed due to pumping errors). Otherwise, the deltas accumulate and the vial can overflow. This additional step guarantees that that volume of liquid never exceeds the end of the efflux tube. During your experiment set up, the length of the tubes out of the cap can provide information about their \"roles\": longest tube is air exchange, shortest tube is efflux, and middle two tubes are influx.","s":"Extra","u":"/user-guide/prepare-vial-for-cultures","h":"#extra","p":699},{"i":729,"t":"The Pioreactor connects to your local network, and the UI is hosted locally on the Raspberry Pi. A priori, there's no access to view the UI from outside your local network (this is a good thing for security reasons). Let's change that. With some extra free services, we can safely connect to our Pioreactor cluster remotely. We've documented 2 ways to do this. Both require command-line access to the leader Pioreactor and some external services. Option 1: Ngrok. Remotely access your UI behind a simple username / password. Option 2: Tailscale. Spin up a simple VPN, and expose your UI to users of your VPN. Also allows for Pioreactors in different locations to be used together over the VPN.","s":"Introduction to remote access","u":"/user-guide/remote-access","h":"#introduction-to-remote-access","p":727},{"i":731,"t":"By allowing remote access to your Pioreactor, you are providing a possible vector for malicious folks to access the UI, and possibly your network. We've built the Pioreactor to minimize these holes, but there are two more additional changes you should make: To disallow users to upload files onto your server, enter the following into your leader: touch /home/pioreactor/.pioreactor/DISALLOW_UI_UPLOADS To disallow users to add plugins to your cluster, enter the following into your leader: touch /home/pioreactor/.pioreactor/DISALLOW_UI_INSTALLS We highly recommend doing both these actions. To remove these blocks, simply delete the files.","s":"Security","u":"/user-guide/remote-access","h":"#security","p":727},{"i":733,"t":"To get the best results and confirm your Pioreactor is working as expected, it's advisable to run a self-test on your Pioreactor after setting it up initially. The self-test routine can catch common errors that may compromise your data collection.","s":"Running a self-test","u":"/user-guide/running-self-test","h":"","p":732},{"i":735,"t":"Start on the Pioreactors page: Insert a closed vial with water and stir bar into the Pioreactor, and click \"Start\". The Pioreactor will start running tests against expected output and report back to you success and failures of those tests. Depending on the results of each test, you'll see success and failures: info The self-test routine is optional. Even with test failures, the Pioreactor is still operational (perhaps not where the test failed though!). We highly recommend a self-test at least after your initial setup.","s":"How to run the self-test routine","u":"/user-guide/running-self-test","h":"#how-to-run-the-self-test-routine","p":732},{"i":737,"t":"Pioreactor HAT is detected checks if the Pioreactor HAT is correctly placed on top of the Raspberry Pi. A non-trivial failure here suggests a problem connection between the HAT and the RPi, a failure with the i2c channel, or a failure with the RP2040 chip on the HAT. If Heating PCB is detected also fails, try disconnecting the Heater PCB flat-flex cable from the HAT (unlock and pull straight out), and trying the test again. Photodiodes are responsive to IR LED checks to ensure that the IR photodiode(s) have a linear relationship with the IR LED's output. The linear relationship is important. Common reasons why this test fails include: Not enough light is entering the PD position (see below for resolutions) The IR LED connected to the the wrong LED output. Make sure that the IR LED is identified correctly in the config.ini A loose (or absent) connection to the Pioreactor HAT, either in the photodiode(s) or the IR LED. The test will also report any valid IR LED & photodiode relationships in the dialog box. For example, IR ⇝ REF means that the REF photodiode has a linear relationship with the IR LED. Similarly, IR ⇝ 45 means the the photodiode in the 45° pocket has a linear relationship with the IR LED. The absence of a relationship here can tell you about what might be wrong. Tips: Try running this test again. Add a slight amount of turbid liquid (milk, culture, tea) to slightly increase the turbidity of the liquid inside. This increases the scatter of the liquid, and will help this test. If it continues to fail, contact us. No ambient IR light detected checks that the photodiodes are detecting a near-0 signal when the IR LED is completely off. This test may fail if a powerful IR signal is shining into or onto the Pioreactor's body (aka the Sun - don't put the Pioreactor in direct sunlight and avoid windows). Also make sure that the caps are on all the Pioreactor's LED pockets. Reference photodiode is the correct magnitude checks, if using the reference photodiode (REF), that the REF signal is less than 0.256 volts when the IR LED is at the level specified in the config.ini's [od_config].[ir_led_intensity] section. If this test fails, confirm that in your config.ini that REF is present for one of the channels under [od_config.photodiode_channel]. check the positioning of the REF photodiode (should be adjacent the the IR LED, snugly inserted, and with a cap). If still failing, try reducing the value in [od_config].[ir_led_intensity]. Reference photodiode is in the correct position checks, if using the reference photodiode (REF), that the REF cable is inserted into the correct photodiode position (channel 1 or 2). The correct position is provided in the config.ini's [od_config.photodiode_channel] section. Note: this is a flakey test, and can fail even when positioned correctly. The test compares the variances of the two signals (from photodiode channels 1 and 2), and the lower variance one is usually the REF. If this test fails, Is your vial in the Pioreactor? Does your vial have water and a stirbar in it? Confirm that in your config.ini that REF is present for one of the channels under [od_config.photodiode_channel]. Photodiode measures near zero signal for clear water checks that a non turbid liquid, like water, doesn't produce a signal (since there is no scatter). This is a new test, and may fail even if everything is okay. Check the following: confirm that your vial contains water (or any very clear liquid) and that your signal photodiode is positioned in 45°, 90°, or 135°. This test won't work for 180°. Heating PCB is detected checks that the heating PCB is correctly attached to the Pioreactor HAT. A non-trivial failure here suggests a problem when the i2c channel, a loose connection, or damage to the heating PCB. See notes for Pioreactor HAT is detected, too. Heating is responsive checks for a linear relationship between the temperature sensor and the PWM heating system. Stirring RPM is responsive checks for a linear relationship between PWM stirring system and the Hall sensor that measure's RPM. If this fails, check that the stirring power is connected correctly (and in the location specified in config.ini's [PWM] section). Another reason for failure is that the magnets are too far away from the base of the vial. See stirring troubleshooting. AUX power supply is appropriate value checks that the AUX power voltage is between 0V and 18V. If no AUX power is connected to the Pioreactor, the default voltage is 5V.","s":"Explanation of each test","u":"/user-guide/running-self-test","h":"#explanation-of-each-test","p":732},{"i":740,"t":"To create a new experiment, click on the drop-down menu on the top of the left-hand bar. Click the \"New experiment\" button. On the next screen, enter your new experiment name. This name should be unique from prior experiment names. Enter optional metadata about your experiment; you can modify the description later, if necessary. Click \"Save\" when done.","s":"Creating an experiment","u":"/user-guide/set-up-an-experiment","h":"#creating-an-experiment","p":738},{"i":742,"t":"The Pioreactors tab will display any active and inactive Pioreactors assigned to the experiment. Click on \"Assign Pioreactors\" to assign pioreactors to the current experiment. Pioreactors that are assigned to another experiment will be unavailable, unless unassigned through the Inventory tab or through it's assigned experiment's Pioreactors tab.","s":"Assigning Pioreactors to your experiment","u":"/user-guide/set-up-an-experiment","h":"#assigning-pioreactors-to-your-experiment","p":738},{"i":744,"t":"When working with small amounts of a microorganism, or when using very turbid media, you can obtain more accurate growth rates by blanking the vial before inoculation. How to record a blank # Insert your sterile vial containing media into the Pioreactor before inoculating with your species of interest. On the website, click the Pioreactors tab on the left-hand menu, and choose one of the active Pioreactors. Select Calibrate, and under the Blanks tab, click Start. The Pioreactor will now record the optical density of the blank vial. Repeat for all the Pioreactors to be used. A notification will appear when a Pioreactor has finished blanking. You can now inoculate your vials and begin your experiment.","s":"(Optional) Blanking","u":"/user-guide/set-up-an-experiment","h":"#optional-blanking","p":738},{"i":747,"t":"tip When starting, it's useful to run a self test to confirm that your Pioreactors are all working as expected. How to run a self-test. On the Pioreactors page, you should see at least one Pioreactor under Active Pioreactors. You can start an activity using the \"Manage\" button. Once started, you can pause (and then resume) or stop jobs. Clicking the \"Manage all Pioreactors\" button will give you control to start and stop activities on all active Pioreactors. The typical sequence of activities to start is: Stirring Temperature automation, and selecting Thermostat Optical density After observing that the optical density looks normal on the Experiment Overview page, Growth rate Any other activities. Any of the automations can be started, or custom jobs you've added to your Pioreactor.","s":"Start activities from the Pioreactors page","u":"/user-guide/set-up-an-experiment","h":"#start-activities-from-the-pioreactors-page","p":738},{"i":749,"t":"If you'd like to change the settings of your activities after you start, navigate back to the Pioreactors tab. Under Manage for a single Pioreactor or Manage all Pioreactors, click the Settings tab. Here you can change the settings of your activities (such as temperature, RPM, and dosing volume) without pausing or stopping the activity. (Optional) If working with more than one Pioreactor in your cluster, it's useful to assign experiment-specific labels in these settings. These labels appear in the user interface, making progress checking and updating easier. The labels can be changed later. Click \"Assign\" when done. tip Use these labels to keep track of treatments on multiple Pioreactors. For example, labels '15C', '25C' and '35C' can be used to differentiate temperature treatments. These labels will be shown on graphs generated in the Overview page on the website. They can be changed in the UI later, too. Ending your experiment​ On the Overview, Pioreactors, and Profiles tabs, the option to Manage experiment is located in the top left corner. The option End experiment will stop all running activities and unassign all Pioreactors from the experiment. warning The option Delete experiment will do the same, while also deleting all experiment data. Note that you will not be able to export any data from a deleted experiment.","s":"Changing settings","u":"/user-guide/set-up-an-experiment","h":"#changing-settings","p":738},{"i":752,"t":"You can expect the setup process to take 10-15 minutes. If you encounter any problems, feel free to email us for support at hello@pioreactor.com. info Before you get started, you'll need to have the following: A Raspberry Pi (our list of recommended Raspberry Pis is here) A blank microSD card (our recommended microSD cards is here) A suitable power supply for the Raspberry Pi (our recommended power supply units are here) A computer with internet access and ability to read & write to a microSD card","s":"Before you begin","u":"/user-guide/software-set-up","h":"#before-you-begin","p":750},{"i":754,"t":"We'll start your blank microSD card. Download the Pioreactor leader & worker image file. info What is an image file? It's a file that contains all the required software preinstalled on it, including an operating system and our custom Pioreactor software. The image will be installed on the microSD card. Download the latest version of Raspberry Pi Imager for your operating system and install it. Open the newly-installed Raspberry Pi Imager. Click Choose Device, and \"No filtering\" at the top. Click Choose OS. Click on Use custom towards the bottom: Select the downloaded Pioreactor image from step 1. Insert your microSD card to your computer. After your microSD card is recognized by your computer, click Choose Storage and select it. Click Next. Click Edit settings: Check Set hostname. Input a unique name for this Pioreactor. Some names that we use for our first Pioreactor: pioreactor01, or leader, or pio01. Don't use pioreactor or raspberrypi. Check Set username and password. Enter the following: username: pioreactor. password: raspberry. Note: You can change the username and password later. Check Configure wireless LAN and enter your network name into SSID network name, WiFi password, and country. Or leave blank if using ethernet. tip If you are having difficulty connecting to a network, like at a university that may not easily allow Raspberry Pi's, there's a built-in solution for creating a local access point). Note that any tutorials that mention wpa_supplicant.conf are out of date. This has been deprecated by Raspberry Pis for a while. We have some further documentation on networking available here. Change timezone to your local timezone. Under the \"Services\" tab, check Enable SSH, and select Use password authentication. Your settings should look something like this: Click Save to save and exit the dialog box. Click \"Yes\" to begin writing. A prompt may appear asking for permission to write, accept it. Writing will take up to 5 minutes. Perfect time for a tea break. Once writing is complete, remove the microSD card, and place it into the Raspberry Pi. Your Raspberry Pi's power should be unplugged before inserting the microSD card. The microSD slot is located on the PWM side of the Pioreactor. Example for a Raspberry Pi A model: Plug power into your Raspberry Pi. LEDs onboard the Raspberry Pi may start to light up momentarily. After a few minutes, your Pioreactor HAT will briefly blink a blue LED, telling us it is ready. info Waited, but didn't see a blue LED blink, or maybe you missed it? Try pressing on the onboard button, near the side labelled \"PWM\", and pictured above. If this lights up the blue LED, you're good to move on. Still not working? Try power-cycling the Raspberry Pi, or email us at hello@pioreactor.com. After observing the blue LED flashing, navigate to http://pioreactor.local in a web browser to visit the web interface. If you are using local-access-point, looking for a pioreactor wifi network and then visit the link. (Not able to load http://pioreactor.local? Read Troubleshooting below). The Pioreactor is now ready for use! Follow this guide to set up your first experiment. If you're using a Pioreactor 20ml v1.0, edit your config.ini to [pioreactor] model=pioreactor_20ml version=1.0 and then reboot.","s":"Setting up your Raspberry Pi","u":"/user-guide/software-set-up","h":"#setting-up-your-raspberry-pi","p":750},{"i":756,"t":"Workers are additional Pioreactors that you can control from a single UI. Together, a leader and workers form a Pioreactor cluster. Step 1. Install the worker software​ Follow the same instructions above, but use a Pioreactor Worker image instead. All the settings are the same, including username and password, but choose a new hostname. See note below: note Choose a hostname that isn't currently being used in your cluster, ex: worker01, worker02, etc. Re-using old names is fine, so long as that worker isn't present in your cluster. Tip: if you plan to have many Pioreactors, use a leading zero in any numbers, like pio01, or worker01, etc. Below is a screenshot of example settings, your settings might be slightly different. If using a local-access-point on your leader Pioreactor, use the wifi ssid pioreactor and password raspberry. After the image is written to the microSD card, place the microSD card into the Raspberry Pi and power it on. The Pioreactor's blue LED will light up and stay on, indicating that it's ready to be connected. Move onto the next step. Step 2. Add worker to cluster using the UI​ Follow the instructions here to add your worker to your Pioreactor cluster. From the command line (Alternative)​ On the leader's command line, the command pio add-pioreactor <new name> will connect the new Pioreactor to the cluster. tip We recommend running a self-test on all Pioreactors after your initial setup to detect any hardware bugs at this point.","s":"Adding additional workers to your cluster","u":"/user-guide/software-set-up","h":"#adding-additional-workers-to-your-cluster","p":750},{"i":758,"t":"My leader Pioreactor never flashes the blue LED​ First, confirm that when you press the HAT button, the blue LED does not show up. If it does, you're good to go. It's likely that the installation failed (due to a settings issue), or there is a problem with the SD card. Double check the settings that you used and try reinstalling the image. Are you using a microSD card with a size larger than 32GB? You may need to reformat it to FAT32. To do this, in the Raspberry Pi Imager, first select \"Erase: format card as FAT32\" under \"Choose OS\". Then proceed with writing the image. My Pioreactor keeps flashing the blue LED​ On a successful start, the Pioreactor will flash its blue LED for about 2 seconds. If you observe the blue LED flashing for longer, something may be wrong. You can diagnose the problem by counting the number of flashes observed. My RPi won't connect to my WiFi.​ Some Raspberry Pis can't connect to Wifi natively, and some Raspberry Pis can only connect to 2.4GHz connections. See table below: If you are using the built-in WiFi in a Raspberry Pi3, a Pi3B+, or Pi Zero W, be aware that the signal strength from the tiny internal antenna may be weaker than other WiFi devices. Try moving your Pioreactor closer to the router as a test. If your network hidden? You will need to check hidden SSID in the configuration in the Raspberry Pi imager. To fix this, you'll need to restart the image installation from the Raspberry Pi Imager. Try power-cycling the Raspberry Pi (unplug and plug back in). If you are on a restrictive network (like at a university), and wish to avoid the network, creating a local access point may be a better option. You may have mis-typed your WiFi credentials. To fix this, you'll need to restart the image installation from the Raspberry Pi Imager. If connecting to a 5GHz WiFi connection, you need to supply a valid country code. See the list here: https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2/. It's possible your SD card is damaged. This can cause all sorts of problems (including failing to boot), not just WiFi issues. The most common cause of SD card failure is probably inserting or removing the SD card while the Pi is powered up. Check out some other possibilities here. I want to change the Pioreactor name on installation of leader​ Easiest solution is to start over. You can edit the name in the RPi Imager, and reflash the image onto the microSD card to remove all previous data. http://pioreactor.local in a web browser is not showing up​ In your browser's address bar, add the http:// in front of the url, like so: http://pioreactor.local. Try appending a backslash as well: http://pioreactor.local/. The UI is hosted on http, not https. Check if you are accessing http ://pioreactor.local, and not https ://pioreactor.local. Try accessing using the url http://<the name of your leader Pioreactor aka hostname>.local. If you know your Raspberry Pi's IP, try http://<IP address of your Raspberry Pi>. Here's information to determine the IP address. When pressing the button on the HAT, does the blue LED show up? If not, installation may have failed. Try installing the image again, and double check the settings. Try power-cycling the Raspberry Pi (unplug and plug back in). In your Raspberry Pi Imager settings, confirm that you clicked \"Set username and password\", and used the username pioreactor. If not, try reinstalling the image. Are you on an older Windows machine? You may need to install a DNS service, but also see workarounds here. Can I plug a monitor into the Raspberry Pi's HDMI port?​ Our current software turns off all external displays (for power and compute reasons), so any external monitor attached to the Pi won't work.","s":"Troubleshooting","u":"/user-guide/software-set-up","h":"#troubleshooting","p":750},{"i":760,"t":"Unlike using Ngrok, this method does not expose your UI to the public internet. To access the UI remotely, you need to join an authenticated VPN. This greatly improves security, but adds a bit of additional work for users. info Tailscale is a really really cool service! You may find yourself using it for other projects, too. Sign up for an account at Tailscale. The free account is fine for now. Once signed up and logged in, visit the Tailscale admin. Install Tailscale on your computer. SSH into your leader Pioreactor. Install Tailscale for Raspberry Pi with the following: curl -fsSL https://tailscale.com/install.sh | sh. You don't need to install anything on the workers. Back in your Tailscale admin, you should see two machines: your computer and the leader Pioreactor. Make note of the ipv4 address for the leader - we will use it below. You should still be able to access http://pioreactor.local without any problems. In your config.ini, add your ipv4 address to the [mqtt] section: [mqtt] ... broker_address=<ipv4 address> ... If you have other Pioreactors in your cluster: you likely won't be adding those to tailscale (only adding the leader is necessary for remote access), so in each of the worker config files, add: [mqtt] broker_address=<leader name>.local And save. This means that your workers will connect \"locally\" (over the local network), but the UI will connect \"remotely\". Now, when you leave the local network, and if you have internet access, you can turn your VPN on and still access http://<ipv4 address>. Troubleshooting: try http://<hostname>, but confirm that magicDNS is on, too. You can use the Tailscale admin to add users to your VPN, too.","s":"Tailscale","u":"/user-guide/tailscale-remote-access","h":"","p":759},{"i":762,"t":"The heater in the Pioreactor wetware can be programmed to control the temperature of the vial in automated ways. Pioreactor is pre-programmed with the following temperature automations. In the below automations, values highlighted like so are configurable.","s":"Temperature automations","u":"/user-guide/temperature-automations","h":"","p":761},{"i":764,"t":"The Thermostat automation will try to maintain a target temperature using a feedback loop. You can select a target temperature (between ambient temperature and 50℃), and the automation will vary the onboard heater to maintain that temperature in the vial. At room temperature, the Pioreactor will be able to achieve up to about 43℃.","s":"Thermostat","u":"/user-guide/temperature-automations","h":"#thermostat","p":761},{"i":766,"t":"This automation is the simplest automation: do not apply any external heating. Reading and logging of temperature will still occur.","s":"Only record temperature","u":"/user-guide/temperature-automations","h":"#only-record-temperature","p":761},{"i":769,"t":"If your Pioreactor stops being responsive (and was previously working), For Raspberry Pi 3A model, is the Pi's green LED constantly on? there should be a short, perhaps caused by damage. Power off, and disconnect the heater PCB's flat-flex cable from the HAT (unlock, and pull straight out), and power on. Is the Pioreactor responsive now? Investigate the heater PCB for damage.","s":"My Pioreactor isn't responsive anymore","u":"/user-guide/troubleshooting-hardware","h":"#my-pioreactor-isnt-responsive-anymore","p":767},{"i":771,"t":"Is your HAT directly connected to the Raspberry Pi, or are you using a long cable to connect them? Long cables tend to degrade signals, which can cause communication problems between the HAT and RPi.","s":"I see a \"Pioreactor HAT must be present\" error, but the HAT is definitely attached.","u":"/user-guide/troubleshooting-hardware","h":"#i-see-a-pioreactor-hat-must-be-present-error-but-the-hat-is-definitely-attached","p":767},{"i":773,"t":"SSH into the Pioreactor that's causing problems. Run pio version -v. Does the firmware section say 0.0? If so, run sudo systemctl restart load_rp2040.service. Try pio version -v again. Continue below if firmware still says 0.0. Disconnect the heater PCB's flat-flex cable from the HAT (unlock, and pull straight out). Try pio version -v again. If this shows something other than 0.0 beside firmware, there could be a problem with your heater PCB. Email us at help@pioreactor.com. See section above.","s":"I see \"The internal ADC/DAC is not responding. Exiting.\"","u":"/user-guide/troubleshooting-hardware","h":"#i-see-the-internal-adcdac-is-not-responding-exiting","p":767},{"i":775,"t":"Check the connection between the 3\" flat-flex-cable and the HAT, and the connection on the heater PCB. It's possible that the connector could have been pulled out by accident.","s":"I see \"Heating PCB must be attached to Pioreactor HAT\" or Heating PCB must be present to measure RPM.\" errors.","u":"/user-guide/troubleshooting-hardware","h":"#i-see-heating-pcb-must-be-attached-to-pioreactor-hat-or-heating-pcb-must-be-present-to-measure-rpm-errors","p":767},{"i":777,"t":"See our stirring troubleshooting docs.","s":"I'm having trouble with Pioreactor's stirring.","u":"/user-guide/troubleshooting-hardware","h":"#im-having-trouble-with-pioreactors-stirring","p":767},{"i":779,"t":"You can improve your Pioreactor temperature sensing capabilities with the Temperature Expansion Kit. This kit allows for faster temperature response times, more granular temperature data, and increasing the maximum culture temperature. Below are instructions on how to assemble the new hardware to your existing Pioreactor. Step 0: before you begin # What's needed to upgrade your Pioreactor with the Pioreactor Expansion Kit: Pioreactor Temperature Expansion HAT 12mm nylon stand-offs thermowell Pt1000 probe A powered-off Pioreactor. A philips head screwdriver Step 1: Expose the Pioreactor HAT # Unplug all wires and cables attached to the Pioreactor HAT. Unscrew the four 6mm nylon screws on the top faceplate. Keep these screws nearby. Remove the top assembly. Keep this nearby. Step 2: Attach the new HAT # Place the new Temperature Expansion HAT onto the existing HAT, making sure the GPIO pins are lined up. It will fit snug, and you can apply pressure onto the corners of the boards. Tip: if the HAT is still hard to put on, you can screw in the 12mm standoffs to help force the new HAT down further. Finish placing the 12mm standoffs in. Place the Pioreactor top assembly back on, and screw back in the 6mm screws. Replug in the cables and wires into the original HAT. Normally: 90° -> PD channel 2 REF -> PD channel 1 IR -> LED channel A Stirring fan -> PWM 1 (unlabelled) Heater PCB flat-flex cable -> flat-flex connector (unlabelled) Step 3: Attach the Pt1000 # Attach the Pt1000 probe's connector to the new Temperature Expansion HAT. The connector only has one orientation that works. In your Pioreactor's vial, screw in the thermowell. info Make sure when the thermowell is straight when being screwed in (that is, perpendicular to the surface of the cap). It may be a tight squeeze. To help screw it in if it's difficult: Once a few threads are inserted, rotate the thermowell back and forwards a few times slowly to provide more clearance. You can use a pair of needle-nose pliers to hold secure the female end of the thermowell (i.e. one tip is inside the thermowell, and one outside), then twist the vial cap. If not already done so, screw in the Pt1000 into the thermowell. You're done the assembly! Next is to install the software. Power up the Pioreactor. Step 4: Install the software # 1. If you install the Kit across your entire Pioreactor cluster In your PioreactorUI, you can install the temperature-expansion-kit-plugin to all Pioreactors in your cluster. 2. If you installed the Kit on individual Pioreactors SSH into the individual Pioreactor, and type pio plugins install temperature-expansion-kit-plugin Important: in either case, Confirm in your configuration that the [temperature_automation.thermostat] values have been updated for the Pioreactors with the new hardware to be (exact values may vary slightly): Kp=0.017 Ki=0.0 Kd=4.0 You can also update the following configuration: [temperature_automation.config] # 50 or 60 only, depending on geographic location. This improves the accuracy. local_ac_hz=60","s":"Adding the Temperature Expansion Upgrade kit","u":"/user-guide/temperature-expansion-kit","h":"","p":778},{"i":787,"t":"First, get the file latest .whl file here onto any computer that can SSH into the Pioreactor. To get this .whl file onto a Pioreactor, use either scp, or FileZilla. Once the .whl file is on the Pioreactor, use pio plugin install temperature_expansion_kit_plugin --source <location of whl file>","s":"I don't have internet access - how can I install the plugin?","u":"/user-guide/temperature-expansion-kit","h":"#i-dont-have-internet-access---how-can-i-install-the-plugin","p":778},{"i":789,"t":"Try unplugging and plugging the probe back into the HAT. Try restarting the Pioreactor. If the error persists, contact us at hello@pioreactor.com","s":"I'm seeing \"Record null temperature. Is the Pt1000 probe connected?\" and the wire is connected.","u":"/user-guide/temperature-expansion-kit","h":"#im-seeing-record-null-temperature-is-the-pt1000-probe-connected-and-the-wire-is-connected","p":778},{"i":792,"t":"It is possible that your mDNS is being blocked or restricted. If possible, log into your router and enable settings that allow \"multicast\", or \"mDNS\", or \"IGMP proxing\". If you are using a the builtin local access point, this solution is not the correct one. Also, if you are able to provide a permanent IPv4 address to your leader, you can get a significant performance boost by setting the configuration some config parameters to the IPv4 address. [cluster.topology] # below is an example, your IPv4 may differ: leader_address=192.168.0.3 [mqtt] broker_address=192.168.0.3","s":"My Pioreactor activities start very slowly from the UI","u":"/user-guide/troubleshooting-networks","h":"#my-pioreactor-activities-start-very-slowly-from-the-ui","p":790},{"i":794,"t":"See our troubleshooting documentation here.","s":"I'm having trouble with the local access point","u":"/user-guide/troubleshooting-networks","h":"#im-having-trouble-with-the-local-access-point","p":790},{"i":796,"t":"Brown-outs and restarts​ If you find that your Pioreactor is halting jobs (eg: the UI says lost and stirring/motors have stopped), or you find that your Pioreactor is restarting itself often, this could be due to brown-outs. Brown-outs are when your power supply is momentarily reduced to the point that the Raspberry Pi shuts down. When the power comes back up, the Raspberry Pi will start up again. This is most likely caused by: An inadequate power supply unit (PSU). You need to use a proper PSU (5V, at least 2.5 Amps), and certainly not a phone charger. We like the Raspberry Pi's official PSU. If you are running a lot of power: high temperature, stirring, pumping often, additional LEDs (or some combination) and you are experiencing brown-outs, we suggest adding an external power supply for the PWM outputs. You can view the PWM's voltage for a Pioreactor under Manage -> System -> Voltage on PWM rail. This should be near 5.0V. Pioreactor restarts when a PWM output is turned on​ If your Pioreactor restarts with a pump, stirring fan, etc. turns out, it's possible there is a short in the connectors. Email us at help@pioreactor.com","s":"Power and restarts","u":"/user-guide/troubleshooting-power","h":"","p":795},{"i":799,"t":"Likely the fan's magnets are striking the 4mm screws above it. See this section if so.","s":"Stirring is making a grinding noise.","u":"/user-guide/troubleshooting-stirring","h":"#stirring-is-making-a-grinding-noise","p":797},{"i":801,"t":"First, with the stirring activity running, carefully examine if the fan below is spinning. If the fan is not spinning, Check to confirm that the fan's cable is in the right PMW channel. You can find the right PWM channel to use in the config.ini, under [PWM] (also check that it is not overwritten in the unit specific config.ini) Does the fan start to spin momentarily, but then stop? You may need to increase the target RPM in the UI. The lower limit of RPM is around 125. Target RPMs below 125 have a tendency to stall. Alternatively, increase the initial_duty_cycle by 10 units or so and try again. for Pioreactor 20ml 1.0: Visually inspect the top of the fan from the side. If you rotate the fan with a pen, is it touching (or nearly touching) the screws above it (see image below)? See this section if so. for Pioreactor 20ml 1.1: you may need to increase the distance between the fan and the vial holder. You can unscrew the M3 30mm screws slightly to increase the distance. Very gently wiggle the connection between the stirring wires and the HAT - does the fan start? It may be a bad connection. Contact us at support@pioreactor.com The fan may be damaged. Contact us at support@pioreactor.com If the fan is spinning: This issue may occur if the fan is positioned too far from the RPM sensors on the heater PCB above it. There should be no-to-very-little visible metal from the screw at the interface between the vial holder and the top faceplate's arms. See image below. Try pushing the fan only slightly higher up using a pen, pencil or thin rod. Avoid moving the fan too high up and hitting the vial holder's screws. Try moderately tightening the screws on the bottom of the top faceplate. Try lowering the initial_duty_cycle in the config.ini to a value like ~20. Are the two magnets still present on the fan? Visually inspect from the side, or unscrew the top faceplate from the vial holder to see better. The heater PCB may be damaged. Contact us at support@pioreactor.com. You can turn off the feedback loop by setting use_rpm=0 in the [stirring] section of your configuration. Set the initial_duty_cycle to some appropriate value (20 to 40), as well.","s":"UI is reporting \"Stirring RPM is 0\", or stirring self-test failed.","u":"/user-guide/troubleshooting-stirring","h":"#ui-is-reporting-stirring-rpm-is-0-or-stirring-self-test-failed","p":797},{"i":803,"t":"Detach the top faceplate. Under the faceplate, slightly unscrew each of the four metal screws. This action will create more space between the magnets and the plastic screws.","s":"The magnets rub against the plastic screws above them, causing the stirring performance to be degraded / stop.","u":"/user-guide/troubleshooting-stirring","h":"#the-magnets-rub-against-the-plastic-screws-above-them-causing-the-stirring-performance-to-be-degraded--stop","p":797},{"i":805,"t":"Check that the vial is pushed down all the way. Try moving the fan closer to the vial holder by gently tightening the screws on the bottom of the top faceplate. The liquid in the vial may be too viscous for the mixing to work.","s":"Stir bar is not spinning","u":"/user-guide/troubleshooting-stirring","h":"#stir-bar-is-not-spinning","p":797},{"i":807,"t":"Consider decreasing the value of Kp in the section stirring.pid in the config.ini by 50%. Are you trying to target a very low RPM? The lower limit of RPM is around 125. Target RPMs below 125 have a tendency to stall. Try performing a stirring calibration.","s":"Stirring is not able to keep a steady RPM","u":"/user-guide/troubleshooting-stirring","h":"#stirring-is-not-able-to-keep-a-steady-rpm","p":797},{"i":809,"t":"Consider reducing your target RPM. Check if the vial is pushed all the way down. From the side profile, check that no metal from the screws is showing ⇒ the vial is straight vertically. Try another stir bar design, like a cross shape.","s":"My stir bar keeps skipping. How can I reduce that?","u":"/user-guide/troubleshooting-stirring","h":"#my-stir-bar-keeps-skipping-how-can-i-reduce-that","p":797},{"i":811,"t":"This is likely caused by a short circuit in the fan's cable assembly. Remove the fan's power cable, and remove the plastic housing by applying pressure on the exposed metal tabs and gently pulling the wires out. Check for any stray wire strands and remove them. Carefully put the plastic housing back on until it clicks (red wire should be positioned closer to the GPIO pins), and try again.","s":"Raspberry Pi shuts off or restarts when stirring is turned on","u":"/user-guide/troubleshooting-stirring","h":"#raspberry-pi-shuts-off-or-restarts-when-stirring-is-turned-on","p":797},{"i":814,"t":"In your browser's address bar, add the http:// infront of the url, like so: http://pioreactor.local. The UI is hosted on http, not http_s_. Check if you are accessing http ://pioreactor.local, and not https ://pioreactor.local. Try accessing using the url http://<the permanent name of your Pioreactor aka hostname>.local If you know your Raspberry Pi's IP, try http://<IP address of your Raspberry Pi>. Here's information to determine the IP address Errors during installation: When pressing the button on the HAT, does the blue LED show up? If not, installation may have failed. See notes here. In your Raspberry Pi Imager settings, confirm that you clicked \"Set username and password\", and used the username pioreactor. If not, try reinstalling the image. Are you on an older Windows machine? You may need to install a DNS service, but also see workarounds here. Try SSHing in and restarting the webserver: sudo systemctl restart lighttpd.service && sudo systemctl status lighttpd.service.","s":"I'm not able to access http://pioreactor.local","u":"/user-guide/troubleshooting-ui","h":"#im-not-able-to-access-httppioreactorlocal","p":812},{"i":816,"t":"This error occurs because your UI can't connect to an internal system, MQTT, that is used for displaying data and actions. Likely you also weren't able to access the UI with http://pioreactor.local, but had to use an IP address as the url. To fix this: Navigate to the Configuration page in the side bar. Find the [mqtt] section, and change the broker_address configuration to your Pioreactor's IP. Ex: [mqtt] broker_address=192.168.0.10 Your IP may be different than the one above. Hit Save. Power-cycle the Pioreactor by rebooting it from the Inventory page. If you are using a remote access service, like ngrok or tailscale​ Likely you didn't fill out the ws parameter in the configuration correctly. See the remote access instructions again.","s":"I see \"Failed to connect to MQTT. ...\" in a pop-up - what can I do?","u":"/user-guide/troubleshooting-ui","h":"#i-see-failed-to-connect-to-mqtt--in-a-pop-up---what-can-i-do","p":812},{"i":818,"t":"Any of the following could solve your problem: Is there a green icon in the top-left of the Pioreactor card? If not, or it's grey, either the Pioreactor is powered off, or the monitor job is not running. If so, try power-cycling the Pioreactor. It's possible that the experiment has changed while the page has been left open - try refreshing the page and try again. If you had trouble accessing the UI (see question above), in your config.ini, change the leader_address field to whatever worked above, an IP for example. Possibly the web server is off. Try logging into your leader and typing sudo systemctl status lighttpd.service Do you also see a \"Failed to connect to MQTT. Is configuration for leader_address correct?\" error pop-up? If so, see question above. Try power-cycling the Pioreactor.","s":"When I click an action in the UI, I don't see any response. Or the button just spins and does nothing.","u":"/user-guide/troubleshooting-ui","h":"#when-i-click-an-action-in-the-ui-i-dont-see-any-response-or-the-button-just-spins-and-does-nothing","p":812},{"i":820,"t":"You can add your own LEDs to the Pioreactor. You might want to do this for the following reasons: Adding white LEDs (or red + blue LEDs) to turn grow algae Adding a while LED to illuminate the culture so you can easily see growth through the window Opto-genetic experiments to add LEDs to trigger expressions info You don't have to worry about your LED interfering with optical density measurements. When the OD Reading job is running, it forces all other LEDs off (setting intensity to 0%) before taking a reading.","s":"Using additional LEDs","u":"/user-guide/using-leds","h":"","p":819},{"i":823,"t":"The Pioreactor comes with a large set of functionality and behaviour to accomplish most projects. For example, continuous culturing, optical density reading, and stable temperatures are available out-of-the-box. However, the specifics and range of how people use bioreactors goes far beyond what we could ever cover. That's why Pioreactor has added a platform so that community members can make their own extensions and share them with others. We call these plugins. (Below is how to install plugins - if you are looking to create your own plugins, see here.) Installing plugins Automations installed via plugins Activities installed via plugins Uninstalling plugins Alternative: putting Python files in the the plugins folder","s":"Using community plugins","u":"/user-guide/using-community-plugins","h":"","p":822},{"i":825,"t":"From your Pioreactor's interface, the \"Plugins\" button on the left navigation bar will display all your currently installed plugins, and some recommended plugins. We also encourage you to explore our forums for more plugins created by the community. You can also use the \"Install plugin by name\" button in the top-right to install a plugin that is not featured on this page.","s":"Installing plugins","u":"/user-guide/using-community-plugins","h":"#installing-plugins","p":822},{"i":827,"t":"Some plugins add new automations to your Pioreactor. After installing, new dosing, LED, or temperature automations will be available in the list of automations available to you.","s":"Automations installed via plugins","u":"/user-guide/using-community-plugins","h":"#automations-installed-via-plugins","p":822},{"i":829,"t":"Some plugins add new activities to your Pioreactor. After installation, an activity's state and settings will show up on each Pioreactor's card. Below, we've installed the pioreactor-air-bubbler plugin: Managing on/off and settings are done just like any other job, in the Manage dialog:","s":"Activities installed via plugins","u":"/user-guide/using-community-plugins","h":"#activities-installed-via-plugins","p":822},{"i":831,"t":"You can uninstall plugins from the same page, too. These will remove the action on the Pioreactor's card, but won't delete the section in your config.ini. Also, if a SQL table was installed with the plugin, the table will not be deleted.","s":"Uninstalling plugins","u":"/user-guide/using-community-plugins","h":"#uninstalling-plugins","p":822},{"i":833,"t":"An alternative way to install a plugin is to place a Python file in the /home/pioreactor/.pioreactor/plugins directory on the Raspberry Pi. This is good for one-off scripts or plugins you are demoing or testing. See more about writing and distributing plugins.","s":"Alternative: putting Python files in the the plugins folder","u":"/user-guide/using-community-plugins","h":"#alternative-putting-python-files-in-the-the-plugins-folder","p":822},{"i":835,"t":"The Pioreactor HAT comes with a connector for the StemmaQT / Qwiic connector that can be used to attach additional hardware for your Pioreactor. See image below: info What is StemmaQT / Qwiic? It's simply a standardized physical connector, the JST SH, with electronic connections to 3.3V, GND and I²C. Many other hardware design companies, like Adafruit and SparkFun, implement StemmaQT / Qwiic on their boards, which expands the StemmaQT / Qwiic ecosystem.","s":"Using the StemmaQT/Qwicc connector","u":"/user-guide/using-stemma-qt","h":"","p":834},{"i":837,"t":"Suppose you are placing your Pioreactor in a CO₂ incubator, and want to record the CO₂ concentration of the incubator. The incubator does monitor the CO₂ concentration, but generally this isn't accessible to other tools. What you can do is purchase an external CO₂ sensor with StemmaQT / Qwiic connectors, like the SCD-40, and attach it to your Pioreactor. The Pioreactor can now read from the CO₂ sensor, and build logging, event-loops, plotting, etc. around the measurements. To read from the sensor, a plugin may be available for it, or you can write a simple Python script like so: note To run the script, you'll first need to install the Python library: sudo pip3 install adafruit-circuitpython-scd4x import sleep import board import adafruit_scd4x from pioreactor.pubsub import publish from pioreactor.whoami import get_unit_name, get_latest_experiment_name i2c = board.I2C() scd4x = adafruit_scd4x.SCD4X(i2c) exp = get_latest_experiment_name() unit = get_unit_name() scd4x.start_periodic_measurement() while True: if scd4x.data_ready: print(\"CO2: %d ppm\" % scd4x.CO2) publish(f\"pioreactor/{unit}/{exp}/scd4x/co2\", scd4x.CO2, retain=True) print(\"Temperature: %0.1f *C\" % scd4x.temperature) publish(f\"pioreactor/{unit}/{exp}/scd4x/temperature\", scd4x.temperature, retain=True) print(\"Humidity: %0.1f %%\" % scd4x.relative_humidity) publish(f\"pioreactor/{unit}/{exp}/scd4x/relative_humidity\", scd4x.relative_humidity, retain=True) print() time.sleep(1) Running this on your Pioreactor will publish the data to MQTT, and thus be available to any other bioreactor job. You could also turn this into a background job to make it even easier to use!","s":"Example","u":"/user-guide/using-stemma-qt","h":"#example","p":834},{"i":844,"t":"We publish new software occasionally that fixes bugs, adds new features, and improves performance. You can update your Pioreactor(s) to the latest software from the UI, or from the command line. We highly recommend keeping your Pioreactor software up to date!","s":"Updating the Pioreactor software","u":"/user-guide/updating-software","h":"","p":843},{"i":846,"t":"info To use this update method, you Raspberry Pi must be able to access the internet. Using a local access point, see method 2 below. When a new software version is released by our team, you will see a red \"badge\" in your UI's sidebar: Upon visiting the Updates page, you can see what version you have installed, and the latest version published by us. You can also read the changelog to see what improvements we've made in the latest releases. If you'd like to update, click on the \"Update to next release\" button. Updating software doesn't interrupt experiments or activities, but we suggest waiting until between experiments to update. Updating from the UI will update all the Pioreactors in your cluster. info The updating process will update to the next release, after your current version. So if your current version is 23.4.1, and there are two more recent releases, say 23.5.1 and 23.6.1, then the update process will update to 23.5.1. You can run the update process again to update to 23.6.1. We do this so that you will get changes folded in from each release we make. Installing previous versions or development versions​ You can install the bleeding-edge software from this page as well. Just select the development build in the drop down. Warning: this version may be unstable (and fun!) Similarly, from the command line, you can install specific versions. See pio update app --help for more.","s":"Method 1: Updating over the internet","u":"/user-guide/updating-software","h":"#method-1-updating-over-the-internet","p":843},{"i":848,"t":"Each time we release a new Pioreactor version, we create a bundle of the required files as a zip file. This zip file can be uploaded to your Pioreactor cluster via the UI. On the Releases page, download the release_xx.xx.xx.zip file for the version you want onto a computer with access to the Pioreactor web UI. In the web UI, visit Updates. In the drop down in the top right, select \"Update from zip file\". Select the zip file from step 1. Click update. Your browser does not support the video tag.","s":"Method 2: Update using a zip file and the UI","u":"/user-guide/updating-software","h":"#method-2-update-using-a-zip-file-and-the-ui","p":843},{"i":850,"t":"On the Releases page, download the release_xx.xx.xx.zip file for the version you want. We need a software tool up upload this release to the Pioreactor. You can use scp on the command line: scp <path to release archive> pioreactor@<leader hostname>.local:/home/pioreactor Skip to 8. below. or a tool like FileZilla. We'll continue with FileZilla below. Download and open FileZilla. Connect to the Pioreactor's local-access-point, pioreactor. Enter the following credentials in the top-right: host: pioreactor.local (or, your <leader hostname>.local or its IP address) username: pioreactor password: raspberry port: 22 Click Quickconnect. You should successfully connect to your Pioreactor's Raspberry Pi (and may need to accept a security pop-up). On the left-hand side is your computer's file system. Find the release_xx.xx.xx.zip file you downloaded earlier, and double click it to upload to the Raspberry Pi (that filesystem is on the right). You should see a successfully uploaded message, and the file should be present on the right-hand side now. You can close FileZilla. SSH into your Pioreactor. Now enter: pio update app --source release_xx.xx.xx.zip (Of course, replace the xx.xx.xx with your version). This will kick off a task to update your software. To update your workers, first we will distribute the release file to all workers: pios cp release_xx.xx.xx.zip -y Finally, run the following to update the software on the workers: pios update app --source release_xx.xx.xx.zip","s":"Method 3: Update using a zip file over scp or sftp","u":"/user-guide/updating-software","h":"#method-3-update-using-a-zip-file-over-scp-or-sftp","p":843},{"i":868,"t":"You can attach up to three peristaltic pumps to your Pioreactor, typically used for: adding fresh media to the vial, removing effluent from the vial, and adding an alternative media to the vial. First decide what you want your new pump to do: add media, remove waste, or add an alternative media. Pumps that are supplied by us will have a connector that connects to the PWM outputs on the Pioreactor hat. Which PWM you connect to is determined by your PWM settings in config.ini. In our case, if we were to use the pump as a media pump, we would connect the pump to PWM channel 2. Setting up the dosing platform # The dosing platform isn't needed, but helps organize your pumps. We sell them in our shop, but it's also open source - so you can 3D print your own! Set the dosing platform on a level surface. Place your Pioreactor in the platform, as shown. Note: a Raspberry Pi B model won't fit. Attach your two pumps' wires to media and waste PWMs on the Pioreactor (your config.ini has the PWM channels these should attach to, see section above). Vertically place each pump into the platform. Note the following: Check the orientation of the pump head: the tubes should be facing out. Each pump's wire should travel up one of the grooves in the side of the holder. The pump will feel snug in the holder. Do this for both pumps. The pumps should be have some gap between them and the Pioreactor, facing opposite directions, and not interfering with each other. Connecting the tubes # For both pumps, the tube that is closer to the Pioreactor's vial is the tube that will connect to the vial. Optional: If the pump→vial tubes seem too long, you can cut them to a preferable length. In the pictures shown, we cut the 9\" tube down to 6\". This reduces media waste and makes the platform more compact. For each pump, attach this tube to the Pioreactor's vial via the luer lock connection. You're done! Note the picture demonstrating the flow of liquid in and out of the Pioreactor's vial. caution When attaching tube ends that contain liquid to the vial, be careful of drops that might escape. We suggest taking the Pioreactor vial out of the vial holder when attaching tubes, to minimize the chance of a drop falling into the vial holder. After attaching, place back into the vial holder. tip If using your pumps for the first time, we suggest letting them run continuously for 10 minutes or so to \"loosen\" the tubing up and check for any problems. Here's how to do this: Unattach the end connected to the vial. Place both ends (source and sick) into a beaker of water, Use the Pioreactor UI to run them continuously.","s":"Viewing pump configuration in config.ini","u":"/user-guide/using-pumps","h":"#viewing-pump-configuration-in-configini","p":866},{"i":872,"t":"Read the calibration instructions for how to calibrate your pumps to move precise mL of liquid. Calibration is required for most dosing automations in the Pioreactor.","s":"Calibrating pumps","u":"/user-guide/using-pumps","h":"#calibrating-pumps","p":866},{"i":874,"t":"caution We strongly recommended you don't run peristaltic pumps continuously for hours at a time. By continuously, we mean \"always moving liquid\". The inner tubing has a lifetime and may wear out during operation, causing a leak. If you need to move liquid continuously for long periods of time, you need a different pump design.","s":"Using pumps in experiments","u":"/user-guide/using-pumps","h":"#using-pumps-in-experiments","p":866},{"i":876,"t":"To avoid contamination, pumps should be sterilized before and after use. Using heat​ You can disassemble the pump head, extract the tubing, and autoclave the tubing. (If it's your first time, make note of how the pumps are put back together) Put the tubing back in, reassemble the head, and your good to go. Using bleach and ethanol​ Create a 10% bleach dilution, or high concentration alcohol, in a container. Place the sink and source tubes of each pump you're sterilizing in the beaker. On the UI, in the Pioreactors tab, click Manage and go to the Dosing tab. Run continuously to cycle the disinfectant solution through each pump that you're using. Interrupt after sufficient cycling, at least 2 minutes. If finishing an experiment, repeat the above with water. If starting an experiment, you'll need to prime the pumps, see the next section. caution It's important to not keep harsh chemicals, like bleach, in the silicone tubing for long. Cleaning pumps should always end with flushing the tubes with water or something inert.","s":"Sterilizing the pumps before and after experiments","u":"/user-guide/using-pumps","h":"#sterilizing-the-pumps-before-and-after-experiments","p":866},{"i":878,"t":"You can attach the source of your media pump to your media bottle and \"prime\" it by running the media pump until media comes out. The sink end can be left in a bleach/ethanol container, or attached to a Pioreactor vial. Likewise, the waste pump can flushed with water, and then attached to the Pioreactor vial and waste bottle. tip Before attaching to media, waste, or vials for your experiments, you can spray the luer lock ends with ethanol. Be careful that no liquid that drips down into the Pioreactor vial holder.","s":"Preparing for experiments","u":"/user-guide/using-pumps","h":"#preparing-for-experiments","p":866},{"i":880,"t":"See documentation on how to run pumps manually from the UI.","s":"Running pumps from the web interface","u":"/user-guide/using-pumps","h":"#running-pumps-from-the-web-interface","p":866},{"i":882,"t":"pio run add_media --ml 3 or, if you wish to run continuously until interrupted (don't leave this running for hours, though). pio run add_media --continuously","s":"Running pumps from the command line","u":"/user-guide/using-pumps","h":"#running-pumps-from-the-command-line","p":866},{"i":884,"t":"Dosing automations, like turbidostats, chemostats, fed-batch, etc., are available to run once your pumps are attached and calibrated. These automations will programmatically add and remove media. Read more about automations.","s":"Programmatically run pumps using automations","u":"/user-guide/using-pumps","h":"#programmatically-run-pumps-using-automations","p":866},{"i":895,"t":"Writing your own custom automations is easy, but requires some knowledge of Python. If you're interested, see our documentation here.","s":"Writing your own 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guides","u":"/user-guide/getting-started","h":"","p":553},{"i":567,"t":"Software installation","u":"/user-guide/getting-started","h":"","p":553},{"i":572,"t":"Pioreactor Unit Activity Data","u":"/user-guide/export-data","h":"#pioreactor-unit-activity-data","p":570},{"i":576,"t":"1. SSHing into your Raspberry Pi","u":"/user-guide/intro-python-scripting","h":"#1-sshing-into-your-raspberry-pi","p":574},{"i":578,"t":"2. Writing our first script.","u":"/user-guide/intro-python-scripting","h":"#2-writing-our-first-script","p":574},{"i":580,"t":"3. Running our Python script","u":"/user-guide/intro-python-scripting","h":"#3-running-our-python-script","p":574},{"i":582,"t":"4. Extending our script: more jobs, changing RPM, and adding lights.","u":"/user-guide/intro-python-scripting","h":"#4-extending-our-script-more-jobs-changing-rpm-and-adding-lights","p":574},{"i":584,"t":"5. Adding an automation","u":"/user-guide/intro-python-scripting","h":"#5-adding-an-automation","p":574},{"i":586,"t":"Conclusion","u":"/user-guide/intro-python-scripting","h":"#conclusion","p":574},{"i":590,"t":"Skip first run?","u":"/user-guide/intro-to-automations","h":"#skip-first-run","p":588},{"i":594,"t":"Need to assemble your Pioreactor?","u":"/user-guide/introduction","h":"#need-to-assemble-your-pioreactor","p":592},{"i":596,"t":"Help with your first experiment?","u":"/user-guide/introduction","h":"#help-with-your-first-experiment","p":592},{"i":598,"t":"Developers","u":"/user-guide/introduction","h":"#developers","p":592},{"i":600,"t":"Looking for further help?","u":"/user-guide/introduction","h":"#looking-for-further-help","p":592},{"i":604,"t":"Silent","u":"/user-guide/led-automations","h":"#silent","p":602},{"i":606,"t":"Light/Dark cycle","u":"/user-guide/led-automations","h":"#lightdark-cycle","p":602},{"i":609,"t":"Dosing","u":"/user-guide/manual-dosing-leds","h":"#dosing","p":608},{"i":611,"t":"LEDs","u":"/user-guide/manual-dosing-leds","h":"#leds","p":608},{"i":615,"t":"Event logs","u":"/user-guide/monitor-experiment","h":"#event-logs","p":613},{"i":617,"t":"Changing settings","u":"/user-guide/monitor-experiment","h":"#changing-settings","p":613},{"i":619,"t":"Identifying Pioreactors in your cluster","u":"/user-guide/monitor-experiment","h":"#identifying-pioreactors-in-your-cluster","p":613},{"i":621,"t":"Troubleshooting","u":"/user-guide/monitor-experiment","h":"#troubleshooting","p":613},{"i":623,"t":"Gradual increase in noise in OD","u":"/user-guide/monitor-experiment","h":"#gradual-increase-in-noise-in-od","p":613},{"i":625,"t":"Initial noise in OD","u":"/user-guide/monitor-experiment","h":"#initial-noise-in-od","p":613},{"i":627,"t":"Random spikes in OD","u":"/user-guide/monitor-experiment","h":"#random-spikes-in-od","p":613},{"i":629,"t":"Temperature fluctuations","u":"/user-guide/monitor-experiment","h":"#temperature-fluctuations","p":613},{"i":631,"t":"Looking for further help?","u":"/user-guide/monitor-experiment","h":"#looking-for-further-help","p":613},{"i":635,"t":"Step 1: Necessary tools  #","u":"/user-guide/hardware-setup-intro","h":"","p":633},{"i":636,"t":"Step 2: Use all the information available to you  #","u":"/user-guide/hardware-setup-intro","h":"","p":633},{"i":637,"t":"Step 3: Electronics protection  #","u":"/user-guide/hardware-setup-intro","h":"","p":633},{"i":638,"t":"Step 4: We are here for you!  #","u":"/user-guide/hardware-setup-intro","h":"","p":633},{"i":641,"t":"General networking tools","u":"/user-guide/networking","h":"#general-networking-tools","p":639},{"i":643,"t":"Connecting to a wifi network using nmcli","u":"/user-guide/networking","h":"#connecting-to-a-wifi-network-using-nmcli","p":639},{"i":645,"t":"Connecting to multiple networks","u":"/user-guide/networking","h":"#connecting-to-multiple-networks","p":639},{"i":647,"t":"Starting the Pioreactor local access point using nmcli","u":"/user-guide/networking","h":"#starting-the-pioreactor-local-access-point-using-nmcli","p":639},{"i":649,"t":"Changing web UI port from 80 to something else","u":"/user-guide/networking","h":"#changing-web-ui-port-from-80-to-something-else","p":639},{"i":651,"t":"Connecting to eduroam","u":"/user-guide/networking","h":"#connecting-to-eduroam","p":639},{"i":656,"t":"Background on optical density","u":"/user-guide/od-normal-growth-rate","h":"#background-on-optical-density","p":655},{"i":658,"t":"Normalization","u":"/user-guide/od-normal-growth-rate","h":"#normalization","p":655},{"i":660,"t":"Blanking","u":"/user-guide/od-normal-growth-rate","h":"#blanking","p":655},{"i":662,"t":"Growth rate","u":"/user-guide/od-normal-growth-rate","h":"#growth-rate","p":655},{"i":665,"t":"Step 1: Optic cables assembly  #","u":"/user-guide/optics-assembly","h":"","p":664},{"i":666,"t":"Step 2: Inserting the bulbs into the vial holder  #","u":"/user-guide/optics-assembly","h":"","p":664},{"i":667,"t":"Step 3: Add the rest of the LED caps  #","u":"/user-guide/optics-assembly","h":"","p":664},{"i":668,"t":"Step 4: Add the window covering (optional)  #","u":"/user-guide/optics-assembly","h":"","p":664},{"i":669,"t":"Step 4: Your done!  #","u":"/user-guide/optics-assembly","h":"","p":664},{"i":672,"t":"Pinch valve options","u":"/user-guide/pinch-valves","h":"#pinch-valve-options","p":670},{"i":674,"t":"Software","u":"/user-guide/pinch-valves","h":"#software","p":670},{"i":676,"t":"Recommended pinch valves","u":"/user-guide/pinch-valves","h":"#recommended-pinch-valves","p":670},{"i":680,"t":"Starting a local access point","u":"/user-guide/local-access-point","h":"#starting-a-local-access-point","p":678},{"i":682,"t":"Access the local access point","u":"/user-guide/local-access-point","h":"#access-the-local-access-point","p":678},{"i":684,"t":"Connecting more Pioreactors to your local access point","u":"/user-guide/local-access-point","h":"#connecting-more-pioreactors-to-your-local-access-point","p":678},{"i":686,"t":"Adding internet access to your local access point","u":"/user-guide/local-access-point","h":"#adding-internet-access-to-your-local-access-point","p":678},{"i":688,"t":"Turning off a local access point","u":"/user-guide/local-access-point","h":"#turning-off-a-local-access-point","p":678},{"i":690,"t":"Changing SSID name or password for your local access point","u":"/user-guide/local-access-point","h":"#changing-ssid-name-or-password-for-your-local-access-point","p":678},{"i":692,"t":"Troubleshooting","u":"/user-guide/local-access-point","h":"#troubleshooting","p":678},{"i":693,"t":"My computer can't connect to the local-access-point","u":"/user-guide/local-access-point","h":"#my-computer-cant-connect-to-the-local-access-point","p":678},{"i":695,"t":"I'm on the network, but can't load the Pioreactor UI at http://pioreactor.local","u":"/user-guide/local-access-point","h":"#im-on-the-network-but-cant-load-the-pioreactor-ui-at-httppioreactorlocal","p":678},{"i":697,"t":"I can't connect a worker to my local access point","u":"/user-guide/local-access-point","h":"#i-cant-connect-a-worker-to-my-local-access-point","p":678},{"i":699,"t":"I'm pretty sure I'm at the limit of ~4-8 clients on my access point - what can I do?","u":"/user-guide/local-access-point","h":"#im-pretty-sure-im-at-the-limit-of-4-8-clients-on-my-access-point---what-can-i-do","p":678},{"i":702,"t":"Step 1: Necessary parts  #","u":"/user-guide/putting-it-together","h":"","p":701},{"i":703,"t":"Step 2: Securing the vial holder  #","u":"/user-guide/putting-it-together","h":"","p":701},{"i":704,"t":"Step 3: Attaching the vial holder to the HAT  #","u":"/user-guide/putting-it-together","h":"","p":701},{"i":705,"t":"Step 4: Connecting heater and stirring to the HAT  #","u":"/user-guide/putting-it-together","h":"","p":701},{"i":707,"t":"1. Preparing the vial","u":"/user-guide/prepare-vial-for-cultures","h":"#1-preparing-the-vial","p":706},{"i":709,"t":"2. Preparing media","u":"/user-guide/prepare-vial-for-cultures","h":"#2-preparing-media","p":706},{"i":711,"t":"3. Sterilization","u":"/user-guide/prepare-vial-for-cultures","h":"#3-sterilization","p":706},{"i":713,"t":"4. Inoculation","u":"/user-guide/prepare-vial-for-cultures","h":"#4-inoculation","p":706},{"i":715,"t":"5. Adjusting tube lengths (Optional)","u":"/user-guide/prepare-vial-for-cultures","h":"#5-adjusting-tube-lengths-optional","p":706},{"i":717,"t":"6. Handling the glass","u":"/user-guide/prepare-vial-for-cultures","h":"#6-handling-the-glass","p":706},{"i":719,"t":"7. Positioning glassware in the Pioreactor sleeve","u":"/user-guide/prepare-vial-for-cultures","h":"#7-positioning-glassware-in-the-pioreactor-sleeve","p":706},{"i":721,"t":"Extra","u":"/user-guide/prepare-vial-for-cultures","h":"#extra","p":706},{"i":724,"t":"Introduction to remote access","u":"/user-guide/remote-access","h":"#introduction-to-remote-access","p":723},{"i":726,"t":"Security","u":"/user-guide/remote-access","h":"#security","p":723},{"i":729,"t":"Step 1: Necessary parts  #","u":"/user-guide/rpi-hat-assembly","h":"","p":728},{"i":730,"t":"Step 2: Assemble the bottom faceplate  #","u":"/user-guide/rpi-hat-assembly","h":"","p":728},{"i":731,"t":"Step 3: Placing the HAT PCB on top  #","u":"/user-guide/rpi-hat-assembly","h":"","p":728},{"i":732,"t":"Step 2: Assemble the bottom faceplate  #","u":"/user-guide/rpi-hat-assembly","h":"","p":728},{"i":733,"t":"Step 3: Placing the HAT PCB ontop  #","u":"/user-guide/rpi-hat-assembly","h":"","p":728},{"i":736,"t":"How to run the self-test routine","u":"/user-guide/running-self-test","h":"#how-to-run-the-self-test-routine","p":734},{"i":738,"t":"Explanation of each test","u":"/user-guide/running-self-test","h":"#explanation-of-each-test","p":734},{"i":742,"t":"Thermostat","u":"/user-guide/temperature-automations","h":"#thermostat","p":740},{"i":744,"t":"Only record temperature","u":"/user-guide/temperature-automations","h":"#only-record-temperature","p":740},{"i":747,"t":"Before you begin","u":"/user-guide/software-set-up","h":"#before-you-begin","p":746},{"i":749,"t":"Setting up your Raspberry Pi","u":"/user-guide/software-set-up","h":"#setting-up-your-raspberry-pi","p":746},{"i":751,"t":"Adding additional workers to your cluster","u":"/user-guide/software-set-up","h":"#adding-additional-workers-to-your-cluster","p":746},{"i":753,"t":"Troubleshooting","u":"/user-guide/software-set-up","h":"#troubleshooting","p":746},{"i":756,"t":"Creating an experiment","u":"/user-guide/set-up-an-experiment","h":"#creating-an-experiment","p":755},{"i":758,"t":"Assigning Pioreactors to your experiment","u":"/user-guide/set-up-an-experiment","h":"#assigning-pioreactors-to-your-experiment","p":755},{"i":760,"t":"(Optional) Blanking","u":"/user-guide/set-up-an-experiment","h":"#optional-blanking","p":755},{"i":762,"t":"How to record a blank  #","u":"/user-guide/set-up-an-experiment","h":"","p":755},{"i":763,"t":"Start activities from the Pioreactors page","u":"/user-guide/set-up-an-experiment","h":"#start-activities-from-the-pioreactors-page","p":755},{"i":765,"t":"Changing settings","u":"/user-guide/set-up-an-experiment","h":"#changing-settings","p":755},{"i":770,"t":"My Pioreactor isn't responsive anymore","u":"/user-guide/troubleshooting-hardware","h":"#my-pioreactor-isnt-responsive-anymore","p":769},{"i":772,"t":"I see a \"Pioreactor HAT must be present\" error, but the HAT is definitely attached.","u":"/user-guide/troubleshooting-hardware","h":"#i-see-a-pioreactor-hat-must-be-present-error-but-the-hat-is-definitely-attached","p":769},{"i":774,"t":"I see \"The internal ADC/DAC is not responding. Exiting.\"","u":"/user-guide/troubleshooting-hardware","h":"#i-see-the-internal-adcdac-is-not-responding-exiting","p":769},{"i":776,"t":"I see \"Heating PCB must be attached to Pioreactor HAT\" or Heating PCB must be present to measure RPM.\" errors.","u":"/user-guide/troubleshooting-hardware","h":"#i-see-heating-pcb-must-be-attached-to-pioreactor-hat-or-heating-pcb-must-be-present-to-measure-rpm-errors","p":769},{"i":778,"t":"I'm having trouble with Pioreactor's stirring.","u":"/user-guide/troubleshooting-hardware","h":"#im-having-trouble-with-pioreactors-stirring","p":769},{"i":782,"t":"Step 0: before you begin  #","u":"/user-guide/temperature-expansion-kit","h":"","p":780},{"i":783,"t":"Step 1: Expose the Pioreactor HAT  #","u":"/user-guide/temperature-expansion-kit","h":"","p":780},{"i":784,"t":"Step 2: Attach the new HAT  #","u":"/user-guide/temperature-expansion-kit","h":"","p":780},{"i":785,"t":"Step 3: Attach the Pt1000  #","u":"/user-guide/temperature-expansion-kit","h":"","p":780},{"i":786,"t":"Step 4: Install the software  #","u":"/user-guide/temperature-expansion-kit","h":"","p":780},{"i":787,"t":"Troubleshooting","u":"/user-guide/temperature-expansion-kit","h":"#troubleshooting","p":780},{"i":788,"t":"I don't have internet access - how can I install the plugin?","u":"/user-guide/temperature-expansion-kit","h":"#i-dont-have-internet-access---how-can-i-install-the-plugin","p":780},{"i":790,"t":"I'm seeing \"Record null temperature. Is the Pt1000 probe connected?\" and the wire is connected.","u":"/user-guide/temperature-expansion-kit","h":"#im-seeing-record-null-temperature-is-the-pt1000-probe-connected-and-the-wire-is-connected","p":780},{"i":793,"t":"My Pioreactor activities start very slowly from the UI","u":"/user-guide/troubleshooting-networks","h":"#my-pioreactor-activities-start-very-slowly-from-the-ui","p":792},{"i":795,"t":"I'm having trouble with the local access point","u":"/user-guide/troubleshooting-networks","h":"#im-having-trouble-with-the-local-access-point","p":792},{"i":798,"t":"Stirring is making a grinding noise.","u":"/user-guide/troubleshooting-stirring","h":"#stirring-is-making-a-grinding-noise","p":797},{"i":800,"t":"UI is reporting \"Stirring RPM is 0\", or stirring self-test failed.","u":"/user-guide/troubleshooting-stirring","h":"#ui-is-reporting-stirring-rpm-is-0-or-stirring-self-test-failed","p":797},{"i":802,"t":"The magnets rub against the plastic screws above them, causing the stirring performance to be degraded / stop.","u":"/user-guide/troubleshooting-stirring","h":"#the-magnets-rub-against-the-plastic-screws-above-them-causing-the-stirring-performance-to-be-degraded--stop","p":797},{"i":804,"t":"Stir bar is not spinning","u":"/user-guide/troubleshooting-stirring","h":"#stir-bar-is-not-spinning","p":797},{"i":806,"t":"Stirring is not able to keep a steady RPM","u":"/user-guide/troubleshooting-stirring","h":"#stirring-is-not-able-to-keep-a-steady-rpm","p":797},{"i":808,"t":"My stir bar keeps skipping. How can I reduce that?","u":"/user-guide/troubleshooting-stirring","h":"#my-stir-bar-keeps-skipping-how-can-i-reduce-that","p":797},{"i":810,"t":"Raspberry Pi shuts off or restarts when stirring is turned on","u":"/user-guide/troubleshooting-stirring","h":"#raspberry-pi-shuts-off-or-restarts-when-stirring-is-turned-on","p":797},{"i":813,"t":"I'm not able to access http://pioreactor.local","u":"/user-guide/troubleshooting-ui","h":"#im-not-able-to-access-httppioreactorlocal","p":812},{"i":815,"t":"I see \"Failed to connect to MQTT. ...\" in a pop-up - what can I do?","u":"/user-guide/troubleshooting-ui","h":"#i-see-failed-to-connect-to-mqtt--in-a-pop-up---what-can-i-do","p":812},{"i":817,"t":"When I click an action in the UI, I don't see any response. Or the button just spins and does nothing.","u":"/user-guide/troubleshooting-ui","h":"#when-i-click-an-action-in-the-ui-i-dont-see-any-response-or-the-button-just-spins-and-does-nothing","p":812},{"i":823,"t":"Method 1: Updating over the internet","u":"/user-guide/updating-software","h":"#method-1-updating-over-the-internet","p":821},{"i":825,"t":"Method 2: Update using a zip file and the UI","u":"/user-guide/updating-software","h":"#method-2-update-using-a-zip-file-and-the-ui","p":821},{"i":827,"t":"Method 3: Update using a zip file over scp or sftp","u":"/user-guide/updating-software","h":"#method-3-update-using-a-zip-file-over-scp-or-sftp","p":821},{"i":831,"t":"Adding LEDs to your Pioreactor  #","u":"/user-guide/using-leds","h":"","p":829},{"i":834,"t":"Installing plugins","u":"/user-guide/using-community-plugins","h":"#installing-plugins","p":832},{"i":836,"t":"Automations installed via plugins","u":"/user-guide/using-community-plugins","h":"#automations-installed-via-plugins","p":832},{"i":838,"t":"Activities installed via plugins","u":"/user-guide/using-community-plugins","h":"#activities-installed-via-plugins","p":832},{"i":840,"t":"Uninstalling plugins","u":"/user-guide/using-community-plugins","h":"#uninstalling-plugins","p":832},{"i":842,"t":"Alternative: putting Python files in the the plugins folder","u":"/user-guide/using-community-plugins","h":"#alternative-putting-python-files-in-the-the-plugins-folder","p":832},{"i":845,"t":"Viewing pump configuration in config.ini","u":"/user-guide/using-pumps","h":"#viewing-pump-configuration-in-configini","p":844},{"i":847,"t":"Setting up the dosing platform  #","u":"/user-guide/using-pumps","h":"","p":844},{"i":848,"t":"Connecting the tubes  #","u":"/user-guide/using-pumps","h":"","p":844},{"i":849,"t":"Calibrating pumps","u":"/user-guide/using-pumps","h":"#calibrating-pumps","p":844},{"i":851,"t":"Using pumps in experiments","u":"/user-guide/using-pumps","h":"#using-pumps-in-experiments","p":844},{"i":853,"t":"Sterilizing the pumps before and after experiments","u":"/user-guide/using-pumps","h":"#sterilizing-the-pumps-before-and-after-experiments","p":844},{"i":855,"t":"Preparing for experiments","u":"/user-guide/using-pumps","h":"#preparing-for-experiments","p":844},{"i":857,"t":"Running pumps from the web interface","u":"/user-guide/using-pumps","h":"#running-pumps-from-the-web-interface","p":844},{"i":859,"t":"Running pumps from the command line","u":"/user-guide/using-pumps","h":"#running-pumps-from-the-command-line","p":844},{"i":861,"t":"Programmatically run pumps using automations","u":"/user-guide/using-pumps","h":"#programmatically-run-pumps-using-automations","p":844},{"i":864,"t":"Step 1: Inserting the O-rings  #","u":"/user-guide/v11-upgrade-building-vial-holder","h":"","p":863},{"i":865,"t":"Step 2: Attach the window cover  #","u":"/user-guide/v11-upgrade-building-vial-holder","h":"","p":863},{"i":866,"t":"Step 3: Place and secure the heater PCB  #","u":"/user-guide/v11-upgrade-building-vial-holder","h":"","p":863},{"i":867,"t":"Step 4: Complete the vial holder  #","u":"/user-guide/v11-upgrade-building-vial-holder","h":"","p":863},{"i":870,"t":"Example","u":"/user-guide/using-stemma-qt","h":"#example","p":868},{"i":873,"t":"Step 1: Upgrade parts  #","u":"/user-guide/v11-upgrade-hardware-setup","h":"","p":872},{"i":874,"t":"Step 2: Use all the information available to you  #","u":"/user-guide/v11-upgrade-hardware-setup","h":"","p":872},{"i":875,"t":"Step 3: Electronics protection  #","u":"/user-guide/v11-upgrade-hardware-setup","h":"","p":872},{"i":876,"t":"Step 4: We are here for you!  #","u":"/user-guide/v11-upgrade-hardware-setup","h":"","p":872},{"i":878,"t":"Step 1: Necessary parts  #","u":"/user-guide/wetware-assembly","h":"","p":877},{"i":879,"t":"Step 2: Placing the heating pad  #","u":"/user-guide/wetware-assembly","h":"","p":877},{"i":880,"t":"Step 3: Securing the heating PCB into the vial holder  #","u":"/user-guide/wetware-assembly","h":"","p":877},{"i":882,"t":"Step 1: Unplug and disassemble the optics system  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":881},{"i":883,"t":"Step 2: Remove the top assembly from the base  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":881},{"i":884,"t":"Step 3: Remove the heater PCB from the vial holder  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":881},{"i":885,"t":"Step 4: Remove the window cover  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":881},{"i":886,"t":"Step 5: Items to be reused  #","u":"/user-guide/v11-upgrade-pioreactor-disassembly","h":"","p":881},{"i":888,"t":"Step 1: Necessary parts  #","u":"/user-guide/v11-upgrade-pioreactor-reassembly","h":"","p":887},{"i":889,"t":"Step 2: Complete the top assembly  #","u":"/user-guide/v11-upgrade-pioreactor-reassembly","h":"","p":887},{"i":890,"t":"Step 3: Button extension  #","u":"/user-guide/v11-upgrade-pioreactor-reassembly","h":"","p":887},{"i":891,"t":"Step 4: Putting it all together  #","u":"/user-guide/v11-upgrade-pioreactor-reassembly","h":"","p":887},{"i":895,"t":"Step 1: Insert optic cables into channels  #","u":"/user-guide/v11-upgrade-optics-assembly","h":"","p":894},{"i":896,"t":"Step 2: Secure bulbs into pockets  #","u":"/user-guide/v11-upgrade-optics-assembly","h":"","p":894},{"i":897,"t":"Step 3: You're done!  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Currently we don't like how much a developer has to implement (or copy and paste) to create a new calibration. We want to make it easier to design new calibrations. Ideally, all calibrations, including od_calibration and pump_calibration, should behave similarly: Interface should have the following: pio run <x>_calibration starts the calibration and saves it keyed by a unique name (see 2. for storage) pio run <x>_calibration list lists all saved calibrations, keyed by their unique name. pio run <x>_calibration display ?name? displays information about the current calibration to be used, or the calibration ?name? if provided pio run <x>_calibration change_current <name> changes the current calibration to <name> calibration. pio run <x>_calibration publish <name> publishes the calibration to the leader. On disk, all run calibrations should be stored in local persistent storage under <x>_calibrations keyed by a unique name, and the current calibration should be stored in <x>_current_calibration, with appropriate key (can use <calibration_type>) that is not the unique name, but something consistent. Note: The name cannot be current. A struct should be created / sub-classed from structs.Calibration that will encode / decode the calibration data blob. When a new calibration is created, a PUT request to /api/calibrations/ should be sent. The body is the json-encoded Calibration struct. When a new calibration is set as current (change_current), a PATCH request to /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name> should be sent. Creating a new calibration should both publish to leader and set as current. 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Fill in what to do before, and after, an OD reading takes place by implementing method action_to_do_before_od_reading and action_to_do_after_od_reading, respectively. class JustPause(BackgroundJobWithDodgingContrib): ... def action_to_do_before_od_reading(self): # example self.logger.debug(\"Pausing\") self.stop_pumping() def action_to_do_after_od_reading(self): # example self.logger.debug(\"Unpausing\") self.start_pumping() We also want some \"buffer\" time before and after an OD reading. For example, if using a bubbler, we want the bubbles to dissipate completely before taking an OD reading. We should stop bubbling early then. To set these times, add the following to your config.ini: [<job_name>] pre_delay_duration=<float> post_delay_duration=<float> enable_dodging_od=1 # 1 if you want the behaviour, 0 to disable it. The diagram of timing, actions, and OD reading, looks like the following: And you're done!","s":"Avoiding when optical density is run","u":"/developer-guide/avoiding-od","h":"","p":3},{"i":6,"t":"With custom background jobs or automations, the goal is to have it available in the web interface, so you and your users don't need to use the command line at all. We've built support for easily adding to the web interface. Based on whether your have created a background job, a script, or an automation, adding it to the UI only involves creating a yaml file and placing it in the correct directory. info You should have already added your plugin's Python code to your Pioreactor by some method presented here.","s":"Adding your plugins to the web interface","u":"/developer-guide/adding-plugins-to-ui","h":"","p":5},{"i":9,"t":"The list of activities, among other things, is sourced from either of two directories: /var/www/pioreactorui/contrib/jobs/, is the source of the \"default\" jobs /home/pioreactor/.pioreactor/plugins/ui/contrib/jobs, is a directory to put custom yaml files for jobs. Placing a new yaml file in either of these folders will populate the page with your new job. Here's an example example.yaml file: --- display_name: Name job_name: job_name_as_defined_in_Python display: true # true to display on the /Pioreactors card source: your_plugin_name description: This description is displayed with the start/stop buttons in Manage / Activities. published_settings: - key: rpm # as defined in Python unit: RPM # label: Stirring speed # human readable name description: This description is displayed with an editable field in Manage / Settings. type: numeric # one of numeric, bool, string, json default: null display: true # true to display on the /Pioreactors card - key: something_else unit: lb label: Something else description: This description is displayed with an editable switch in Manage / Settings. type: bool # one of numeric, bool, string, json default: null display: true # true to display on the /Pioreactors card Saving it to either directory above, and refreshing the page:","s":"Adding a custom background job to the list of activities","u":"/developer-guide/adding-plugins-to-ui","h":"#adding-a-custom-background-job-to-the-list-of-activities","p":5},{"i":11,"t":"Placing a new yaml file in either of the following folders will populate the UI with your new job. /var/www/pioreactorui/contrib/jobs/, is the source of the \"default\" jobs /home/pioreactor/.pioreactor/plugins/ui/contrib/jobs/, is a directory to put custom plugins. --- display_name: Example Script display: true job_name: my_script source: Example Script description: Run my custom script. published_settings: [] See more information on the structure of your script here","s":"Adding a custom Python script to the list of activities","u":"/developer-guide/adding-plugins-to-ui","h":"#adding-a-custom-python-script-to-the-list-of-activities","p":5},{"i":14,"t":"Suppose we wish to add our new automation, either installed from a package or via the plugins folder, to the drop-down list of automations users can choose from: This list is sourced from yaml files located on the leader's Raspberry Pi, in either of two directories: /var/www/pioreactorui/contrib/automations/, is the source of the our built-in automations /home/pioreactor/.pioreactor/plugins/ui/contrib/automations/{led,dosing,temperature}, is a directory to put yaml files for custom automations. Placing your yaml file in either folder above will populate the dropdown list in the UI with your new automation. Here's an example example.yaml file: --- display_name: My Automations Name # human readable name automation_name: my_automations_name # the corresponding name of the automation from the Python code. source: my_plugin_name description: Provide a meaningful description of what the automation does, when to use it, how it works... fields: - key: duration # key is the same as the keyword in the Python code. default: 30 unit: min label: Duration between events - key: target_od default: 1.5 unit: AU label: Target OD - key: volume default: 0.75 unit: mL label: Max volume - key: intensity default: 50 unit: \"%\" # note: percent signs needs to be quoted. label: Intensity of PWM If this file was saved to the folder /home/pioreactor/.pioreactor/plugins/ui/contrib/automations/dosing, we would see the following in the web interface (after refreshing): More examples of automation yaml files here.","s":"Adding a custom automation to the drop-down of automations","u":"/developer-guide/adding-plugins-to-ui","h":"#adding-a-custom-automation-to-the-drop-down-of-automations","p":5},{"i":17,"t":"If your plugin produces data (or is some novel transformation of existing data), you can also add a new chart to the Overview page. See documentation here.","s":"Adding a chart to display a new data source","u":"/developer-guide/adding-plugins-to-ui","h":"#adding-a-chart-to-display-a-new-data-source","p":5},{"i":19,"t":"If the UI isn't display the data from your yaml, you may have introduced a yaml file that is not being read correctly. Look for error logs on the Overview page. There is a 30sec cache, so it may take up to 30sec to see new changes in the UI.","s":"Troubleshooting","u":"/developer-guide/adding-plugins-to-ui","h":"#troubleshooting","p":5},{"i":22,"t":"You can add custom charts to the UI. Below is an example of adding a chart that displays historical and real-time CO2 sensor data.","s":"Adding basic time series charts","u":"/developer-guide/chart-to-ui","h":"","p":21},{"i":24,"t":"Create a yaml file with the following fields, and place it in /home/pioreactor/.pioreactor/plugins/ui/contrib/charts. (Plugins can put the yaml file under ui/contrib/charts in there project folder - it will be added upon installation.) chart_key: a unique identifier for the chart being added, string. data_source: the SQL table to read historical data from. The data source must have a timestamp, pioreactor_unit, and experiment column, along with a numeric column to plot (see below), string. data_source_column: the column in data_source to read and display, string. title: title on the chart, string y_axis_label: the y-axis label, string fixed_decimals: How many decimals to display, integer. mqtt_topic: a truncated MQTT topic to read live data from - stripped of the pioreactor/<unit>/<experiment> part. Ex: co2_readings/ppm if the entire MQTT topic is pioreactor/<unit>/<experiment>/co2_readings/ppm, string. payload_key: (Optional) If the MQTT topic is json blobs, use the payload_key to retrieve the data from the blob, string. interpolation: (Optional) the interpolation to use between points, default is stepAfter, string. y_axis_domain: (Optional) specify a starting y-axis domain. Must be an array, like [0.0, 0.5]. y_transformation: (Optional) an inline JS function to transform the y data. Default is the identity function, string. See examples of yaml files here and here.","s":"Step 1","u":"/developer-guide/chart-to-ui","h":"#step-1","p":21},{"i":26,"t":"In your config.ini, add your chart key under [ui.overview.charts] and assign it 1. Example: [ui.overview.charts] # show/hide charts on the PioreactorUI dashboard # 1 is show, 0 is hide ... co2_readings=1 ...","s":"Step 2","u":"/developer-guide/chart-to-ui","h":"#step-2","p":21},{"i":28,"t":"If the UI stops displaying data, you may have introduced a yaml file that is not being read correctly. Check out the Pioreactor UI logs by sshing into the leader, and running: tail /var/log/pioreactorui.log The last few lines should tell you about if a field is missing, a wrong type, etc. There is a 30sec cache, so it may take up to 30sec to see new changes in the UI.","s":"Troubleshooting","u":"/developer-guide/chart-to-ui","h":"#troubleshooting","p":21},{"i":30,"t":"The Pioreactor has a few different ways to store data (depending on the requirements). They are:","s":"Introduction","u":"/developer-guide/data-stores-intro","h":"","p":29},{"i":32,"t":"The most important datastore is the SQLite3 database on the leader, located at /home/pioreactor/.pioreactor/storage/. This database stores historical data, jobs changes, logs, experiments, etc. The background job mqtt_to_db_streaming picks up data from MQTT (like OD readings), and puts them into the database. The CLI command pio db will open up the SQLite terminal to query the database directly. Backups of the database​ The Pioreactor software will automatically backup the SQLite database via a scheduale cron job. The backup is hosted locally on the Raspberry Pi, however if there if the cluster has active worker Pioreactors, the database backup is duplicated to (at most) two workers as well. This level of redundancy means that if the leader's microSD card fails, the database can be recovered from backups stored off the card.","s":"SQLite3","u":"/developer-guide/data-stores-intro","h":"#sqlite3","p":29},{"i":34,"t":"SQLite3 is also used by the library diskcache. This is essentially a fast key-value store on the Raspberry Pi. For Pioreactor, we use it to store \"machine-specific\" data, like calibration curves, locks on GPIOs, state of LEDs, jobs running, etc. Instead of one large file containing all these keys, we have split them into multiple locations based on category and level of persistence. The persistent databases are stored in /home/pioreactor/.pioreactor/storage and the temporary databases are in /tmp. You can access them from Python using pioreactor.utils.local_persistant_storage and pioreactor.utils.local_intermittent_storage, respectively. info What are temporary and persistent? Something like GPIO locks or LED state are physically reset between cycles of the Raspberry Pi. So when the Pi power-cycles, the state is wiped, and by have the database in /tmp, the databases are wiped as well. You can use pio view-cache <name> to view the contents of <name>, and pio clear-cache <name> <key> to clear contents.","s":"Local key-value datastore","u":"/developer-guide/data-stores-intro","h":"#local-key-value-datastore","p":29},{"i":36,"t":"The inter- and intra-Pioreactor communications are handled by MQTT, a pub/sub service. The MQTT broker is on the leader Pioreactor (pio mqtt will stream the latest messages to your terminal). MQTT is used to transfer data between workers and leader, and even between process on the workers (ex: OD readings are created on worker, send to leader, and then sent back to worker's growth_rate_calculating job. This does create minor latency, and certainly more risk of data loss, but simplifies the design of the system overall). A principle we have stood by is to not let MQTT turn into our database. That is, we shouldn't store important information in MQTT only (also use mqtt_to_db_streaming job to store important data in the SQLite3 database, or handle it locally using local_intermitant_storage or local_persistance_storage), we shouldn't store information in MQTT that is \"machine-specific\", like calibrations (better to use local_intermitant_storage or local_persistance_storage) we shouldn't use MQTT as a source of truth (trust the database, local_intermitant_storage or local_persistance_storage more). Serialization of MQTT messages​ We make a configuration change so MQTT data is not persisted through leader power-cycles. Authentication​ The Mosquitto broker has a username/password of pioreactor / raspberry.","s":"MQTT","u":"/developer-guide/data-stores-intro","h":"#mqtt","p":29},{"i":38,"t":"The execute method attached to any automation can return either None, or a AutomationEvent. If the latter, the event will be published to MQTT as a published setting, i.e under the topic pioreactor/<unit>/<experiment>/dosing_automation/latest_event. This can be used to downstream events that want to know about what events are occurring. It may make more sense to look at a specific execute. This is from the builtin Turbidostat automation: class Turbidostat(DosingAutomationJob): ... def execute(self) -> Optional[events.DilutionEvent]: if self.latest_od >= self.target_od: self.execute_io_action(media_ml=self.volume, waste_ml=self.volume) return events.DilutionEvent( f\"latest OD={self.latest_od:.2f} >= target OD={self.target_od:.2f}\", {'latest_od': self.latest_od, 'target_od': self.target_od} ) else: return When execute runs, either a DilutionEvent or nothing is returned. All events take up two (optional) arguments: a message, and a dictionary of arbitrary data. In this case, we've included a small message of why the dosing did or did not occur, and included some metadata about the optical densities. After execute returns an event, it will be published to MQTT. For example: pioreactor/unit/demo_exp/dosing_automation/latest_event {\"event_name\":\"NoEvent\",\"message\":\"latest OD=0.98 < target OD=1.00\",\"data\":{\"latest_od\":0.98,\"target_od\":1.0}} This can be listed in other jobs, and acted on, if needed.","s":"Automation events","u":"/developer-guide/events","h":"","p":37},{"i":40,"t":"Pioreactor ships with some default events. They are located in pioreactor.automation.events. Events are simple subclass of events.AutomationEvent, so events behave and look the same, except for their name. You can create custom automations, too: From pioreactor.automations.events import AutomationEvent class MyExampleEvent(AutomationEvent): pass class MyAutomation(...): ... def execute(self): ... event = MyExampleEvent(\"my message\", {'some_data': 1.0}) return event","s":"Using events, and creating your own","u":"/developer-guide/events","h":"#using-events-and-creating-your-own","p":37},{"i":42,"t":"Name Chip Address ADC RP2040 0x30 DAC RP2040 0x30 TEMP TMP1075 0x4F","s":"I²C addresses","u":"/developer-guide/i2c-addresses","h":"","p":41},{"i":44,"t":"You can add a hook to what happens when the button is pressed on the Pioreactor HAT. For example, you could do things like: Flash an LED on when the button is pressed Cycle media: turn on both media and waste pumps for as long as the button is compressed for Pause a job, example: pause OD reading so you can take the vial out of the sleeve to inspect Spike the culture via dosing To do this, you need to write a small plugin that can be placed in the Pioreactor's /home/pioreactor/.pioreactor/plugins folder. Here's an example on how to turn on LED channel B for as long as the button is compressed: \"\"\" The background job Monitor is the job that listens to button state changes. There are hooks in that class to add callbacks for button down and button up. \"\"\" from pioreactor.background_jobs.monitor import Monitor from pioreactor.actions.led_intensity import led_intensity def on(*args): led_intensity({'B': 20}, verbose=False, source_of_event=\"button\") def off(*args): led_intensity({'B': 0}, verbose=False, source_of_event=\"button\") Monitor.add_pre_button_callback(on) Monitor.add_post_button_callback(off) An example to pause a job over MQTT: from pioreactor.background_jobs.monitor import Monitor from pioreactor.pubsub import publish from pioreactor.whoami import get_latest_experiment_name, get_unit_name target=\"od_reading\" def pause(*args): publish(f\"pioreactor/{get_unit_name()}/{get_latest_experiment_name()}/{target}/$state/set\", \"sleeping\") def unpause(*args): publish(f\"pioreactor/{get_unit_name()}/{get_latest_experiment_name()}/{target}/$state/set\", \"ready\") Monitor.add_pre_button_callback(pause) Monitor.add_post_button_callback(unpause)","s":"Adding behaviour to the HAT's button","u":"/developer-guide/hat-button","h":"","p":43},{"i":46,"t":"Below is a list of important locations and files on the filesystem for the Pioreactor:","s":"Important locations on the filesystem","u":"/developer-guide/filesystem-locations","h":"","p":45},{"i":48,"t":"/var/www/pioreactorui/ is the source of the web-app. /var/www/pioreactorui/.env holds some configuration for the UI. /var/www/pioreactorui/contrib/ holds yaml files that display automation data, job data, and chart data. /home/pioreactor/.pioreactor/plugins/ui/contrib/ also holds yaml files, like the above.","s":"UI","u":"/developer-guide/filesystem-locations","h":"#ui","p":45},{"i":50,"t":"/var/log/pioreactor.log is the log file for the Pioreactor app /var/log/pioreactorui.log is the log file for the Pioreactor UI","s":"Logs","u":"/developer-guide/filesystem-locations","h":"#logs","p":45},{"i":52,"t":"/home/pioreactor/.pioreactor/storage/ holds the main database, backup of the database, and persistent caches. /tmp/ holds temporary caches. Files in here are not kept between reboots.","s":"Storage","u":"/developer-guide/filesystem-locations","h":"#storage","p":45},{"i":54,"t":"/usr/local/bin/ store bash scripts that are used when working with the filesystem: installing plugins, updating code, etc.","s":"Bash scripts","u":"/developer-guide/filesystem-locations","h":"#bash-scripts","p":45},{"i":56,"t":"/home/pioreactor/.pioreactor/ holds all configuration files for the Pioreactor UI and app, the main one being config.ini","s":"Config","u":"/developer-guide/filesystem-locations","h":"#config","p":45},{"i":58,"t":"/home/pioreactor/.pioreactor/plugins/ is where Python files can be added. /home/pioreactor/.pioreactor/plugins/ui/contrib/ also holds UI yaml files for custom Python code.","s":"Plugins","u":"/developer-guide/filesystem-locations","h":"#plugins","p":45},{"i":60,"t":"/home/pioreactor/.pioreactor/experiment_profiles/ is where experiment profiles (yaml) are stored.","s":"Experiment profiles","u":"/developer-guide/filesystem-locations","h":"#experiment-profiles","p":45},{"i":63,"t":"The Pioreactor runs ontop of a Raspberry Pi. We provide the operating system that runs on the Raspberry Pi as downloadable images. The operating system the latest version of Raspberry Pi OS (a fork of Debian Bookworm at the time of writing) with our custom modifications.","s":"Operating system","u":"/developer-guide/important-concepts","h":"#operating-system","p":61},{"i":65,"t":"The Pioreactor software works as follows: Different jobs, like stirring, OD reading, dosing, etc. are controlled by separate Python objects. Some jobs will passively listen for events from other jobs, and change their behavior in response, for example, dosing automations listen to OD readings, and may respond by dosing or not dosing. The main \"control plane\" for the Pioreactor software is the command line interface, pio. For example, when the user starts a activity from the UI, the web server will run pio run <some activity> --arguments, which launches a Python process that will instantiate the object the controls the activity. Because each activity is a separate Python process, we can modify an activity before running it by changing files on the filesystem.","s":"An initial mental model of Pioreactor software","u":"/developer-guide/important-concepts","h":"#an-initial-mental-model-of-pioreactor-software","p":61},{"i":67,"t":"One of the Raspberry Pi's is assigned as the \"leader\", and this hosts most of the services: web server, MQTT broker, database, etc. It also sends commands to any \"workers\". The leader can also be a worker. Together, the leader and all the workers are called a \"cluster\". A cluster can be a small as a single leader+worker. See more information about clusters here.","s":"Cluster topology","u":"/developer-guide/important-concepts","h":"#cluster-topology","p":61},{"i":69,"t":"The Raspberry Pis communicate through the local network (in more advanced cases, this network is hosted on the leader). Users control the Pioreactor cluster while being on the same network, and accessing the web UI or the command line of the Pioreactors.","s":"Networking","u":"/developer-guide/important-concepts","h":"#networking","p":61},{"i":71,"t":"MQTT is message-broker system that the Pioreactor uses to communicate between Pioreactors and between processes. Think of it as an in-memory event log, and any software in the cluster can interact with it. The leader Pioreactor hosts the message-broker (using the software Mosquitto), and worker Pioreactors (which are called MQTT clients) will read and write to it. On the leader's command line, you can view the event log with pio mqtt. The Pioreactor UI also connects to MQTT, and uses it to push and pull live data from the activities in each Pioreactor (states of activities, settings, graphs, etc).","s":"MQTT","u":"/developer-guide/important-concepts","h":"#mqtt","p":61},{"i":74,"t":"Automations are specialized background jobs with a simplified interface for controlling some part of the Pioreactor. Whereas there is really only one way to control stirring in the Pioreactor (on, off, and constant), there are many ways to modify dosing to get different microbiological outcomes. Similarly with LEDs: there are many ways researchers want to control LEDs to change microorganisms. Same with temperature. For that reason, we've built an automation interface to make developing automations easier. You'll see an example of this simplified design when we build one in the next page.","s":"Automations","u":"/developer-guide/intro-automations","h":"#automations","p":72},{"i":76,"t":"Because we often want to change automations during an experiment, there is a Controller object (a background job) that initializes and teardowns automations during an experiment. For each automation type: dosing, temperature, and LED, there is a corresponding controller: DosingController, TemperatureController, and LEDController, respectively. Running these looks like: from pioreactor.background_jobs.dosing_control import DosingController dc = DosingController( dosing_automation=\"turbidostat\", # name of the automation, see next page duration=30, # how often `execute` runs, in minutes target_od=2.0, # kwarg that the turbidostat automation needs volume=0.5, # kwarg that the turbidostat automation needs ) The controller will start the automation (and publish information about to MQTT via published_settings), and if requested, will stop the automation and start a new one. Using the controllers is the preferred way to start and stop automations, rather than invoking the automations directly. Since the automation in the controller is part of published_settings, you can change the automation over MQTT by publishing to a MQTT topic. For example, if you wish to change the dosing automation from turbidostat to chemostat, publish the following JSON payload to pioreactor/<unit>/<experiment>/dosing_control/automation/set { \"automation_name\":\"chemostat\", \"args\": { \"volume: 1, \"duration\": 20 } }","s":"Controllers","u":"/developer-guide/intro-automations","h":"#controllers","p":72},{"i":78,"t":"Pioreactor plugins are a way to distribute code to others (or yourself), and avoid having to use the command line each time you invoke your custom code - you should be able to just use the web interface. There are two ways to distribute a plugin:","s":"Working with plugins","u":"/developer-guide/intro-plugins","h":"","p":77},{"i":80,"t":"On each Pioreactor's Raspberry Pi is a folder at /home/pioreactor/.pioreactor/plugins. When the Pioreactor software starts, any Python files in this folder are read and loaded into memory. If you were to include an automation in here, or a background job (with the click CLI component), they would be available globally. Why would you want to distribute code this way? It's a great way to test or develop your code instead of committing to other distribution methods: short iterations times, tight feedback loop, and code runs in the production environment. Two downsides are that it's harder to distribute your code to the rest of the community, and that it doesn't have the same deployment pipeline (adding configs, etc.) caution The Pioreactor software will load and run each Python file in /plugins on each invocation of pio. Don't have long-running or blocking code without wrapping it in a function or if __name__ == \"__main__\". For example: # my plugin code.py #❌ don't do this import time time.sleep(100) # ✅ this is okay import time def sleep(): time.sleep(100) # ✅ also is okay import time if __name__ == \"__main__\": time.sleep(100)","s":"1. Adding Python files to plugins folder","u":"/developer-guide/intro-plugins","h":"#1-adding-python-files-to-plugins-folder","p":77},{"i":82,"t":"Here's an example: place the following code into the file /home/pioreactor/.pioreactor/plugins/demo_job.py # -*- coding: utf-8 -*- import click from pioreactor.whoami import get_unit_name, get_latest_experiment_name from pioreactor.background_jobs.base import BackgroundJob __plugin_summary__ = \"Just a demo job\" __plugin_version__ = \"0.0.1\" __plugin_name__ = \"Demo job\" __plugin_author__ = \"Cam Davidson-Pilon\" __plugin_homepage__ = \"https://docs.pioreactor.com\" class DemoJob(BackgroundJob): job_name=\"demo_job\" def __init__(self, unit, experiment, **kwargs): super().__init__(unit=unit, experiment=experiment) def on_ready(self): self.logger.debug(\"Hello, world!\") def on_disconnected(self): self.logger.debug(\"Goodbye, world!\") @click.command(name=\"demo_job\", help=__plugin_summary__) def click_demo_job(): job = DemoJob( unit=get_unit_name(), experiment=get_latest_experiment_name(), ) job.block_until_disconnected() You should be able to execute the following from the command line now: pio run demo_job. Finally, in your web interface under plugins, you should see \"Demo Job\" installed. info A full introduction to writing jobs is available. info How do you add this to your /pioreactors page in the UI? See here.","s":"Custom background jobs","u":"/developer-guide/intro-plugins","h":"#custom-background-jobs","p":77},{"i":84,"t":"If you are interested in creating a Python script to control multiple jobs, like in a previous Python scripting example, you can create a file called example_script.py in the /home/pioreactor/.pioreactor/plugins/ folder: import time import click from pioreactor.background_jobs.stirring import start_stirring from pioreactor.background_jobs.od_reading import start_od_reading from pioreactor.actions.led_intensity import led_intensity from pioreactor.background_jobs.temperature_control import start_temperature_control __plugin_summary__ = \"My example script to control stirring, OD and temperature\" __plugin_version__ = \"0.0.1\" __plugin_name__ = \"Example Script\" __plugin_author__ = \"Cam Davidson-Pilon\" __plugin_homepage__ = \"https://docs.pioreactor.com\" @click.command(name=\"my_script\", help=__plugin_summary__) # the name field is used in the invocation `pio run X` def click_my_script(): led_intensity({\"B\": 50}) stirrer = start_stirring(target_rpm=400) od_reader = start_od_reading(\"90\", \"REF\") temp_controller = start_temperature_control(\"thermostat\", target_temperature=32) time.sleep(10) stirrer.set_target_rpm(300) stirrer.block_until_disconnected() You should be able to execute the following from the command line now: pio run my_script. (The my_script is from the @click.command line, you can change it there). important The function that click.command wraps should have it's name prepended by click_. Ex: def click_my_script is okay, but def my_script is not. info How do you add this to your /pioreactors page in the UI? See here.","s":"Custom scripts","u":"/developer-guide/intro-plugins","h":"#custom-scripts","p":77},{"i":86,"t":"Here's an example of adding a custom automation: place the following code into the file /home/pioreactor/.pioreactor/plugins/demo_automation.py # -*- coding: utf-8 -*- from pioreactor.automations.dosing.base import DosingAutomationContrib __plugin_summary__ = \"A demo dosing automation\" __plugin_version__ = \"0.0.1\" __plugin_name__ = \"Demo Dosing Automation\" __plugin_author__ = \"Cam Davidson-Pilon\" __plugin_homepage__ = \"https://docs.pioreactor.com\" class DemoAutomation(DosingAutomationContrib): automation_name = \"demo\" def __init__(self, volume, **kwargs): super().__init__(**kwargs) self.volume = volume def execute(self): self.logger(\"Here I would execute...\") You should be able to execute the following from the command line now: pio run dosing_control --automation-name demo --volume 10 info A full introduction to writing automations is available. info How do you add this to your /pioreactors page in the UI? See here.","s":"Custom automations","u":"/developer-guide/intro-plugins","h":"#custom-automations","p":77},{"i":88,"t":"An alternative to placing Python files in the plugins folder is to bundle your code into a Python package that can be installed over the internet. This is the best way to ship your code to many users, and is pretty easy! We have a full guide on how to create a Pioreactor Python package.","s":"2. pip-installable plugins","u":"/developer-guide/intro-plugins","h":"#2-pip-installable-plugins","p":77},{"i":90,"t":"The core unit of \"work\" in the Pioreactor software is a background job (called activities in the web interface). Background jobs include od_reading, monitor, automation controllers, all the automations themselves, etc. Often, a community plugin is a background job (or multiple jobs) that gives your bioreactor new abilities. There are a few important features of background jobs to be highlighted if you intend on working with them.","s":"Introduction to background jobs","u":"/developer-guide/intro-background-jobs","h":"","p":89},{"i":92,"t":"All background jobs inherit from the base class pioreactor.background_jobs.base.BackgroundJob. This class controls most of the behind-the-scenes behaviour of the class. Typically, we structure background job code such that the Python file has a single background job class and a command-line interface. See examples here.","s":"Inheritance and file structure","u":"/developer-guide/intro-background-jobs","h":"#inheritance-and-file-structure","p":89},{"i":94,"t":"All subclasses of BackgroundJob have the logger attribute that can be used to log messages. These messages are printed to the console, sent to MQTT, sometimes displayed in the UI, and all are stored permanently in the Pioreactor database. Here's how: # use for debugging job.logger.debug(\"A debug message - displayed in the console\") # use for providing relevant updates job.logger.info(\"An info message - this is display in the Recent Logs table in the UI\") # use for successes or important updates job.logger.notice(\"A notice message - this is displayed in the UI in a green popup\") # use for when something doesn't look correct, but will continue. job.logger.warning(\"A debug message - this is displayed in the UI in a yellow popup\") # use for when something is wrong and you take over control from the user job.logger.error(\"A debug message - this is displayed in the UI in a red popup\")","s":"Logging","u":"/developer-guide/intro-background-jobs","h":"#logging","p":89},{"i":96,"t":"A background job can be in one of five different states: init: the job is initializing. The job starts in this state. ready: the job is prepared to do \"work\", or currently doing \"work\" sleeping: the job's work is paused (ex: when the stirring job is in state sleeping, it turns off its power.) This state is called \"paused\" in the web interface. disconnected: the job has disconnected from services (MQTT, databases, etc.) and cleaned itself up successfully. lost: the job did not disconnect gracefully. Something may be wrong. Here's how the states can transition to each other: ┌──────────┐ │ │ ┌──────────────────────┬───────► lost ◄────────┐ │ │ │ │ │ │ │ └─────▲────┘ │ │ │ │ │ ┌────┴─────┐ ┌─────┴──────┐ │ ┌───────┴──────┐ │ │ │ │ │ │ │ │ init ├──────────► ready ├──────┼─────► disconnected │ │ │ │ │ │ │ │ └──────────┘ └────┬──▲────┘ │ └──────▲───────┘ │ │ │ │ │ │ │ │ │ │ │ │ ┌────▼──┴────┬──────┘ │ │ │ │ │ sleeping ├───────────────────┘ │ │ └────────────┘ The author can optionally define hooks when a job moves between states, and when it enters a new state. For example, the method .on_ready_to_sleeping() is called when the job moves from ready to sleeping. Similarly, the method .on_sleeping() is called when the jobs enters state sleeping. By default, these methods are empty. The recommended way to move a job between states is with job.set_state(job.READY). This will invoke any hooks that exist between the states. State can also be changed remotely over MQTT - we'll get to that point later.","s":"State of a job","u":"/developer-guide/intro-background-jobs","h":"#state-of-a-job","p":89},{"i":98,"t":"On job creation, the job will connect to MQTT to allow for publishing and subscribing. The attribute sub_client is for subscribing from MQTT, and pub_client is for publishing to MQTT. Internally, sub_client and pub_client are Paho client objects. Since publishing is so common, we also expose a .publish method: job = SomeBackgroundJob(unit, experiment) job.publish(f\"pioreactor/{job.unit}/{job.experiment}/...\", payload) Another common pattern is to subscribe to a MQTT topic, and execute a threaded callback whenever a message comes in from that topic. This is done with the .subscribe_and_callback method. By convention, this is most often used in a .start_passive_listeners method: from pioreactor.background_jobs.base import BackgroundJob class SomeBackgroundJob(BackgroundJob): def __init__(self, ...): ... self.start_passive_listeners() def response_to_dosing_event(self, msg): # change self in response, etc. ... def start_passive_listeners(self): self.subscribe_and_callback( self.response_to_dosing_event, f\"pioreactor/{self.unit}/{self.experiment}/dosing_events\", )","s":"Publish & subscribe, also known as pub/sub","u":"/developer-guide/intro-background-jobs","h":"#publish--subscribe-also-known-as-pubsub","p":89},{"i":100,"t":"A common task is when we have a job running, say stirring job, and we want to dynamically update an attribute, like the target RPM, without restarting the job. We also want to know the value of a job's attribute when it changes. For example, in the stirring job, we'd like to know what the actual RPM is. This can't be edited externally (it's a measured value...), but we want the value available for other jobs to use, for the web interface to display, or to sink it into a database. These two tasks, updating attributes and reading attributes in real-time, are so common that we've wrapped the logic into the parent BackgroundJob class, and allow job authors to tell us what attributes they wish to update and/or read. In the class definition, the attribute published_settings defines which class attributes they would like to track. For example, the job responsible for stirring looks like: class Stirrer(BackgroundJob): published_settings = { \"target_rpm\": {\"datatype\": \"json\", \"settable\": True, \"unit\": \"RPM\"}, \"measured_rpm\": {\"datatype\": \"json\", \"settable\": False, \"unit\": \"RPM\"}, \"duty_cycle\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"%\"}, } ... Thus the attributes target_rpm, measured_rpm, duty_cycle are all published to MQTT when they change, but only duty_cycle and target_rpm are able to be updated over MQTT (as defined by settable). The \"datatype\" field is normally one of: \"string\", \"float\", \"integer\", \"json\", \"boolean\" (full list in pioreactor/types.py). The \"settable\" field sets whether this attribute can be changed externally. The \"unit\" field is the unit of measurement, if any. This key is optional, and can be omitted. Also, there is an optional \"persist\" key (not shown above), which contains a boolean describing if the value should be kept in MQTT after the job exits, default False. When a class' attribute that's present in published_settings changes, a MQTT message is published under the topic pioreactor/{self.unit}/{self.experiment}/{self.job_name}/{attr} with payload equal to the new value of the attribute. This is how the web interface is provided real-time data. For updating an attribute, the BackgroundJob parent class listens to the MQTT topic: pioreactor/{self.unit}/{self.experiment}/{self.job_name}/+/set (the + is a MQTT wildcard), and when a message comes in, the class will check if the attribute (defined by +) is settable. If so, a lookup is done to see if a class method called set_<attr> is defined, and if present, calls that, with the only argument the message's payload. Otherwise, a simple assignment is done: self.<attr> = payload. The utility of a set_<attr> method is when changing the attribute requires more logic (ex: changing a PID controller's set point, see example here). info state is special attribute that is automatically appended to published_settings (with settable: True and persist: True) so the state of the job can always be updated and read from MQTT. Over MQTT, the field is called referenced as pioreactor/{unit}/{experiment}/{job_name}/$state - note the $. When the job disconnects and cleans up, the published settings in MQTT are removed by sending an empty payload to the respective topics (unless persist: True, see above.)","s":"Publishing attributes to MQTT","u":"/developer-guide/intro-background-jobs","h":"#publishing-attributes-to-mqtt","p":89},{"i":102,"t":"Only a single instance of a background job, indexed by the job's name, can be running on a Raspberry Pi. For example, only a single Monitor background job can run, likewise only a single ODReading can run. (It's not clear what running multiple ODReadings means, or how they will interact with the hardware - poorly we expect). The uniqueness is across processes, too. So if a script is running ODReading, then pio run od_reading will fail. note This uniqueness constraint is enforced in the current version of the software. It's possible we will see a reason to remove the uniqueness constraint in a future version - let us know if you want to see this, too!","s":"Uniqueness","u":"/developer-guide/intro-background-jobs","h":"#uniqueness","p":89},{"i":104,"t":"Background jobs make lots of connections to MQTT, GPIOs, hardware, and other external systems. It's important to treat background jobs as objects that need to be cleaned up these connections properly. If your jobs needs to clean up something, you can put it into the on_disconnected function: from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class HappyJob(BackgroundJob): def __init__(self, ...): # connect to a hardware self.hardware_connection = Hardware() self.hardware_connection.connect() # set LED on, too led_intensity({\"A\": 10}) def on_disconnected(self): self.hardware_connection.disconnect() led_intensity({\"A\": 0}) on_disconnected is called and connections are closed when the job exits (see below). There are two ways to use a background job that will ensure jobs are cleaned up correctly on exit: job = SomeBackgroundJob(unit, experiment) ... job.clean_up() # all cleaned up - state is set to disconnected alternatively, with a context manager: with SomeBackgroundJob(unit, experiment) as job: ... # all cleaned up - state is set to disconnected The job is also cleaned up when the Python process exits. caution The following will cause problems: #❌ don't do this def function_that_doesnt_clean_up(): job = SomeBackgroundJob(unit, experiment) # job not cleaned up return True value = function_that_doesnt_clean_up() ... In the above, the job SomeBackgroundJob isn't disconnected, and state hasn't changed - nor can you access the job anymore (no accessible references). Do this instead: # ✅ this is okay def function_that_does_clean_up(): with SomeBackgroundJob(unit, experiment) as job: ... return True value = function_that_does_clean_up() Blocking​ Often we want the job to wait and blocks, so as to wait for user commands or MQTT messages. We can accomplish this with job.block_until_disconnected() This blocks the execution until the job is disconnected (either a MQTT state change, or a signal from the OS).","s":"Entry & exit","u":"/developer-guide/intro-background-jobs","h":"#entry--exit","p":89},{"i":106,"t":"Often we want the job to wait and blocks, so as to wait for user commands or MQTT messages. We can accomplish this with job.block_until_disconnected() This blocks the execution until the job is disconnected (either a MQTT state change, or a signal from the OS).","s":"Blocking","u":"/developer-guide/intro-background-jobs","h":"#blocking","p":89},{"i":108,"t":"This documentation is for those who want to get the most customization out of their Pioreactor, use the Pioreactor core software for their own project, understand how the pieces work, contribute back code to the open-source Pioreactor software.","s":"Introduction for developers","u":"/developer-guide/introduction","h":"","p":107},{"i":110,"t":"Our code base is all open source, and available on GitHub. Pioreactor core, written in Python. Pioreactor user interface, a React app written in JS.","s":"Open source","u":"/developer-guide/introduction","h":"#open-source","p":107},{"i":112,"t":"Any suggestions or comments can be added to our Issue Tracker. If you're up for it, feel free to send a pull request, too!","s":"Have edits, corrections, or suggestions?","u":"/developer-guide/introduction","h":"#have-edits-corrections-or-suggestions","p":107},{"i":115,"t":"Confirm that Python3 is installed, and is greater or equal to version 3.9. python3 --version will print the version. To install the Pioreactor codebase locally, it should be enough to clone the repo pioreactor/pioreactor. git clone https://github.com/Pioreactor/pioreactor.git && cd pioreactor Install the core software are necessary packages (useful to do this in a virtualenv!): pip3 install -e . pip3 install -r requirements/requirements_dev.txt In the pioreactor folder, create a folder called .pioreactor/ and .pioreactor/storage. mkdir .pioreactor mkdir .pioreactor/storage The configuration file that is used is config.dev.ini, and is provided in the repository.","s":"Local development","u":"/developer-guide/local-development","h":"#local-development","p":113},{"i":117,"t":"You will need to install MQTT and have a broker running locally. On OSX, homebrew can be used to install the MQTT broker mosquitto. On Windows, it can be installed from this download page. info The mosquitto broker should be running whenever you invoke the Pioreactor software locally, else you'll likely get some connection refused error. The CLI tools mosquitto_pub and mosquitto_sub should work as well.","s":"MQTT","u":"/developer-guide/local-development","h":"#mqtt","p":113},{"i":119,"t":"With pio TESTING=1 pio run <job name> You can also modify to hostname and experiment with TESTING=1 \\ HOSTNAME=<whatever> \\ EXPERIMENT=<up to you> \\ pio run <job name> With python TESTING=1 python <your script>.py You can also modify to hostname and experiment with TESTING=1 \\ HOSTNAME=<whatever> \\ EXPERIMENT=<up to you> \\ python <your script>.py info If invoking from a different directory from pioreactor/, you'll need to have a config.dev.ini file locally. I usually copy my pioreactor/config.dev.ini to wherever I am working. Or you can use an environment argument GLOBAL_CONFIG=./config.dev.ini pio ...","s":"Running jobs locally","u":"/developer-guide/local-development","h":"#running-jobs-locally","p":113},{"i":121,"t":"py.test pioreactor/tests","s":"Testing","u":"/developer-guide/local-development","h":"#testing","p":113},{"i":123,"t":"Create a folder in the pioreactor folder called plugins_dev. In this folder, you can place python files that will run whenever pio is invoked (similar to the plugins folder at .pioreactor/plugins on the Raspberry Pi, see docs here)","s":"Plugins development","u":"/developer-guide/local-development","h":"#plugins-development","p":113},{"i":125,"t":"Raspberry Pi images are built in the Pioreactor/CustoPizer repo. Nightly builds are available at nightly.pioreactor.com.","s":"Raspberry Pi Images","u":"/developer-guide/local-development","h":"#raspberry-pi-images","p":113},{"i":128,"t":"Here's an example: from pioreactor.utils import local_intermittent_storage, local_peristant_storage with local_intermittent_storage(\"my_cache\") as cache: cache['key'] = \"value\" print(cache['key']) with local_peristant_storage(\"my_longterm_storage\") as cache: cache['key'] = \"value\" You can use pio view-cache <name> to view the contents of <name>, and pio clear-cache <name> <key> to clear contents.","s":"How do I write and read from the local storage?","u":"/developer-guide/local-storage","h":"#how-do-i-write-and-read-from-the-local-storage","p":126},{"i":130,"t":"local_intermittent_storage is data that won't, or shouldn't, exist after a reboot. For example: the state of GPIO pins. At a hardware level, this is reset after each reboot, and so should data associated with it. Whereas local_peristant_storage is data that should exist between reboots. This is data like calibration data, or OD blank data.","s":"What's the difference between local_intermittent_storage and local_peristant_storage?","u":"/developer-guide/local-storage","h":"#whats-the-difference-between-local_intermittent_storage-and-local_peristant_storage","p":126},{"i":133,"t":"We suggest using the following prefix: pioreactor/{unit name or $broadcast}/{experiment name or $experiment}/ ...","s":"How do you structure topics for MQTT?","u":"/developer-guide/mqtt","h":"#how-do-you-structure-topics-for-mqtt","p":131},{"i":135,"t":"If you're writing code for Job, you can simply use Job's methods: def some_method(self, ...): ... self.publish(f\"pioreactor/{self.unit}/{self.experiment}/{self.job_name}/more/topics\", payload) If writing a script: from pioreactor.utils import publish publish(f\"pioreactor/{unit}/{experiment}/more/topics\", payload)","s":"How do I publish data to MQTT?","u":"/developer-guide/mqtt","h":"#how-do-i-publish-data-to-mqtt","p":131},{"i":138,"t":"If you have a Raspberry Pi available, you can quickly boot up a near-exact environment to a Pioreactor. We can mock out the hardware needed, but everything else will work: networking, the Pioreactor UI, MQTT, running jobs, plugins, etc. Install the Pioreactor software on to a microSD card by following the instructions here. Power the Raspberry Pi. Since there's no HAT hardware, there won't be a blue blinking LED. The Raspberry Pi will still connect to the network you provided in the setup. SSH into the Raspberry Pi. Instructions on how to SSH in. You should also be able to visit http://pioreactor.local Once SSH'ed in, we need to add some \"mocking\" packages. Enter the following: sudo pip3 install fake-rpi The environment variable TESTING will determine if the Pioreactor should run in \"testing\" mode (i.e. mock out hardware required, and fake some data). We also need to specify the location of the config.ini file with the GLOBAL_CONFIG env variable. For example, we can mock the stirring job by entering: TESTING=1 GLOBAL_CONFIG=/home/pioreactor/.pioreactor/config.ini pio run stirring However, the experiment needs to be mocked out too: TESTING=1 \\ GLOBAL_CONFIG=/home/pioreactor/.pioreactor/config.ini \\ EXPERMENT=\"Demo Experiment\" \\ pio run stirring That's a lot of typing variables, so you could move these environment variables to ~/.profile: nano ~/.profile And add anywhere: export TESTING=1 export GLOBAL_CONFIG=/home/pioreactor/.pioreactor/config.ini export EXPERMENT=\"Demo Experiment\" And finally enter: source ~/.profile Now you can do pio run stirring without having to enter in the environment variables.","s":"Developing without hardware","u":"/developer-guide/pi-development","h":"#developing-without-hardware","p":136},{"i":141,"t":"Runpio db on the leader to open up the database shell. You can quit with .q.","s":"How do I access the SQlite3 database?","u":"/developer-guide/sqlite3","h":"#how-do-i-access-the-sqlite3-database","p":139},{"i":143,"t":"You can either use .tables in the sqlite shell, or visit all the tables schemas here.","s":"Where is a list of tables on the database?","u":"/developer-guide/sqlite3","h":"#where-is-a-list-of-tables-on-the-database","p":139},{"i":145,"t":"Using the sqlite shell (pio db), you can execute any SQL statements, including creating new tables. Plugins can also automatically create new tables when installed, see instructions here.","s":"How can I add new SQL tables?","u":"/developer-guide/sqlite3","h":"#how-can-i-add-new-sql-tables","p":139},{"i":147,"t":"The Pioreactor job mqtt_to_db_streaming handles how to get data into the sqlite3 database. This job listens to specific topics in MQTT, and writes it to the database. We've implemented hooks into mqtt_to_db_streaming job for you to added your own topics. In your code: a parser, usually called parser, function that accepts a MQTT topic and payload, and returns a dictionary that maps to the tables schema. a TopicToParserToTable object is created with the MQTT topics to listen to, the parser, and the table name to load to. This TopicToParserToTable is provided to register_source_to_sink. Example below for a CO2 sensor: ... from pioreactor.background_jobs.leader.mqtt_to_db_streaming import produce_metadata from pioreactor.background_jobs.leader.mqtt_to_db_streaming import register_source_to_sink from pioreactor.background_jobs.leader.mqtt_to_db_streaming import TopicToParserToTable from pioreactor.utils import timing ... def parser(topic, payload) -> dict: metadata = produce_metadata(topic) return { \"experiment\": metadata.experiment, \"pioreactor_unit\": metadata.pioreactor_unit, \"timestamp\": timing.current_utc_timestamp(), \"co2_reading_ppm\": float(payload), } register_source_to_sink( TopicToParserToTable( [\"pioreactor/+/+/scd_reading/co2\", \"pioreactor/+/+/co2_reading/co2\"], parser, \"co2_readings\", ) ) You can place this into the ~/.pioreactor/plugins folder. The next time mqtt_to_db_streaming starts, it will starts listening to the specific topics.","s":"How do I populate my own SQL tables?","u":"/developer-guide/sqlite3","h":"#how-do-i-populate-my-own-sql-tables","p":139},{"i":149,"t":"The web UI is hosted on the leader Pioreactor. Here are the details:","s":"Overview","u":"/developer-guide/web-ui-introduction","h":"","p":148},{"i":151,"t":"The web server we use is lighttpd, and hosted from /var/www/pioreactorui. This folder is actually a git repo, and pulls from pioreactorui GH repo. Systemd controls starting and restarting lighttpd. The lighttpd conf file is located in /etc/lighttpd/conf-enabled/50-pioreactorui.conf. Error logs (though not helpful) are in /var/log/lighttpd/error.log. The default protocol is http served on port 80. To use https requires a certificate, and is out of scope for this project. If you'd change the protocol or the port, you'll need up tell the software too: look in the config.ini under [ui] section. How to change the web UI port","s":"Web server","u":"/developer-guide/web-ui-introduction","h":"#web-server","p":148},{"i":153,"t":"The backend app is a Flask app, with entry point in /var/www/pioreactorui/main.fcgi. The app uses Huey as background workers to perform pio tasks, save to disk, etc. Huey is controlled by systemd huey.service. The API is available here","s":"Backend","u":"/developer-guide/web-ui-introduction","h":"#backend","p":148},{"i":155,"t":"The frontend is a React app, built with Material UI components. The source code is at pioreactorui_frontend. A lot of the \"data\" for the frontend comes from YAML files on the RPi's filesystem. For example, all the charts, activities, and automations are defined in their own YAML file in a contrib folder on the filesystem. This way, it's easy to add new data to the frontend without having to write new JS.","s":"Frontend","u":"/developer-guide/web-ui-introduction","h":"#frontend","p":148},{"i":157,"t":"To allow for pioreactor.local to be an alias for <leader hostname>.local, we use mdns provided by avahi. There is a systemd service, avahi_alias.service, that will point pioreactor.local to <leader hostname>.local.","s":"DNS name resolution to pioreactor.local","u":"/developer-guide/web-ui-introduction","h":"#dns-name-resolution-to-pioreactorlocal","p":148},{"i":159,"t":"To update on the UI on Pioreactor leader, use pio update ui. This also restarts the server. To restart: sudo systemctl restart lighttp && sudo systemctl restart huey","s":"Updating and restarting the web UI","u":"/developer-guide/web-ui-introduction","h":"#updating-and-restarting-the-web-ui","p":148},{"i":161,"t":"Start up logs from systemd are in sudo systemctl status lighttpd.service. Logs for the backend and background workers are located in /var/log/pioreactorui.log.","s":"Logs","u":"/developer-guide/web-ui-introduction","h":"#logs","p":148},{"i":164,"t":"If you'd like to contribute your plugin to the community, this is done easily by creating a Python package and uploading to PyPI. Let's walk through this!","s":"Turning your plugins into a Python package to share","u":"/developer-guide/plugin-as-python-package","h":"","p":163},{"i":166,"t":"Your plugin name should be all lowercase, and have underscores divide any words. Example: pireactor_relay_plugin is fine, but pioreactor-relay-plugin is not, nor is Pioreactor-Relay-Plugin. However, your distribution package name should be lowercase and have dashes instead of underscores (it's a Python thing: I agree, this is confusing, I'll walk you through it). You can just replace any underscores with dashes: so our example distribution package name is pioreactor-relay-plugin. Later in these steps, we'll reference these names as follows: PLUGIN_NAME: should be the name in all lowercase with underscores. Example: pioreactor_relay_plugin DISTRIBUTION-NAME: should be the name in all lowercase with dashes. Example: pioreactor-relay-plugin","s":"Choosing a plugin name","u":"/developer-guide/plugin-as-python-package","h":"#choosing-a-plugin-name","p":163},{"i":168,"t":"tip Note that the way files are organized may depend on if your plugin is an automation or a background job. Plugins can install both automations and jobs. Consider an example plugin: a plugin named pioreactor_relay_plugin that implements a background job which just turns on or off a PWM channel. Follow the file organization here: CamDavidsonPilon/pioreactor-relay-plugin. Here's a general directory outline of how your files should be organized for a job: 📁 <DISTRIBUTION-NAME (with dashes)> ├─ 📁 <PLUGIN_NAME> │ ├─ 📁 ui │ │ ├─ 📁 contrib │ │ │ ├─ 📁 jobs │ │ │ │ ├─ 📝 <PLUGIN_NAME>.yaml │ ├─ 📝 __init__.py │ ├─ 📝 additional_config.ini │ ├─ 📝 my_plugin_code.py ├─ 📝 LICENSE.txt ├─ 📝 MANIFEST.in ├─ 📝 README.md ├─ 📝 setup.py The directory outline is very similar for an automation plugin &#151 the only difference is the location of the .yaml file. 📁 <DISTRIBUTION-NAME with dashes> ├─ 📁 <PLUGIN_NAME> │ ├─ 📁 ui │ │ ├─ 📁 contrib │ │ │ ├─ 📁 automations │ │ │ │ ├─ 📁 <AUTOMATION TYPE (one of {dosing, led, temperature})> │ │ │ │ │ ├─ 📝 <PLUGIN_NAME>.yaml │ ├─ 📝 __init__.py │ ├─ 📝 additional_config.ini │ ├─ 📝 my_plugin_code.py ├─ 📝 LICENSE.txt ├─ 📝 README.md ├─ 📝 MANIFEST.in ├─ 📝 setup.py Start by creating a new folder for your plugin, equal to the distribution name (the name with dashes). In our case, we named it pioreactor-relay-plugin. This top level folder will contain five important parts: 1. The subfolder <PLUGIN_NAME> containing your plugin's code​ Within the top level directory, we created a sub-directory called <PLUGIN_NAME>. 2. A license text file, named LICENSE.txt​ A common license for software is the MIT license. 3. A MANIFEST file, named MANIFEST.in​ When creating a Python package, there's a default set of files that are included. To assure that our additional configuration and yaml files are included, create a MANIFEST.in file and paste the following: recursive-include <PLUGIN_NAME>/ui/ *.yaml include <PLUGIN_NAME>/additional_config.ini 4. A README.md​ Write a few notes with general information on your plugin to guide users. Call out any additional installation steps, or hardware required. This is a markdown document. 5. A Python setup.py file​ Create a Python file called setup.py and copy & paste the following. Make changes based on your own plugin information. # -*- coding: utf-8 -*- from setuptools import setup, find_packages setup( name=\"<DISTRIBUTION-NAME (with dashes)>\", version=\"<VERSION>\", license_files = ('LICENSE.txt',), description=\"<DESCRIPTION OF PLUGIN>\", long_description=open(\"README.md\").read(), long_description_content_type=\"text/markdown\", author_email=\"<EMAIL>\", author=\"<NAME>\", url=\"<A HOMEPAGE>\", packages=find_packages(), include_package_data=True, install_requires=[], # PROVIDE OTHER PYTHON REQUIREMENTS, ex: \"pioreactor>=23.6.0\", \"numpy>=1.0\" entry_points={ \"pioreactor.plugins\": \"<PLUGIN_NAME> = <PLUGIN_NAME>\" }, )","s":"Organizing your files","u":"/developer-guide/plugin-as-python-package","h":"#organizing-your-files","p":163},{"i":170,"t":"1. Your plugins Python files​ This Python file contains the core code for your plugin. If your plugin is implementing a background job, then there should be a function decorated with @click.command at the bottom of the file. See example here. For discovery reasons, this function's name should start with click_. 2. A Python __init__.py file​ If implementing an automation: Import the Class of your automation file: from <SUBFOLDER CONTAINING PLUGIN>.<PYTHON FILE NAME> import <CLASS NAME> If implementing a job: This will contain an import statement such as the following: from <PLUGIN_NAME>.<PYTHON FILE NAME> import <PLUGIN CLICK FUNCTION> This imports the function within our plugin file that executes our plugin action. Example for the relay plugin: from pioreactor_relay_plugin.relay import click_relay where click_relay is the function decorated with @click.command. 3. Optional: A configuration file, named additional_config.ini​ This configuration file will contain additional configs that we want to add to our list of existing Configurations on the Pioreactor web interface. This file will be merged with the existing config.ini when the plugin is installed. tip A convention we've tried to follow is to use the section name convention of [<job_name>.config] or [<automation_name>.config] in the configuration files. For example, our relay job has [relay.config] in its additional_config.ini and settings under it. 4. Optional: Adding details for the UI​ If implementing a job:​ Within <PLUGIN_NAME> folder, create subfolders named ui/contrib/jobs. For a job, create a .yaml file that looks like the following format. The name of the yaml can be anything, but convention is to use the <job_name>.yaml: --- display_name: # human readable name job_name: # `job_name` as defined in your Python file display: # bool; true to display on the /Pioreactors card source: # name of your plugin description: # description of what your plugin does published_settings: - key: # as defined in Python unit: # unit (ml, lux, AU, etc.) label: # human readable name description: # description of your setting type: # one of numeric, boolean, string, json default: # provide a default value, often null display: # bool; true to display on the /Pioreactors card - key: ... unit: ... ... There are lots of examples of job yaml files here. If implementing an automation:​ In the case of creating an automation plugin, create subfolder(s) with ui/contrib/automations/<AUTOMATION TYPE>, where AUTOMATION TYPE is one of dosing, led, or temperature depending on your automation type. Create a yaml file with the following convention. The name of the yaml file can be anything, but by convention it's <automation_name>.yaml. --- display_name: # human readable name automation_name: # automation name as defined in your Python files source: # name of your plugin description: # description of your plugin fields: - key: # as defined in Python unit: # unit of your key label: # human readable name description: # description of your key - key: ... unit: ... There are lots of examples of automation yaml files here. 5. Optional: adding tables to the SQL store​ You can also add a file called additional_sql.sql that will run against the SQLite database. For example, a CO₂ sensor may want to create a new table in the database to store its sensor data. It's additional_sql.sql may look like: CREATE TABLE IF NOT EXISTS co2_readings ( experiment TEXT NOT NULL, pioreactor_unit TEXT NOT NULL, timestamp TEXT NOT NULL, co2_reading_ppm REAL ); You also need to tell Pioreactor software how to populate this table from your source of data. Include the following in your code such that it executes when the plugin is loaded: a parser function that accepts a MQTT topic and payload, and returns a dictionary that maps to the new tables schema. a TopicToParserToTable object is created with the MQTT topics to listen to, the parser, and the table name to load to. This TopicToParserToTable is provided to register_source_to_sink. Example below for a CO2 sensor: ... from pioreactor.background_jobs.leader.mqtt_to_db_streaming import produce_metadata from pioreactor.background_jobs.leader.mqtt_to_db_streaming import register_source_to_sink from pioreactor.background_jobs.leader.mqtt_to_db_streaming import TopicToParserToTable from pioreactor.utils import timing ... def parser(topic, payload) -> dict: metadata = produce_metadata(topic) return { \"experiment\": metadata.experiment, \"pioreactor_unit\": metadata.pioreactor_unit, \"timestamp\": timing.current_utc_timestamp(), \"co2_reading_ppm\": float(payload), } register_source_to_sink( TopicToParserToTable( [\"pioreactor/+/+/scd_reading/co2\", \"pioreactor/+/+/co2_reading/co2\"], parser, \"co2_readings\", ) ) ... note You also need to add the following to your MANIFEST.in: ... include <PLUGIN_NAME>/additional_sql.sql See an example plugin that uses this idea here. 6. Optional: adding a custom chart to the UI​ To add a chart that display real-time and historical data (provided by MQTT and SQL store respectively), you can do the following: In a new folder named ui/contrib/charts in your project, add a YAML file as described here. The name of the file can by the chart_key field, append with .yaml. In your additional_config.ini, add a new entry to be merged: [ui.overview.charts] <your chart key>=1 info You'll need to make sure your database table has the necessary fields. See details under data_source in the docs here. See an example plugin that uses this idea here. 7. Optional: adding post_install and pre_uninstall bash scripts.​ If your plugin needs to edit the operating system, you can include either of the following files: post_install.sh, or pre_uninstall.sh. We have used these files to enable systemd services such that the job being installed will start at startup. Example post_install.sh and pre_uninstall.sh. You'll need to append to your MANIFEST.in, too: include <PLUGIN_NAME>/post_install.sh include <PLUGIN_NAME>/pre_uninstall.sh For an example, see the logs2slack plugin's repository. 8. Optional: only installing on leader Pioreactor.​ Some plugins may only want to be installed on the leader. For example, if they are changing the UI or database. To signal that a plugin should only be installed on the leader (and no-op on workers), add an empty file named LEADER_ONLY to the folder. You'll need to append to your MANIFEST.in, too: include <PLUGIN_NAME>/LEADER_ONLY For an example, see the logs2slack plugin's repository.","s":"Contents of the subfolder, <PLUGIN_NAME>","u":"/developer-guide/plugin-as-python-package","h":"#contents-of-the-subfolder-plugin_name","p":163},{"i":172,"t":"Create an account on https://pypi.org/. Make sure to verify your email. On your command line, type the following: pip install twine pip install --upgrade build python -m build --wheel This creates a .whl file in a dist/ folder (that will be created). Next, we upload the whl file to PyPI: twine upload dist/<THE .WHL FILE> You will then be prompted for a username and password. Use the credentials for your PyPI account. Then, your package is uploaded and viewable at the link provided in the output! Note Before you build a new wheel, it's good practice to clean up your previous build. This can be done using python setup.py clean --all on the command line.","s":"Create a Python package on PyPI","u":"/developer-guide/plugin-as-python-package","h":"#create-a-python-package-on-pypi","p":163},{"i":174,"t":"A plugin can be installed through the command line on a leader using pio: pio plugin install <DISTRIBUTION-NAME OR PLUGIN_NAME> To install a given plugin on the leader and all workers connected to the leader in a cluster, pios plugins install can be used. pios plugin install <DISTRIBUTION-NAME OR PLUGIN_NAME>","s":"Installing your Python package on your cluster","u":"/developer-guide/plugin-as-python-package","h":"#installing-your-python-package-on-your-cluster","p":163},{"i":176,"t":"To give your plugin further reach, we've provided an option to add it to the web interface. You will need to edit the plugins.json file within our Pioreactor repository, list-of-plugins. There are two ways to do this: Create an issue to have us edit the plugins.json file for you. Fork from our repository to edit the plugins.json file, then create a pull request. In both cases, we will evaluate your plugin to ensure code quality and all requirements are met. Once your plugin is accepted, it will appear on the Plugins tab on the Pioreactor web interface. Users in the community can now easily click Install to download your plugin onto their Pioreactors!","s":"Sharing your plugin with the community","u":"/developer-guide/plugin-as-python-package","h":"#sharing-your-plugin-with-the-community","p":163},{"i":179,"t":"Endpoint Methods Rule --------------------------------------- ------- ------------------------------------------------------------------------- able_to_install_plugins_from_ui GET /api/allow_ui_installs create_or_update_new_calibrations PUT /api/calibrations get_available_calibrations_type_by_unit GET /api/calibrations/<pioreactor_unit> get_available_calibrations_of_type GET /api/calibrations/<pioreactor_unit>/<calibration_type> get_calibration_by_name GET /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name> patch_calibrations PATCH /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name> get_current_calibrations_of_type GET /api/calibrations/<pioreactor_unit>/<calibration_type>/current get_configs GET /api/configs get_config GET /api/configs/<filename> update_config PATCH /api/configs/<filename> get_automation_contrib GET /api/contrib/automations/<automation_type> get_charts_contrib GET /api/contrib/charts create_experiment_profile POST /api/contrib/experiment_profiles get_experiment_profiles GET /api/contrib/experiment_profiles get_experiment_profile GET /api/contrib/experiment_profiles/<filename> delete_experiment_profile DELETE /api/contrib/experiment_profiles/<filename> get_job_contrib GET /api/contrib/jobs get_experiments GET /api/experiments create_experiment POST /api/experiments delete_experiment DELETE /api/experiments/<experiment> update_experiment PATCH /api/experiments/<experiment> get_logs GET /api/experiments/<experiment>/logs get_media_rates GET /api/experiments/<experiment>/media_rates get_fallback_time_series GET /api/experiments/<experiment>/time_series/<data_source>/<column> get_growth_rates GET /api/experiments/<experiment>/time_series/growth_rates get_od_readings GET /api/experiments/<experiment>/time_series/od_readings get_od_readings_filtered GET /api/experiments/<experiment>/time_series/od_readings_filtered get_temperature_readings GET /api/experiments/<experiment>/time_series/temperature_readings get_unit_labels GET /api/experiments/<experiment>/unit_labels upsert_unit_labels PUT /api/experiments/<experiment>/unit_labels get_logs_for_unit_and_experiment GET /api/experiments/<experiment>/units/<unit>/logs get_list_of_workers_for_experiment GET /api/experiments/<experiment>/workers add_worker_to_experiment PUT /api/experiments/<experiment>/workers remove_workers_from_experiment DELETE /api/experiments/<experiment>/workers remove_worker_from_experiment DELETE /api/experiments/<experiment>/workers/<pioreactor_unit> stop_worker_in_experiment POST /api/experiments/<experiment>/workers/<worker>/stop stop_all_in_experiment POST /api/experiments/<experiment>/workers/stop get_experiments_worker_assignments GET /api/experiments/assignment_count get_latest_experiment GET /api/experiments/latest export_datasets POST /api/export_datasets get_historical_config_for GET /api/historical_configs/<filename> get_historical_media_used GET /api/historical_media get_historical_organisms_used GET /api/historical_organisms is_local_access_point_active GET /api/is_local_access_point_active install_plugin POST /api/plugins/install get_installed_plugins GET /api/plugins/installed get_plugin GET /api/plugins/installed/<filename> uninstall_plugin POST /api/plugins/uninstall setup_worker_pioreactor POST /api/setup_worker_pioreactor reboot_unit POST /api/units/<unit>/reboot shutdown_unit POST /api/units/<unit>/shutdown update_app POST /api/update_app update_app_from_release_archive POST /api/update_app_from_release_archive update_app_to_develop POST /api/update_app_to_develop upload POST /api/upload get_app_version GET /api/versions/app get_ui_version GET /api/versions/ui get_list_of_workers GET /api/workers add_worker PUT /api/workers delete_worker DELETE /api/workers/<pioreactor_unit> get_worker GET /api/workers/<pioreactor_unit> get_experiment_assignment_for_worker GET /api/workers/<pioreactor_unit>/experiment change_worker_status PUT /api/workers/<pioreactor_unit>/is_active run_job_on_unit PATCH /api/workers/<unit>/experiments/<experiment>/jobs/<job>/run stop_job_on_unit PATCH /api/workers/<unit>/jobs/<job>/stop get_workers_and_experiment_assignments GET /api/workers/assignments static GET /static/<path:filename> From python3 -m flask --debug --app main routes -s rule","s":"All endpoints","u":"/developer-guide/web-ui-api","h":"#all-endpoints","p":177},{"i":181,"t":"Let's design a simple LED automation for Light/Dark cycles. The basic idea is that the LED automation \"wakes up\" (specifically: it runs its execute method) every hour, and on specific hours, turns on or turns off the white light LEDs.","s":"Another example writing a new automation","u":"/developer-guide/writing-automations-2","h":"","p":180},{"i":183,"t":"Imports at the top of the file! # -*- coding: utf-8 -*- from __future__ import annotations from pioreactor.automations.led.base import LEDAutomationJobContrib from pioreactor.whoami import get_unit_name, get_latest_experiment_name from pioreactor.automations import events Define a new class as a subclass of LEDAutomationJobContrib. We use LEDAutomationJobContrib since this is a 3rd party automation. We give the new class a descriptive name. The automation_name attribute is necessary - and is often just the camel case version of the class name. class LightDarkCycle(LEDAutomationJobContrib): automation_name = \"light_dark_cycle\" Define our published_settings for this class. This is a dictionary of LightDarkCycle attributes that we can modify/inspect from MQTT (and hence from the UI, or from the leader Pioreactor). Not all attributes need to go in here - only the ones that users may want to modify mid-experiment. Later in this post, we'll see what each of these attributes does. published_settings = { \"duration\": {\"datatype\": \"float\", \"settable\": False, \"unit\": \"min\"}, \"light_intensity\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"%\"}, \"light_duration_hours\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"h\"}, \"dark_duration_hours\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"h\"}, } Create the __init__, with the attributes we'll need. def __init__(self, light_intensity: float, light_duration_hours: int, dark_duration_hours: int, **kwargs): super().__init__(**kwargs) self.hours_online = -1 self.light_active = False self.channels = [\"B\", \"C\"] self.set_light_intensity(light_intensity) self.light_duration_hours = float(light_duration_hours) self.dark_duration_hours = float(dark_duration_hours) hours_online will keep track of how many elapsed hours have gone by. light_active keeps track of whether the LEDs are currently on or off channels refers to which LED channels on the Pioreactor HAT we are using. light_duration_hours: the number of hours to keep the light on for, typically 16 dark_duration_hours: the number of hours to keep the light off for, typically 8 light_intensity: the level of intensity, as a percent, of the LEDs when turned on. We define the execute function, which is what runs every duration minutes. In the function, we increment hours_online by 1 (since it runs every 60 minutes), and ask a separate function, trigger_leds, to handle turning on and off LEDs. The execute can return an Event, which is useful for logging and testing purposes. def execute(self): self.hours_online += 1 event = self.trigger_leds(self.hours_online) return event The other class function, trigger_leds, role is to: determine if we should turn on LEDs, turn off LEDs, or do nothing. If we are changing LEDs status (on to off, or off to on), perform that task. return an Event, with some description of what occurred (even if nothing changed). To do 1., we think about the total hours passed modulo how long our cycle is. That is, if our cycle lasts 24 hours (which might be the result of choosing 16h light + 8h dark), then the hour 33 is really the same as hour 9, likewise the hour 123 is the same as hour 3: we take the hour modulo the duration. We then ask, is this hour in the dark period, or the light period, of the cycle? We also ask if the lights_active is on, or off, respectively? If so, we change the status of the LEDs. For example, if we should be in the dark period, but our LEDs are on, well, we turn them off, and return a ChangeLEDIntensity event. The function set_led_intensity is from the parent class, and is a helper function. def trigger_leds(self, hours: int) -> events.Event: cycle_duration: int = self.light_duration_hours + self.dark_duration_hours if ((hours % cycle_duration) < self.light_duration_hours) and (not self.light_active): self.light_active = True for channel in self.channels: self.set_led_intensity(channel, self.light_intensity) return events.ChangedLedIntensity(f\"{hours}h: turned on LEDs\") elif ((hours % cycle_duration) >= self.light_duration_hours) and (self.light_active): self.light_active = False for channel in self.channels: self.set_led_intensity(channel, 0) return events.ChangedLedIntensity(f\"{hours}h: turned off LEDs\") else: return events.NoEvent(f\"{hours}h: no change\") We also need to define that set_light_intensity function above. This function is automatically called whenever we change light_intensity (see note below). We need additional logic to immediately change the light_intensity when asked, otherwise, the LEDs wouldn't actually update until the next execute is called, which could be an hour away. def set_light_intensity(self, intensity) -> None: self.light_intensity = float(intensity) if self.light_active: # update now! for channel in self.channels: self.set_led_intensity(channel, self.light_intensity) else: pass info Updates over MQTT either update the attribute directly, i.e. :self.<attr> = new_value, or, if defined, the method set_<attr>(new_value) is called instead. This is what is happening with set_light_intensity. Using set_<attr> methods is useful when you have additional logic that needs to be accomplished when an attribute changes. That's the end of the class! In total, our file looks like: # -*- coding: utf-8 -*- from __future__ import annotations from pioreactor.automations.led.base import LEDAutomationJobContrib from pioreactor.automations import events class LightDarkCycle(LEDAutomationJobContrib): \"\"\" Follows as h light / h dark cycle. Starts dark. \"\"\" automation_name = \"light_dark_cycle\" published_settings = { \"duration\": {\"datatype\": \"float\", \"settable\": False, \"unit\": \"min\"}, # doesn't make sense to change duration. \"light_intensity\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"%\"}, \"light_duration_hours\": {\"datatype\": \"int\", \"settable\": True, \"unit\": \"h\"}, \"dark_duration_hours\": {\"datatype\": \"int\", \"settable\": True, \"unit\": \"h\"}, } def __init__(self, light_intensity: float, light_duration_hours: int, dark_duration_hours: int, **kwargs): super().__init__(**kwargs) self.hours_online: int = -1 self.light_active: bool = False self.channels = [\"B\", \"C\"] self.set_light_intensity(light_intensity) self.light_duration_hours = float(light_duration_hours) self.dark_duration_hours = float(dark_duration_hours) def trigger_leds(self, hours: int) -> events.Event: cycle_duration: int = self.light_duration_hours + self.dark_duration_hours if ((hours % cycle_duration) < self.light_duration_hours) and (not self.light_active): self.light_active = True for channel in self.channels: self.set_led_intensity(channel, self.light_intensity) return events.ChangedLedIntensity(f\"{hours}h: turned on LEDs\") elif ((hours % cycle_duration) >= self.light_duration_hours) and (self.light_active): self.light_active = False for channel in self.channels: self.set_led_intensity(channel, 0) return events.ChangedLedIntensity(f\"{hours}h: turned off LEDs\") else: return events.NoEvent(f\"{hours}h: no change\") def set_light_intensity(self, intensity) -> None: self.light_intensity = float(intensity) if self.light_active: # update now! for channel in self.channels: self.set_led_intensity(channel, self.light_intensity) else: pass def execute(self) -> events.Event: self.hours_online += 1 event = self.trigger_leds(self.hours_online) return event","s":"The Code","u":"/developer-guide/writing-automations-2","h":"#the-code","p":180},{"i":185,"t":"Setting up your Pioreactor is easy: attach LEDs to LED channels B and C, and stick them in pockets X2 and X3.","s":"Setting up the Pioreactor","u":"/developer-guide/writing-automations-2","h":"#setting-up-the-pioreactor","p":180},{"i":187,"t":"Let's save this file to our Pioreactor plugin folder, by accessing the Pioreactor's command line, typing nano ~/.pioreactor/plugins/light_dark_cycle.py, and pasting in the code above. You can test the automation from the Pioreactor's command line by executing: pio run led_control --automation-name light_dark_cycle --light_intensity 45 --light_duration_hours 16 --dark_duration_hours 8","s":"Running the automation","u":"/developer-guide/writing-automations-2","h":"#running-the-automation","p":180},{"i":189,"t":"To add your automation to the UI so it appears in the automation drop-down, follow the the steps here.","s":"Adding the automation to the UI","u":"/developer-guide/writing-automations-2","h":"#adding-the-automation-to-the-ui","p":180},{"i":191,"t":"The following provides solutions to: using a different pumping system for the Pioreactor instead of our peristaltic pumps adding additional pumps to the Pioreactor (i.e., more than media and alt-media). These additional pumps may be provided via another system, for example an Arduino.","s":"Custom & additional pumps for dosing automations","u":"/developer-guide/writing-pump-software","h":"","p":190},{"i":193,"t":"The first thing to do is to add a hook to your custom pump into Pioreactor's software. To do this, we attach new functions to a dosing automation that are invoked when execute_io_action is called. These functions will call your logic that runs the external pump. Specifically, if we wish to overwrite the media pump, we create a function called add_media_to_bioreactor, with signature (cls, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client: pioreactor.pubsub.Client) -> float) To see this in an example: from pioreactor.automations.dosing.base import DosingAutomationJob class CustomPumper(DosingAutomationJob): automation_name = \"custom_pumper\" def __init__(self, **kwargs): super().__init__(**kwargs) def add_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # overrides the built in add_media_to_bioreactor # add your custom logic here. Example could be interfacing with i2c, serial, PWM, etc. ... pwm = PWM(...) self.logger.info(f\"pumping {ml}\") return ml def execute(self): self.execute_io_action(media_ml=1.0, waste_ml=1.0) Whenever execute_io_action is called upon to add media, the custom function add_media_to_bioreactor is invoked. Similar logic applies to alt_media. Overriding waste uses a different name, as the next example shows: class CustomPumper(DosingAutomationJob): automation_name = \"custom_pumper\" def add_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # overrides the built in add_media_to_bioreactor ... return ml def add_alt_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # overrides the built in remove_waste_from_bioreactor ... return ml def remove_waste_from_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # overrides the built in remove_waste_from_bioreactor ... return ml def __init__(self, **kwargs): super().__init__(**kwargs) def execute(self): self.execute_io_action(media_ml=1.0, alt_media_ml=1.0, waste_ml=2.0)","s":"Using external pumps with a custom automation","u":"/developer-guide/writing-pump-software","h":"#using-external-pumps-with-a-custom-automation","p":190},{"i":195,"t":"In general, we can use this same pattern to add even more pumps to the Pioreactor software, beyond media and alt-media. Let's say we have a third pump, salty-media, that we wish to also use along with media and alt-media. We define the function add_salty_media_to_bioreactor with the same signature above: class ThreePumps(DosingAutomationJob): automation_name = \"three_pumps\" def add_salty_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float: # call an external pump, via i2c, serial, GPIO, etc., # or pumping_functions.add_salt_media ... return ml def __init__(self, **kwargs): super().__init__(**kwargs) With this function defined, we can invoke execute_io_action with an additional kwarg, salty_media_ml: def execute(self): results = self.execute_io_action(waste_ml=3.0, media_ml=1.0, alt_media_ml=1.0, salty_media_ml=1.0) Notice the salty_media_ml=1.0 kwarg: this represents how much salty-media volume to add (your pump is responsible to dosing the correct volume). (Note in the above example, media and alt-media are not overwritten, so would use the \"traditional\" peristaltic pump system provided.) info In general, execute_io_action will try to call a function called add_<name>_to_bioreactor if provided with a kwarg <name>_ml.","s":"Adding additional pumps beyond media and alt-media","u":"/developer-guide/writing-pump-software","h":"#adding-additional-pumps-beyond-media-and-alt-media","p":190},{"i":197,"t":"Since the behaviour of the Pioreactor is controlled by Python objects, you can write Python scripts that use those objects. Here's a simple example of starting the stirring by creating the Stirrer object: from pioreactor.background_jobs.stirring import Stirrer, RpmFromFrequency from pioreactor.whoami import get_unit_name from pioreactor.whoami import get_latest_experiment_name unit = get_unit_name() experiment = get_latest_experiment_name() st = Stirrer( target_rpm=300, unit=unit, experiment=experiment, rpm_calculator=RpmFromFrequency() ) st.start_stirring() st.block_until_disconnected() # pauses the execution, but stirring continues Save this code to a local file on your Pioreactor's Raspberry Pi called stirring_script.py. Then, running python stirring_scripy.py, you should see that stirring on the Pioreactor starts. With the script running, you should also updates on the Pioreactor UI (ex: see pioreactor.local/pioreactors page). Typing ctrl-c will exit the script. info What is get_unit_name and get_latest_experiment_name? These are helper functions that get the current name of the Pioreactor, and the current experiment name, respectively. Using the current experiment name will ensure that your data shows up in the UI, and is correctly stored in the database. Automations​ Using automations requires you to invoke them with a Controller. For example, below we start a chemostat with some specific parameters, and set the target temperature to 30C. from pioreactor.background_jobs.dosing_control import DosingController from pioreactor.background_jobs.temperature_control import TemperatureController from pioreactor.whoami import get_latest_experiment_name unit = get_unit_name() experiment = get_latest_experiment_name() dc = DosingController( \"chemostat\", # automation name duration=1, # every minute, volume=1, # dose 1mL unit=unit, experiment=experiment, ) tc = TemperatureController( \"thermostat\", target_temperature=30, unit=unit, experiment=experiment ) dc.block_until_disconnected()","s":"Writing scripts","u":"/developer-guide/writing-scripts","h":"","p":196},{"i":199,"t":"On the command line, you can run your script with python your_script.py If you want to run the script in the background (so you can close terminal and the job continues in the background), use python your_script.py >/dev/null 2>&1 & disown You can also use the Pioreactor's plugin architecture to control the start and stop of the script.","s":"Starting a long-running script","u":"/developer-guide/writing-scripts","h":"#starting-a-long-running-script","p":196},{"i":201,"t":"RepeatedTimer: this class allows you to scheduale a function to run every N seconds in a non-blocking manner.","s":"Useful utility objects","u":"/developer-guide/writing-scripts","h":"#useful-utility-objects","p":196},{"i":203,"t":"Success Goal Use caffeine-containing liquids to inhibit the growth of your culture.","s":"Caffeine inhibition","u":"/experiments/caffeine-inhibition","h":"","p":202},{"i":205,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix Caffeine-containing liquids (tea, coffee)","s":"Requirements","u":"/experiments/caffeine-inhibition","h":"#requirements","p":202},{"i":208,"t":"Yeasts are versatile eukaryotes that have biological systems synonymous to those found in humans. Substances that affect us are likely to affect yeast as well, so yeasts are commonly used in research to study certain behaviours. Let's take a look at yeast reactions to caffeine, and model these behaviours using our Pioreactor! Caffeine is the most common stimulant in the world, and is found in many consumed items such as coffees, teas, chocolates, and even within certain medication. Ponder this: what do you expect to happen when caffeine is added to yeast cultures? We know that we feel more awake and focused after consumption, but have your students think about why this happens. Think about both the positives and negatives of consuming coffee and form a hypothesis on how yeast cultures will react to caffeine addition. Also consider the other components of black tea","s":"Introduction","u":"/experiments/caffeine-inhibition","h":"#introduction","p":202},{"i":210,"t":"We used two Pioreactors and two vials containing 15 mL of YPD media. We added 1 mL DI water to one vial and 1 mL steeped black tea to another. For the steeped black tea, a teabag was steeped in 250 mL hot water for 5 minutes before inoculation. Finally, we inoculated with 100 uL yeast slurry using a micropipette.","s":"Experiment","u":"/experiments/caffeine-inhibition","h":"#experiment","p":202},{"i":212,"t":"The growth rate chart clearly demonstrates an inhibition of growth occuring in the sample containing tea:","s":"Results","u":"/experiments/caffeine-inhibition","h":"#results","p":202},{"i":214,"t":"We recommend trying different amounts of tea, coffee, or other caffeine containing liquids to evaluate effects of caffeine concentrations. For example, how does adding one drop of black coffee compare to one drop of black tea? For a larger study, also consider giving your students a collection of common substances (vinegar, teas, salt, sugars) and see how these can boost or reduce growth rates.","s":"Recommendations","u":"/experiments/caffeine-inhibition","h":"#recommendations","p":202},{"i":216,"t":"Prepare identical sterile stocks in vials with your media of choice. Add some amount (a few drops to 1 mL) of a liquid containing caffeine to a vial. Add the same amount of DI water to another vial. If the media appears different before inoculation, we recommend you blank your vials before adding your culture. Inoculate each vial with a very small amount of your microorganism, using best practices to avoid other contamination. In our example, a yeast stock solution can be made by diluting a small amount of yeast in 15mL of YPD stock media, then a drop of this stock solution can be added to your vials. Wipe the vials and place them in the Pioreactors. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start Stirring activity, Temperature automation activity (set to an optimal temperature; ex. 30°C) and OD reading activity. Confirm that everything looks normal (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/caffeine-inhibition","h":"#detailed-procedure","p":202},{"i":218,"t":"Success goal Determine the maximum specific growth rate of your culture using turbidostat strategies and pump extentions of the Pioreactor.","s":"Continuous cultures using a turbidostat","u":"/experiments/continuous-cultures-using-turbidostat","h":"","p":217},{"i":220,"t":"# One available Pioreactor Two peristaltic pumps: One media pump One waste pump Two liquid containers: One labelled \"media\" One labelled \"waste\" Scale to calibrate, if needed","s":"Requirements","u":"/experiments/continuous-cultures-using-turbidostat","h":"#requirements","p":217},{"i":223,"t":"Your Pioreactor can be transformed into a turbidostat, where pumps are used to replenish media around a target OD, creating a continuous culture. Due to the abundance of resources and lack of rate-limiting nutrients, the specific growth rate of a species is maximized. Learn more about the differences in bioreactor strategies here! This setup is a powerful tool that tests the limits of population growth. Students can investigate the specific maximum growth rate of a species and evaluate what innate biological processes are limiting growth.","s":"Introduction","u":"/experiments/continuous-cultures-using-turbidostat","h":"#introduction","p":217},{"i":225,"t":"In our turbidostat system, we studied a small vial of YPD media inoculated with 4 drops of a yeast slurry. We set our volume to be exchanged to be 1 mL when the target OD was reached. This means at our target OD, 1 mL of media in the vial would be removed, and 1 mL of fresh media is added. We initially set our turbidostat target OD to 2 AU. To demonstrate how quickly our system can adapt, we changed our target OD to 3.5 AU after 6 hours. A higher target OD allows the culture to become more turbid.","s":"Experiment","u":"/experiments/continuous-cultures-using-turbidostat","h":"#experiment","p":217},{"i":227,"t":"After 16 hours, the following results are recorded: FYI: Why does normalized OD look like that? After the time period set by you (the Time between dosing), the system assesses the normalized OD. As the normalized OD approaches the target OD, an automated amount of new media is added and waste is removed. The next time the system \"wakes up\", the OD will equals/be close to the set target OD. Over time, we expect faster growing yeast to out-compete slower growing yeast, resulting in an increase in maximum growth rate. As seen above, the growth rate improves from 0.30 h⁻¹ to 0.41 h⁻¹ in the span of 15 hours.","s":"Results","u":"/experiments/continuous-cultures-using-turbidostat","h":"#results","p":217},{"i":229,"t":"There is a myriad of further applications for turbidostats, such as characterization of species, directed evolution, responses to stimuli (gene-regulating metabolites) and so much more. We encourage you to choose species and media compositions to suit your interests. Have fun!","s":"Recommendations","u":"/experiments/continuous-cultures-using-turbidostat","h":"#recommendations","p":217},{"i":231,"t":"Add media into your media container. Sterilize by autoclaving. Adjust the tube lengths on the cap of your small sterile vial such that one just touches the media, while another sits above the media. Inoculate your small sterile vial with drops of your culture. Wipe vial and place in the Pioreactor. For your media pump: Attach the source tube to your media container. Attach the sink tube to the vial cap tube that sits above the media. For your waste pump: Attach the source tube to the vial cap tube that touches the media. Attach the sink tube to your waste container. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Select Manage, start Stirring activity and OD reading activity. Confirm everything looks correct, then start the Growth rate activity. Start the Dosing automation. Change automation to Turbidostat. Set your Volume and Target OD. You can change the parameters of the turbidostat automation in the Settings tab. Changes will take effect immediately.","s":"Detailed procedure","u":"/experiments/continuous-cultures-using-turbidostat","h":"#detailed-procedure","p":217},{"i":233,"t":"Success goal This experiment will show the growth curve of algae over a 20h:4h day/night cycle, at two different intensities (4% and 8%).","s":"Algae day and night cycles","u":"/experiments/algae-day-night-cycle","h":"","p":232},{"i":235,"t":"# At least one available Pioreactor Algae Media for algae; for ex. Bold's Basal Medium (BBM) Two LED cables per Pioreactor.","s":"Requirements","u":"/experiments/algae-day-night-cycle","h":"#requirements","p":232},{"i":238,"t":"Adding two LED bulbs onto your base Pioreactor will transform it into a photo-bioreactor, giving you the ability to grow species that require light! In this experiment, we will monitor algae using our Day/Night plugin. There are two main phases that will be observed between the light being on (\"day\") and off (\"night\"). Exponential growth will occur during the “day” as algae biomass is accumulated through photosynthesis), and stalled growth will occur “overnight”, where algae reproduce, but don't accumulate biomass. This should make for some interestingly patterned OD readings!","s":"Introduction","u":"/experiments/algae-day-night-cycle","h":"#introduction","p":232},{"i":240,"t":"We started off with a culture of Chlorella vulgaris that we grew in a tissue culture flask using Bold's Basal Medium. We then used 10 mL of BBM per vial, then inoculated with 1 mL of our culture. With two Pioreactors, we started our experiment using the Day/Night plugin and chose light intensities of 4% and 8%. We kept stirring high to avoid formation of flocculants that could impede our OD readings. Typical experiments use a 16h:8h day night cycle, but we've adjusted the time period to 20h:4h. The experiment takes place over a few days, so results were seen after a week.","s":"Experiment","u":"/experiments/algae-day-night-cycle","h":"#experiment","p":232},{"i":242,"t":"For this style of experiment, let's investigate our normalized OD results: Adjusting just one factor (light intensity) where one is twice as high as the other yielded an approximate doubling of growth in the vial subjected to higher light intensity!","s":"Results","u":"/experiments/algae-day-night-cycle","h":"#results","p":232},{"i":244,"t":"Your Pioreactor is capable of controling a wide diversity of lighting effects on algae or other photosynthesizing microorganisms. The addition of the Day/Night cycle plugin and the ability to use LEDs opens a range of photobioreactor experiments! You can adjust intensities, photoperiods, and even switch out types of bulbs across the light spectrum to study effects of colours or UV lights.","s":"Recommendations","u":"/experiments/algae-day-night-cycle","h":"#recommendations","p":232},{"i":246,"t":"Attach two LED cables into channels C and D. Insert the bulbs into the X2 and X3 pockets and secure them in place with the pocket caps. While on, some light leaking is acceptable. Prepare a sterile stock of media for algae. We used Bold’s Basal Medium (BBM). Aim for 10 to 12 mL of media per each vial/Pioreactor you will be using. This is to allow more headspace for oxygen! Add 1 mL of your algae culture to each vial. Wipe the vials and place them in the Pioreactor. Visit pioreactor.local and start a new experiment. Click the Plugins tab on the left and install the led_cycle plugin. This will add the Day/Night feature when you begin LED automations. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start Stirring activity and OD reading activity. Optional Start the Temperature automation activity set on an optimal temperature. Start the LED automation at the bottom of the Activities list in Manage. Select Day/Night Cycle from the drop down menu, and set your desired Intensity (no more than 12% works best!) or Light and Dark duration (16h:8h is optimal). This automation creates a day/night cycle ideal for algae growth. Confirm that everything looks normal on the Overview page (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Optional Change the names of the Pioreactor in the UI to organize your vials. Watch the growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/algae-day-night-cycle","h":"#detailed-procedure","p":232},{"i":248,"t":"Success Goal Conduct a simple control test to evaluate results between Pioreactors, using the same media composition, culture, and activities.","s":"Control testing","u":"/experiments/control-testing","h":"","p":247},{"i":250,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix","s":"Requirements","u":"/experiments/control-testing","h":"#requirements","p":247},{"i":253,"t":"Like any biotechnology, sources of error exist due to slight differences between Pioreactors. This can include bulb intensity variations, minute differences in the Pioreactor plastics, and even slight differences between vials! We can minimize how these differences affect our experiment through calibrations (check out available calibrations) and test these differences by conducting control tests. Control tests for the Pioreactor, unlike typical experiments, look at two or more instruments under the same conditions to determine any variances. This is an important statistical consideration when comparing data between several Pioreactors for research purposes. Ideally, we'd expect Pioreactors run under the same conditions to have very similar results. If results are dissimilar, we can begin to investigate sources of error by manipulating internal factors (such as configurations).","s":"Introduction","u":"/experiments/control-testing","h":"#introduction","p":247},{"i":255,"t":"The experiment is simple: place identical sterile vials into your Pioreactors, inoculated with the same amount of culture. Set stirring at the same RPM, temperature, and turn on OD reading and growth rate. With all factors the same, you should see similar normalized OD and growth rate graphs being generated.","s":"Experiment","u":"/experiments/control-testing","h":"#experiment","p":247},{"i":257,"t":"Here are graphs we generated though our A/A test: These kinds of tests make it easy to identify any unusual activity occuring in a specific Pioreactor (i.e, if it is missing an LED, temperature malfunctions, etc). In our case, though, both ran almost identically! Thus, we conclude that reliable comparisons can be drawn between these Pioreactors.","s":"Results","u":"/experiments/control-testing","h":"#results","p":247},{"i":259,"t":"Prepare identical sterile stocks in vials with your media of choice. Inoculate each vial with a very small amount of your microorganism, using best practices to avoid other contamination. In our example, a yeast stock solution can be made by diluting a small amount of yeast in 15mL of YPD stock media, then a drop of this stock solution can be added to your vials. Wipe the vials and place them in the Pioreactors. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start Stirring activity, Temperature automation activity (set to an optimal temperature; ex. 30°C) and OD reading activity. Confirm that everything looks normal (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/control-testing","h":"#detailed-procedure","p":247},{"i":262,"t":"For this introductory example, we'll create a background job that controls an LED in channel A on the Pioreactor HAT. When the job ends (either by us exiting, or via a MQTT signal), the LED will turn off. We start with some imports, and a class definition: from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" We've given the class the simple name of IntroJob. Our background job must inherit from BackgroundJob. All jobs require a job_name: the job_name is usually the snake-case of the class name. Next we'll define some initial attributes: from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" We declare that the intensity attribute is to be published and controllable over MQTT. We'll see this in action later. We also set intensity to be 0 initially, and use channel A to control. Next we add the __init__, which should always accept at least unit and experiment (as strings). unit refers to the name of the Pioreactor (the hostname), and experiment is the experiment the job is associated to. from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" def __init__(self, unit, experiment): super().__init__(unit=unit, experiment=experiment) We call super to initialize the super class, BackgroundJob, with the unit, and experiment. Next, we define a function, set_intensity that will be called whenever intensity is changed remotely (we'll do this later). The set_intensity function updates intensity and will change the onboard LED power for channel A. Remember, whenever the attribute intensity changes, it's published to MQTT. from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" def __init__(self, unit, experiment): super().__init__(unit=unit, experiment=experiment) def set_intensity(self, intensity): self.intensity = intensity led_intensity(channels=self.LED_channel, intensities=self.intensity) Next, we create the \"on exit\" behaviour (turn off LED) by overwriting the on_disconnected function. from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" def __init__(self, unit, experiment): super().__init__(unit=unit, experiment=experiment) def set_intensity(self, intensity): self.intensity = intensity led_intensity(channels=self.LED_channel, intensities=self.intensity) def on_disconnected(self): self.set_intensity(0) Finally, we add a small script at the bottom to run our new job when the Python file is invoked: from pioreactor.background_jobs.base import BackgroundJob from pioreactor.actions.led_intensity import led_intensity class IntroJob(BackgroundJob): job_name=\"intro_job\" published_settings = { 'intensity': {'datatype': \"float\", \"unit\": \"%\", \"settable\": True} } intensity = 0 LED_channel = \"A\" def __init__(self, unit, experiment): super().__init__(unit=unit, experiment=experiment) def set_intensity(self, intensity): self.intensity = intensity led_intensity(channels=self.LED_channel, intensities=self.intensity) def on_disconnected(self): self.set_intensity(0) if __name__ == \"__main__\": from pioreactor.whoami import get_unit_name from pioreactor.whoami import get_latest_experiment_name job = IntroJob(unit=get_unit_name(), experiment=get_latest_experiment_name()) job.block_until_disconnected() If you save this code in a file called intro_job.py, we can run it from the command line: python3 intro_job.py. In another terminal window, try the following: pio mqtt -t \"pioreactor/+/+/intro_job/#\" You should see some metadata about this job ($state is ready, some info about intensity), but also you should see the current value of intensity, namely 0. You can cancel the job with ctrl-c in the original terminal window. Adding an additional line in intro_job.py: if __name__ == \"__main__\": from pioreactor.whoami import get_unit_name from pioreactor.whoami import get_latest_experiment_name job = IntroJob(unit=get_unit_name(), experiment=get_latest_experiment_name()) job.set_intensity(10) job.block_until_disconnected() And rerunning the job, you should see MQTT have updated intensity data.","s":"Introductory example","u":"/developer-guide/writing-background-jobs","h":"#introductory-example","p":260},{"i":264,"t":"We'll explain how a more advanced background job is written using the example application of a job that controls an external motor (the load). This motor may control a larger stirrer, or shaker, or air-pump, but is regulated by the amount of voltage applied - that is, the more voltage applied, the more output from the motor. The Pioreactor HAT has four available pulse-width modulation (PWM) outputs, with programmable frequency and duty cycle (DC). For this example, we'll set a frequency that works for the motor. We also wish to increase the DC in proportion to the normalized optical density (this may represent needing to add more air, or shaking, as the culture's oxygen requirements increase). Let's start with the some imports and the class' __init__: from pioreactor.background_jobs.base import BackgroundJob class MotorDriver(BackgroundJob): job_name=\"motor_driver\" def __init__(self, hz, initial_duty_cycle, unit, experiment, **kwargs): super().__init__(unit=unit, experiment=experiment) self.hz = hz self._initial_duty_cycle = initial_duty_cycle self.duty_cycle = initial_duty_cycle ... We see that the __init__ requires the two parameters for PWM: hz and an inital_duty_cycle. One rarely changes the hertz of PWM, so its fixed - but we do often change the duty cycle, so we create a variable self.duty_cycle and assign it the initial_duty_cycle. We also need to supply the unit name (the hostname), and the experiment name. We'll populate these at run time later. Finally, we need a job_name to pass to the super class, BackgroundJob. This should be unique from other jobs that may run. Often we use the \"snake_case\" of the class name as the job name. We give it the job name motor_driver. We next initialize the PWM code (this is still in the __init__) that controls the PWM outputs on the HAT, and add more imports: from pioreactor.hardware_mappings import PWM_TO_PIN from pioreactor.utils.pwm import PWM from pioreactor.config import config ... def __init__(...) ... pwm_pin = PWM_TO_PIN[config[\"PWM_reverse\", \"motor_driver\"]] self.pwm = PWM(pwm_pin, self.hz) self.pwm.lock() ... The PWM_TO_PIN is lookup that maps settings in your config.ini to the Raspberry Pi's GPIO pins (which we use for the output PWM). Which means we also need update the [PWM] section in your config.ini: [PWM] 1=motor_driver 2=media 3=alt_media 4=waste 5=heater In the above code, we next initialize the PWM class. This is an abstraction to make working with the PWM hardware easier. For example, the next line, self.pwm.lock(), will put a lock on that Raspberry Pi GPIO pin, making it difficult for other processes to use it by mistake. We haven't started the PWM yet, we'll do that later. Next, we want to include the behavior to update the duty cycle when we get new normalized OD readings. This is typically done with a callback when a new MQTT message is received. See code below: def __init__(...) ... ... self.start_passive_listeners() ... def start_passive_listeners(self): self.logger.debug(\"Listening for od_filtered topics\") self.subscribe_and_callback( self.update_duty_cycle_by_normalized_od, f\"pioreactor/{self.unit}/{self.experiment}/growth_rate_calculating/od_filtered\", ) Note the self.logger.debug(...) line. Each background job has a Python logger that will log to four places: MQTT, the SQLite3 database, the terminal, and the log file on disk. See Python's logging module for more. The callback, update_duty_cycle_by_normalized_od, needs to be written: import json ... def update_duty_cycle_by_normalized_od(self, message): payload = json.loads(message.payload) if self.state == self.READY: self.set_duty_cycle(payload[\"od_filtered\"] * self._initial_duty_cycle) def set_duty_cycle(self, new_duty_cycle): self.duty_cycle = clamp(0, float(new_duty_cycle), 100) self.pwm.change_duty_cycle(self.duty_cycle) self.logger.debug(f\"new dc: {self.duty_cycle}\") In the callback, update_duty_cycle_by_normalized_od, we accept the message object. The message has two important properties: topic and payload. We only care about the payload, which is a string of json. We de-serialize the json to a dict. We only want to update the duty cycle if the job is in state READY (read about states here). If this is true, we call set_duty_cycle to update our duty cycle. This method handles the logic of clamping the value to be between 0 and 100, and we've stuck a debug in there so we can watch it change. What is the relationship between normalized OD and duty cycle. We do something naive, and just multiple the initial duty cycle by the normalized OD. So if the initial_duty_cycle is 10%, and the culture has 3.5x, then our new duty cycle is 35%. It is very naive. Finally, we need to think about changing states. What should our job do when the user pauses the job? How do we safely disconnect from the PWM? We use the state callback methods to handle these changes: def on_init_to_ready(self): self.pwm.start(self.duty_cycle) def on_ready_to_sleeping(self): self._previous_duty_cycle = self.duty_cycle self.set_duty_cycle(0) def on_sleeping_to_ready(self): self.set_duty_cycle(self._previous_duty_cycle) def on_disconnected(self): self.pwm.clean_up() After the job moves from init to ready (implicitly done after the __init__ finishes), the function on_init_to_ready is called. This starts the PWM, which starts the motor. When we sleep (pause), we record the last duty_cycle value, and use that to populate the duty_cycle when we re-start the job. Let's recap what we have so far, and save this to a file called motor_driver.py (ideally we save it in /home/pioreactor/.pioreactor/plugins/: # -*- coding: utf-8 -*- import json from pioreactor.config import config from pioreactor.background_jobs.base import BackgroundJob from pioreactor.hardware_mappings import PWM_TO_PIN from pioreactor.utils.pwm import PWM from pioreactor.utils import clamp class MotorDriver(BackgroundJob): job_name=\"motor_driver\" published_settings = { \"duty_cycle\": {\"datatype\": \"float\", \"settable\": False, \"unit\": \"%\"}, } _previous_duty_cycle: None def __init__(self, hz, initial_duty_cycle, unit, experiment, **kwargs): super().__init__(unit=unit, experiment=experiment) self.hz = hz self._initial_duty_cycle = initial_duty_cycle self.duty_cycle = initial_duty_cycle self.pwm_pin = PWM_TO_PIN[config[\"PWM_reverse\", \"motor_driver\"]] self.pwm = PWM(self.pwm_pin, self.hz) self.pwm.lock() self.start_passive_listeners() def update_duty_cycle_by_normalized_od(self, message): payload = json.loads(message.payload) if self.state == self.READY: self.set_duty_cycle(payload[\"od_filtered\"] * self._initial_duty_cycle) def set_duty_cycle(self, new_duty_cycle): self.duty_cycle = clamp(0, float(new_duty_cycle), 100) self.pwm.change_duty_cycle(self.duty_cycle) self.logger.debug(f\"new dc: {self.duty_cycle}\") def start_passive_listeners(self): self.logger.debug(\"Listening for od_filtered topics\") self.subscribe_and_callback( self.update_duty_cycle_by_normalized_od, f\"pioreactor/{self.unit}/{self.experiment}/growth_rate_calculating/od_filtered\", ) def on_init_to_ready(self): self.pwm.start(self.duty_cycle) def on_ready_to_sleeping(self): self._previous_duty_cycle = self.duty_cycle self.set_duty_cycle(0) def on_sleeping_to_ready(self): self.set_duty_cycle(self._previous_duty_cycle) def on_disconnected(self): self.logger.debug(\"disconnecting... will clean up PWM\") self.pwm.clean_up() This class works as is, but we also want to develop a command line interface for it so we can run it like pio run motor_driver. At the bottom of the file, we add: import click @click.command(name=\"motor_driver\") @click.option( \"--initial-dc\", default=config.getfloat(\"motor_driver\", \"initial_duty_cycle\"), show_default=True, type=click.FloatRange(0, 100, clamp=True), ) @click.option( \"--hz\", default=config.getfloat(\"motor_driver\", \"hz\"), show_default=True, type=click.FloatRange(1, 10_000, clamp=True), ) def click_motor_driver(initial_dc, hz): \"\"\" Start the external motor \"\"\" from pioreactor.whoami import get_unit_name, get_latest_experiment_name job = MotorDriver( hz=hz, initial_duty_cycle=initial_dc, unit=get_unit_name(), experiment=get_latest_experiment_name(), ) job.block_until_disconnected() Note the helper functions get_unit_name and get_latest_experiment_name to get the metadata for the class. The method block_until_disconnected will halt the program at that line (and only continue when a keyboard interrupt is detected). If you save it in the plugins folder, you can now execute: pio run motor_driver --initial-dc 10 and it should just work! You can exit with ctrl-c, and note that the on_disconnect is called when you do this. Adding published_settings​ Suppose we wish to monitor, or log, or just otherwise publish the duty_cycle from the MotorDriver class. We can \"register\" the attribute duty_cycle in the published_settings: class MotorDriver(BackgroundJob): ... published_settings = { \"duty_cycle\": {\"datatype\": \"float\", \"settable\": False, \"unit\": \"%\"}, } def __init__(...) If you open up the MQTT stream using pio mqtt, you should see duty_cycle appear under the topic pioreactor/<unit>/<experiment>/motor_driver/duty_cycle.","s":"More advanced example","u":"/developer-guide/writing-background-jobs","h":"#more-advanced-example","p":260},{"i":266,"t":"Now that you've set up your Pioreactor, you can start a brand new experiment. Explore the sidebar for experiments you can perform with your Pioreactor. We encourage you to expand on the sample protocols we provided using your own cultures and media. info If you haven't already, please reference the Experiment basics page for information on media preparation, sterilization, and using the Pioreactor UI.","s":"Biology experiments and protocols","u":"/experiments/introduction","h":"","p":265},{"i":268,"t":"This entire site is open-source, and any suggestions or comments can be added to our Issue Tracker. If you're up for it, feel free to send a pull request, too!","s":"Have edits, corrections, or suggestions?","u":"/experiments/introduction","h":"#have-edits-corrections-or-suggestions","p":265},{"i":270,"t":"Success goal Use a turbidostat system with selective pressures to study evolutionary principles.","s":"Directed evolution of salt-tolerant yeast","u":"/experiments/directed-evolution-salt-tolerance","h":"","p":269},{"i":272,"t":"# Two available Pioreactors Dry baker's yeast Table salt YPD media Scale (accurate to 0.1) Two peristaltic pumps: One media pump One waste pump Two liquid containers: One labelled \"media\" One labelled \"waste\"","s":"Requirements","u":"/experiments/directed-evolution-salt-tolerance","h":"#requirements","p":269},{"i":275,"t":"Let's consider how we can combine our Pioreactor abilities to explore more complex ideas: Our turbidostat allows us to perform long-term experiments without the concern of limiting nutrients or space. By itself, there are no selective pressures to stop our cultures from reaching their maximum specific growth rate. We can introduce a selective pressure (like salt) that would reduce the growth rate. Over time, we will see our cultures adapt to the new salt conditions.","s":"Introduction","u":"/experiments/directed-evolution-salt-tolerance","h":"#introduction","p":269},{"i":277,"t":"Turbidostats remove and add media periodically to keep our culture size low and nutrient availability high. We inoculated some drops of baker's yeast into a vial, then set the turbidostat pumps to add and remove 1 mL of media to achieve our target OD of 2 AU. Once your culture has acclimated, inoculate new vials to compare the newly-grown salt-tolerant strain to the wild type strain.","s":"Experiment","u":"/experiments/directed-evolution-salt-tolerance","h":"#experiment","p":269},{"i":279,"t":"The following normalized OD graph resulted from our turbidostat using salted media: A maximum growth rate of 0.6 h⁻¹ was reached. In contrast, when you look back at our secondary level salt experiment, the 4.5% w/v salt vial only reached 0.29 h⁻¹ before the stationary phase occured. This is because our previous experiment selected for salt tolerant yeast, but the culture reached stationary phase before any long term adaptation could be observed. Using the turbidostat system to supply new nutrients and keep the population low, we were able to double the maximum growth rate! Our yeast culture exhibited an adaptation to grow in high salt, indicating our turbidostat yeast culture has gained a higher fitness in 4% w/v salted media. We then grew batch cultures of our new, salt-tolerant yeast, alongside our original (wildtype) yeast culture in 2 Pioreactors using 4% w/v salt media. Here's our result: You can see just how effective our turbidostat system was in creating an environment that pushed yeast into becoming more salt tolerant.","s":"Results","u":"/experiments/directed-evolution-salt-tolerance","h":"#results","p":269},{"i":281,"t":"Part 1: Growing your turbidostat culture​ Prepare one liquid container of 5% w/v YPD broth with 4% w/v salt. Sterilize by autoclaving, along with your sample vial. Sterilize and setup your pumps. Once cooled, fill your sample vial with the autoclaved media by setting the Add media value to 14 mL. Inoculate the sample vial with baker's yeast. Visit pioreactor.local and start a new experiment. Click Manage and Start the Dosing automation. Change the automation type to Turbidostat. Set your Volume and Target OD. End the experiment once the maximum specific growth rate has increased suffienctly. This may take a day or more. note The maximum specific growth rate will increase over time, as faster-growing yeast outcompete slow-growing yeast. Part 2: Comparing batch cultures​ Inoculate one vial of sterile salted YPD media with the new, salt-tolerant yeast. Inoculate a second vial of sterile salted YPD media with the wild type yeast. Determine their growth rates using two Pioreactors. You should be able to observe that the yeast from the turbidostat are quicker to grow in the salt heavy media.","s":"Detailed procedure","u":"/experiments/directed-evolution-salt-tolerance","h":"#detailed-procedure","p":269},{"i":283,"t":"Success Goal Conduct a simple comparison of yeast growth between a low percent and high percent YPD media.","s":"Comparing concentrations of media","u":"/experiments/low-vs-high-conc-media","h":"","p":282},{"i":285,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix","s":"Requirements","u":"/experiments/low-vs-high-conc-media","h":"#requirements","p":282},{"i":288,"t":"The most accessible introductory experiment you can conduct with basic supplies is comparing concentrations of media. In this particular example, we will use YPD media and grow yeast cultures, but any media/culture you have readily available will work! YPD is a common complete media used to propagate yeast cultures, containing peptone and sugars nexcessary for yeast growth. Now consider creating two YPD media compositions: one with 1% YPD w/v, and one with 5% YPD w/v. We can easily infer that a culture grown in 5% YPD will flourish more than one grown in 1% &#151 but let's expore our hypothesis further! Discuss with your students the following ideas: How would both cultures start off? Will one have a faster rate than another? Why? Will one reach a higher growth rate? Why or why not? How long will it take for the culture in 5% YPD to slow in growth? Compared to the culture in 1% YPD?","s":"Introduction","u":"/experiments/low-vs-high-conc-media","h":"#introduction","p":282},{"i":290,"t":"We created 1% YPD by adding 0.15 grams of YPD broth powder to 15 mL: \\text \\{w/v \\%\\}= \\frac \\{\\text\\{mass\\}\\}\\{\\text \\{volume\\}\\} {mass}={0.01}×{15 {mL}}\\text \\{mass\\} = \\{0.01\\} \\times \\{15 \\:\\text \\{mL\\}\\}{mass}={0.01}×{15{mL}}{mass}=0.15 {grams}\\text \\{mass\\} = 0.15 \\:\\text \\{grams\\}{mass}=0.15{grams} Using the same logic, 5% YPD was created by adding 0.75 grams to 15 mL. We inoculated both with 100 uL of a yeast slurry using a micropipette. If this is unavailable, a dropped will work as well!","s":"Experiment","u":"/experiments/low-vs-high-conc-media","h":"#experiment","p":282},{"i":292,"t":"As expected, growth diminished earlier for the culture inoculated in 1% YPD:","s":"Results","u":"/experiments/low-vs-high-conc-media","h":"#results","p":282},{"i":294,"t":"Consider lower or higher bounds for your media compositions. How much sooner will yeast stop growing in 0.5% YPD? Can we test when yeast growth is halted by YPD concentration versus reaching a peak turbidity?","s":"Recommendations","u":"/experiments/low-vs-high-conc-media","h":"#recommendations","p":282},{"i":296,"t":"Prepare a sterile stock of two different concentrations of your media of choice. If the media appears different before inoculation, we recommend you blank your vials before adding your culture. Inoculate each vial with a very small amount of your microorganism, using best practices to avoid other contamination. In our example, a yeast stock solution can be made by diluting a small amount of yeast in 15mL of YPD stock media, then a drop of this stock solution can be added to your vials. Wipe the vials and place them in the Pioreactors. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Calibrate for each Pioreactor and under the Blanks tab, click Start. Select Manage all Pioreactors, and start Stirring activity, Temperature automation activity (set to an optimal temperature; ex. 30°C) and OD reading activity. Confirm that everything looks normal (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Optional: you can change the names of the Pioreactor in the UI to display the percent of media. Students can watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/low-vs-high-conc-media","h":"#detailed-procedure","p":282},{"i":298,"t":"An automation is a hands-off way to adjust the environment for the microbes. We currently support three types of automations: dosing, LED, and temperature. In this section, we'll develop a simple dosing automation.","s":"Writing a new automation","u":"/developer-guide/writing-automations-1","h":"","p":297},{"i":300,"t":"Writing an automation involves creating a Python class and overriding specific methods. It would be helpful to be somewhat familiar with Python classes before beginning. Here's an example of a (naive) turbidostat automation, i.e. it will add fresh media and remove old media when an optical density threshold is exceeded. The full code is below, and we'll go through each line of code after: from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): automation_name = \"naive_turbidostat\" published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, } def __init__(self, target_od, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) def execute(self): if self.latest_od > self.target_od: self.execute_io_action(media_ml=1.0, waste_ml=1.0) First important thing is to subclass from DosingAutomationJobContrib: from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): ... The DosingAutomationJobContrib is a subclass of a BackgroundJob. The -Contrib part is a small detail to specify that it's a third-party automation (i.e. you are developing it, not us.) We need a \"key\" to i) distinguish this from other automations, and ii) be able to be communicate between systems (think: the web UI in JavaScript to Python, and back). The automation_name attribute does this for us. Normally, it's the snakecase of the class name. automation_name = \"naive_turbidostat\" The published_settings tells the Pioreactor software what class attributes are published to MQTT, and if they are editable via MQTT (we will try editing over MQTT later). This is important if you wish to dynamically change attributes of an automation during an experiment, for example: from the web interface. Our class has the following: ... published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, } ... The associated metadata says that the class attribute target_od is a float, is editable via MQTT (so it can be changed using the web interface), and it has units od. Next, we define how to initialize our automation class. Here we can add settings we want to accept from the user: what is our initial target optical density. Note the boilerplate **kwargs, and super() are important. def __init__(self, target_od, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) Finally, every duration (specified in the controller, later in this section) minutes, the function execute will run. duration can be kept low (ex: to often check for some condition), or used to set some periodic task (ex: a chemostat doses every X minutes). The execute contains the core logic of the automation. In our simple case, we want to dilute the vial if we have exceed the latest_od: def execute(self): if self.latest_od > self.target_od: self.execute_io_action(media_ml=1.0, waste_ml=1.0) Since we are working with a fixed volume, media_ml must equal waste_ml, else an error will be thrown. What is latest_od attribute? Our class, when active, is listening to new optical densities being recorded. Hence when execute runs, we'll have access to the most up-to-date value of optical density. Likewise, there are also latest_normalized_od and latest_growth_rate attributes that update when a new growth-rate value is calculated. All three attributes are defined and maintained in the parent class.","s":"Creating our first custom automation","u":"/developer-guide/writing-automations-1","h":"#creating-our-first-custom-automation","p":297},{"i":302,"t":"How do we run this automation now? Let's copy the code into a file called naive_turbidostat.py and place it into the folder ~/.pioreactor/plugins. info You can create this file on your Pioreactor's Raspberry Pi: after accessing the Raspberry Pi's command line, typing nano ~/.pioreactor/plugins/naive_turbidostat.py, and pasting in the code below. # -*- coding: utf-8 -*- from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): automation_name = \"naive_turbidostat\" published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, } def __init__(self, target_od, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) def execute(self): if self.latest_od > self.target_od: self.execute_io_action(media_ml=1.0, waste_ml=1.0) Run the script with pio run dosing_control --automation-name naive_turbidostat --target-od 0.5. This will start the job. After a moment, you may notice that warnings are thrown - that's because there's no optical density measurements being produced! You can use crtl-c to stop the job. Editing attributes over MQTT (optional)​ We'll demonstrate the ability to dynamically change the target_od attribute using MQTT. For each member of published_settings, the DosingAutomationJobContrib class listens to the MQTT topic: pioreactor/<unit name>/<experiment>/dosing_automation/<attribute>/set We'll use mosquitto_pub to publish a message to this topic. So, with the Python script running, open a new command line, and enter the following: mosquitto_pub -t \"pioreactor/test_unit/test_experiment/dosing_automation/target_od/set\" -m 5.0 -u pioreactor -P raspberry You should see some logs in the Python console report that the target_od was changed. Also, a the value of 5.0 is published and retained to the topic pioreactor/test_unit/test_experiment/dosing_automation/target_od Why is this useful? This is how the web interface updates settings in running activities. Other Pioreactor activities can update each other's settings. External programs or apps can monitor and update settings this way, too.","s":"Running the automation","u":"/developer-guide/writing-automations-1","h":"#running-the-automation","p":297},{"i":304,"t":"To add your automation to the UI so it appears in the automation drop-down, follow the the steps here.","s":"Adding the automation to the UI","u":"/developer-guide/writing-automations-1","h":"#adding-the-automation-to-the-ui","p":297},{"i":306,"t":"Below are some extensions, with additions highlighted. Dynamic volume exchanged​ Exchanging 1ml each time may not be enough, so we add volume to the published_settings. Now, from the UI, we can dynamically adjust the volume. from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): automation_name = \"naive_turbidostat\" published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, \"volume\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"mL\"}, } def __init__(self, target_od, volume, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) self.volume = float(volume) def execute(self): if self.latest_od > self.target_od: self.execute_io_action(media_ml=self.volume, waste_ml=self.volume) Using latest_growth_rate​ If our growth rate is high, we may want to modify the volume exchanged to keep up. A naive solution: we can bump up the exchanged volume if the growth rate is high. Much better would be a dynamic solution, or a feedback loop. from pioreactor.automations.dosing.base import DosingAutomationJobContrib class NaiveTurbidostat(DosingAutomationJobContrib): automation_name = \"naive_turbidostat\" published_settings = { \"target_od\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"od\"}, \"volume\": {\"datatype\": \"float\", \"settable\": True, \"unit\": \"mL\"}, } def __init__(self, target_od, volume, **kwargs): super().__init__(**kwargs) self.target_od = float(target_od) self.volume = float(volume) def execute(self): if self.latest_od > self.target_od: if self.latest_growth_rate > 0.2: self.execute_io_action(media_ml=2 * self.volume, waste_ml=2 * self.volume) else: self.execute_io_action(media_ml=self.volume, waste_ml=self.volume)","s":"Extensions of our custom automation","u":"/developer-guide/writing-automations-1","h":"#extensions-of-our-custom-automation","p":297},{"i":308,"t":"Success Goal Apply turbidostat functions with temperature cycling to study yeast behaviour in a more natural temperature environment.","s":"Temperature cycling of continuous cultures","u":"/experiments/temp-cycle","h":"","p":307},{"i":310,"t":"Two available Pioreactors Four peristaltic pumps: Two media pumps Two waste pumps Two liquid containers: One labelled \"media\" One labelled \"waste\" Scale to calibrate, if needed Culture of choice (ex. Baker's Yeast) Media of choice (ex. YPD)","s":"Requirements","u":"/experiments/temp-cycle","h":"#requirements","p":307},{"i":312,"t":"Observations of cultures in lab settings are often disconnected from real world behaviours. In nature, cultures are subjected to many cyclic changes tied to the day and night cycle. We can mimic these cycled environments using plugins on our Pioreactor. We created a plugin that cycles the temperature between 30°C and 40°C sinusoidally over a 24 hour period. Together with turbidostat media cycling, the maximum specific growth rate can be characterized between a culture held at a static temperature versus a culture undergoing temperature cycling. This experiment explores concepts described in Knutson et al., (2018).","s":"Introduction","u":"/experiments/temp-cycle","h":"#introduction","p":307},{"i":314,"t":"Check out our blog post for an in-depth evaluation of our experiment!","s":"Experiment","u":"/experiments/temp-cycle","h":"#experiment","p":307},{"i":316,"t":"Once we exported our data, we charted our yeast growth rate against the temperature readings to generate the following graph:","s":"Results","u":"/experiments/temp-cycle","h":"#results","p":307},{"i":319,"t":"Add media into your media container. Sterilize by autoclaving. Adjust the tube lengths on the cap of your small sterile vial such that one just touches the media, while another sits above the media. Inoculate your small sterile vial with drops of your culture. Wipe vial and place in the Pioreactor. For your media pump: Attach the source tube to your media container. Attach the sink tube to the vial cap tube that sits above the media. For your waste pump: Attach the source tube to the vial cap tube that touches the media. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Select Manage, start Stirring activity and OD reading activity. Install the cycle_temp plugin from the Plugins tab. This will give you a new option in your Temperature automation activity. Under Manage > Activities > Temperature automation, select Cycle Temp from the drop down menu. Click Start. Confirm everything looks correct, then start the Growth rate activity. Start the Dosing automation. Change automation to Turbidostat. Set your Volume and Target OD. You can change the parameters of the turbidostat automation in the Settings tab. Changes will take effect immediately.","s":"Detailed procedure","u":"/experiments/temp-cycle","h":"#detailed-procedure","p":307},{"i":321,"t":"Knutson, C. M., McLaughlin, E. M., & Barney, B. M. (2018). Effect of temperature control on green algae grown under continuous culture. Algal research, 35, 301-308. https://doi.org/10.1016/j.algal.2018.08.020","s":"References","u":"/experiments/temp-cycle","h":"#references","p":307},{"i":324,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix Table salt Scale (accurate to 0.1)","s":"Requirements","u":"/experiments/salt-stress-on-yeast","h":"#requirements","p":322},{"i":327,"t":"In early biology classes, students learn the core concepts of osmolarity across a cell's membrane. The cell's environment can contain different concentrations of impermeable molecules, creating osmotic pressure and resulting in water entering or leaving the cell. You can quantitatively measure this effect on growth rate using your Pioreactor! The inside and outside of a cell are separated by the cell's semi-permeable membrane. Only water and certain molecules can pass through via active or passive transport (diffusion). All other molecules are impermeable and cannot pass through the membrane. We'll refer to these as solutes. Through the process of osmosis, water (our solvent) is drawn across a cell's membrane towards higher concentrations of solutes, until an equilibrium is reached. If the concentration of solutes inside and outside a cell is the same, then the cell is in an isotonic solution. Less external solutes or more solutes create hypotonic and hypertonic solutions, respectively. Increasing salt content to create a hypertonic solution will slow the yeast's fermentation or reproductive activities, leading to slower growth. As salt is added in excess, yeast cells will fail to grow; yeast needs water and their cell volume eventually becomes too small for growth.","s":"Introduction","u":"/experiments/salt-stress-on-yeast","h":"#introduction","p":322},{"i":329,"t":"We performed this experiment using five Pioreactors and vials containing 15 mL of sterile YPD stock and salt concentrations of 0%, 1.5%, 3%, 4.5%, and 6% w/v. A sample calculation is as follows: \\text \\{w/v \\%\\}= \\frac \\{\\text\\{mass\\}\\}\\{\\text \\{volume\\}\\} To create a salt concentration of 3% w/v for 15 mL of media: 0.03 = \\frac \\{\\text\\{mass\\}\\}\\{15 mL\\}{mass}=0.45g\\text \\{mass\\} = 0.45 g{mass}=0.45g Therefore, 0.45 grams of table salt is needed for 3% w/v of salt. To each vial, 0g, 0.225g, 0.45g, 0.675g and 0.9g of table salt were added, repectively. They were then innoculated with one drop of rehydrated active yeast (0.500 g of dry yeast in a 15 mL YPD broth vial). The Temperature automation was set on Thermostat at 32.5°C.","s":"Experiment","u":"/experiments/salt-stress-on-yeast","h":"#experiment","p":322},{"i":331,"t":"After approximately 26 hours, the following growth rates were recorded: We can summarize our results in the following table to highlight our data: Salt percent (w/v) Peak growth rate (h⁻¹) Time to reach stationary phase 0% (control) 0.78 8 hours 1.5% 0.67 8.3 hours 3% 0.49 11.5 hours 4.5% 0.29 17 hours 6% 0.22 24 hours The highest growth was recorded in the vial at 0% salt w/v (no salt stress), at approximately 0.78 h⁻¹. The phases of growth (lag, log phase) occured quickly and the stationary phase was reached in the smallest time frame of about 8 hours. As the salt percentage increased, the peak growth rate decreased and the time to reach the stationary phase was extended. These time increases are non-linear; between 0% and 1.5% salt, the stationary phase was reached within an increment of half an hour &#151 however 4.5% and 6% salt had a large increment of 7 hours (from 17 to 24 hours).","s":"Results","u":"/experiments/salt-stress-on-yeast","h":"#results","p":322},{"i":333,"t":"The flexibility of the Pioreactor means you can do much more with this simple concept! Here are some recommendations: performing the experiment over a longer period of time, or with higher salt percentages; papers commonly go up to 10%. exploring pretreated cells (by growing one culture in a saltier environment, then comparing a non-treated culture to the treated culture under the same conditions). See our experiment on directed evolution. considering different species and how they react to the same salt conditions.","s":"Recommendations","u":"/experiments/salt-stress-on-yeast","h":"#recommendations","p":322},{"i":335,"t":"Prepare a stock of 50g YPD / 1L distilled water. Aim for 20ml × the number of Pioreactors you are using, as each Pioreactor will require about 15mL of media. Divide this stock into small vials, then sterilize by autoclaving. Allow stock to cool. Weigh table salt to add to your media. This amount can be calculated as per the example above. Divide the stock into the sterilized vials and add salt. Mix the salt with gentle shaking or by using the Stirring function on the Pioreactor. Dilute a small amount of yeast in 15mL of YPD stock media. This can be stored in a fridge for future use. Using sterile techniqes, add 3-4 drops of this yeast solution to your vials. Wipe the vials and place them in the Pioreactor. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start: Stirring activity OD reading activity Temperature automation activity Confirm that everything looks normal on the Overview page (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. Watch the growth progress on the Overview page!","s":"Detailed procedure","u":"/experiments/salt-stress-on-yeast","h":"#detailed-procedure","p":322},{"i":337,"t":"Success Goal Demonstrate the effect of temperature on yeast growth. tip Requirements​ # At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix Introduction​ Students may have a prior belief that temperature effects are linear. For example: a culture at 10℃ will grow at half the rate compared to a culture at 20℃, and a third the rate at 30℃. In reality, cells have a range of temperatures it will do well at, and temperatures too cold or too hot will lead to slower growth rates. This experiment would show the non-linear effect of temperature on growth (and relate it to how refrigerators halt spoilage for so long!). Students and the teacher can pick temperatures to test beforehand. info The Pioreactor doesn't cool samples, so it can't achieve temperatures below your ambient temperature. If you want to test low temperatures, you can place the Pioreactor in a fridge, or in a cooler with ice packs (making sure the electronics won't get wet).","s":"Yeast growth at varying temperatures","u":"/experiments/yeast-growth-by-temperature","h":"","p":336},{"i":339,"t":"# At least two available Pioreactors Dry baker's yeast YPD broth mix, or any other media mix","s":"Requirements","u":"/experiments/yeast-growth-by-temperature","h":"#requirements","p":336},{"i":342,"t":"Students may have a prior belief that temperature effects are linear. For example: a culture at 10℃ will grow at half the rate compared to a culture at 20℃, and a third the rate at 30℃. In reality, cells have a range of temperatures it will do well at, and temperatures too cold or too hot will lead to slower growth rates. This experiment would show the non-linear effect of temperature on growth (and relate it to how refrigerators halt spoilage for so long!). Students and the teacher can pick temperatures to test beforehand. info The Pioreactor doesn't cool samples, so it can't achieve temperatures below your ambient temperature. If you want to test low temperatures, you can place the Pioreactor in a fridge, or in a cooler with ice packs (making sure the electronics won't get wet).","s":"Introduction","u":"/experiments/yeast-growth-by-temperature","h":"#introduction","p":336},{"i":344,"t":"The following experiment was performed using four Pioreactors. Four vials containing 15 mL of the sterile YPD stock were inoculated with 1 drop of rehydrated active yeast (0.500 g of dry yeast in a 15mL YPD broth vial). They were grown at temperatures of 28°C, 32°C, 36°C and 40°C.","s":"Experiment","u":"/experiments/yeast-growth-by-temperature","h":"#experiment","p":336},{"i":346,"t":"Over the course of 12 hours, the following graphs were recorded: Though subtle, non-linear patterns of growth rate are observed between the temperatures. Key data points are summarized in the following table: Temperature Peak growth rate (h⁻¹) Time to reach stationary phase 28°C 0.65 9 hours 32°C 0.73 8.5 hours 36°C 0.76 7.5 hours 40°C 0.59 9.5 hours Rather than increasing as temperature increases, the highest growth rates form a bell curve, with the highest overall growth rate of 0.76 h⁻¹ occurring at 36°C. It decreases at 40°C since this temperature lies outside of the ideal temperature range for yeast. The time it takes for each culture to reach the stationary phase is also related to the peak growth rates. Cultures that peaked higher did so in a quicker time frame, thus reaching the stationary phase sooner! Consider the extremes in this case: what would happen if we drop the temperature? Increased it to 50°C? How does this relate to cooking and food storage?","s":"Results","u":"/experiments/yeast-growth-by-temperature","h":"#results","p":336},{"i":348,"t":"We chose a relatively small temperature range that mostly aligned with optimal temperatures for yeast growth. We encourage you to explore temperatures outside of this range, whether by cooling the Pioreactor externally (using ice/a cooler) or increasing the temperature (the maximum that can be reached is room temperature plus 20°C). Keep in mind to not get the electronics of your Pioreactor wet! Elevate your Pioreactor to protect it from any spills.","s":"Recommendations","u":"/experiments/yeast-growth-by-temperature","h":"#recommendations","p":336},{"i":350,"t":"Prepare a stock of 50g YPD / 1L distilled water. Aim for 20ml × the number of Pioreactors you are using, as each Pioreactor will require about 15mL of media. Divide this stock into small vials, then sterilize by autoclaving. Allow stock to cool. Dilute a small amount of yeast in 15mL of YPD stock media. Sterily add 3-4 drops of this yeast solution to your vials. Wipe the vials and place them in the Pioreactor. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start: Stirring activity OD reading activity Select Manage on an individual Pioreactor. Turn on the Temperature automation activity on Thermostat, selecting your temperature of interest. Confirm that everything looks normal on the Overview page (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. Optional: you can change the names of the Pioreactor in the UI to display the target temperature. Students can watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/yeast-growth-by-temperature","h":"#detailed-procedure","p":336},{"i":352,"t":"Info You can expect the assembly to take approximately 20-30 minutes.","s":"Before you begin assembly","u":"/user-guide/20ml-v11-hardware-setup-intro","h":"","p":351},{"i":380,"t":"Below is a list of activities that come available with the Pioreactor. Additionally, you can add activities using plugins. Read more about using plugins. Stirring: this starts the stirring in the Pioreactor. After starting to stir, you can change the stirring speed in the Settings tab. You can modify the default stirring speed in the configuration settings. We recommend keeping the stirring range of 150 RPM to 600 RPM. Optical density: this turns on the system that measures culture density. Readings will start to populate the Experiment Overview page. It's useful to inspect the first few minutes of readings to ensure the readings are as expected (e.g., the readings aren't erratic, and the stirring speed is appropriate, etc.). Growth Rate: this activity requires that stirring and optical density be running as well. This starts the calculation of a normalized optical density, and the implied growth rate. Both calculations will populate the Experiment Overview page. Temperature automation: turning on a temperature automation will start collecting temperature readings. For example, the Thermostat automation will use a feedback loop to stabilize the Pioreactor to a set temperature. Pausing an automation will cease both any active heating and temperature data collection. Stopping an automation will stop the heating and temperature collection. To change a running temperature automation, use the \"Change Temperature Automation\" button. Read more about specific temperature automations. Dosing automation: turning on a dosing automation to start listening periodically for dosing triggers. A dosing automation requires at least 1 pump to be available and calibrated. More about using pumps. Pausing a dosing automation will stop any currently, and future, dosing occurring until the automation is unpaused. Read more about the different types of dosing automations. LED automation: turning on a LED automation to start listening periodically for LED change triggers. Read more about LED automations.","s":"Activities","u":"/user-guide/activities","h":"","p":379},{"i":382,"t":"The PWM output default to 5V (specifically, it's tied to the power supply, so it may be 5.1V, 5.2V etc. See your power supply). You are able to use 12V pumps successfully even at 5V output. However, you can also use the AUX power connection to change the PWM output. Note that the inner tubing on pumps is often different from the outer tubing. For example, for the peristaltic pumps that we supply: Interior tubing dimensions: 3.3mm OD, 1mm ID Exterior tubing dimensions: 1/8\" OD, 1/16\" ID Pumps that we have used and we like: note These pumps require some assembly to work with the Pioreactor Adafruit","s":"More on peristaltic pumps","u":"/user-guide/addition-hardware-pumps","h":"","p":381},{"i":384,"t":"Plugins offer a powerful way to extend your Pioreactor. Below is a list of our favourite plugins. Visit the guide on how to install plugins into your Pioreactor.","s":"List of available plugins","u":"/user-guide/available-plugins","h":"","p":383},{"i":386,"t":"Success goal Explore the ethanol fermentation process and practice dilution calculations for media preparation.","s":"Yeast growth in ethanol","u":"/experiments/yeast-in-ethanol","h":"","p":385},{"i":388,"t":"At least two available Pioreactors Dry baker's yeast Ethanol (95% rubbing alcohol) Distilled water","s":"Requirements","u":"/experiments/yeast-in-ethanol","h":"#requirements","p":385},{"i":390,"t":"To get their energy, yeast species are fermentors; they take sugars and oxygen and metabolize them into ethanol and carbon dioxide. We've used these products to create many goods in the food industry, such as breads and beers! While we have found many applications for yeast products, yeasts themselves see these as waste products. These waste products can accumulate, leading to what's called the \"staling effect\" where yeasts can't grow because of an over-accumulation of their own waste. We know that most yeasts can tolerate an alcohol concentration of 10-15% before dying. Now, let's choose some alcohol concentrations and explore this inhibition using our Pioreactor! We've included two methods to calculate ethanol precentages; teachers can prepare this beforehand or allow their students to calculate it themselves.","s":"Introduction","u":"/experiments/yeast-in-ethanol","h":"#introduction","p":385},{"i":392,"t":"We conducted an experiment using 4 Pioreactors and vials with ethanol concentrations of 0%, 4%, and 6%. After adding 15 mL YPD stock into each vial, we calculated the amount of ethanol to use per vial using Method 1 below. Method 2 can be done instead to simplify the procedure.","s":"Experiment","u":"/experiments/yeast-in-ethanol","h":"#experiment","p":385},{"i":394,"t":"The first concentration of 0% ethanol is easy &#151 we just add 1 mL of distilled water. For the rest, the following calculations were done to determine the volume of ethanol to add to each vial: {[{ethanol}]}{{media volume+ethanol volume}}={ethanol%}\\frac\\{[\\text\\{ethanol\\}]\\}\\{\\text\\{media\\thickspace volume + ethanol\\thickspace volume\\}\\}=\\text\\{ethanol \\%\\}[{​{ethanol}]}{{mediavolume+ethanolvolume}}={ethanol%} In our case, we have 15 mL of YPD broth per vial, and want to add 1 mL of diluted ethanol; we want to determine our final concentration of ethanol in 1 mL to get an overall 2% concentration in our complete, 16 mL of media. For 2%: {[{ethanol}]}{{15mL+1mL}}={2%}\\frac\\{[\\text\\{ethanol\\}]\\}\\{\\text\\{15 mL + 1 mL\\}\\}=\\text\\{2\\%\\}[{​{ethanol}]}{{15mL+1mL}}={2%}[{ethanol}]=32%[\\text\\{ethanol\\}]=32\\%[{ethanol}]=32% Now, we know we want our 1 mL of dilute ethanol concentration to equal 32%. Since we're starting with an initial concentration of 95%, we can apply the following dilution equation to figure out the concentration of 95% ethanol to use: Initial volume (Vi)= ? Initial concentration (Ci)= 95% Final volume (Vf)= 1 mL Final concentration (Cf)= 32% Now we substitute our variables into the equation Ci Vi = Cf Vf: Vi={(32%)({1mL})}{95%}V_i = \\frac\\{(32\\%)(\\text\\{1 mL\\})\\}\\{95\\%\\}Vi​=({​32%)({1mL})}{95%}Vi={0.34mL}V_i = \\text\\{0.34 mL\\}Vi​={0.34mL} So the composition to create 2% ethanol media is: 15 mL YPD stock 0.34 mL of 95% ethanol 0.66 mL distilled water (1 mL - 0.34 mL) tip If you don't have a small enough resolution on your measuring tools, you can increase the total amount of ethanol dilution. For example, instead of making 1 mL diluted ethanol, we used 3.4 mL of 95% ethanol and 6.6 mL of distilled water measured in a graduated cylindar to create a total 10 mL diluted ethanol. From that, we mixed well and added 1 mL into our vial. We repeated this for 4% and 6% ethanol concentrations.","s":"Method 1","u":"/experiments/yeast-in-ethanol","h":"#method-1","p":385},{"i":396,"t":"Instead of finding the exact ethanol amounts to add to create a specific ethanol percentage, we can keep halving the ethanol solution and calculate the ethanol percentage afterwards. For example: Vial 1: 1 mL of 95% ethanol Vial 2: 0.5 mL of 95% ethanol; 0.5 mL distilled water Vial 3: 0.25 mL of 95% ethanol; 0.75 mL distilled water Vial 4: 1 mL distilled water To calculate the resulting ethanol percentage: {[{ethanol}]}{{media volume+ethanol volume}}={ethanol%}\\frac\\{[\\text\\{ethanol\\}]\\}\\{\\text\\{media\\thickspace volume + ethanol\\thickspace volume\\}\\}=\\text\\{ethanol \\%\\}[{​{ethanol}]}{{mediavolume+ethanolvolume}}={ethanol%} Substitute the [ethanol] value for half of 95% (or 47.5%): {47.5%}{{15mL+1mL}}={ethanol%}\\frac\\{47.5\\%\\}\\{\\text\\{15 mL + 1 mL\\}\\} = \\text\\{ethanol \\%\\}4{​7.5%}{{15mL+1mL}}={ethanol%}{ethanol%}≈3%\\text\\{ethanol \\%\\} \\approx 3\\%{ethanol%}≈3% This technique produces halving ethanol percentages of 0%, 1.5%, 3%, and 6% to be studied on a cluster of 4 Pioreactors.","s":"Method 2","u":"/experiments/yeast-in-ethanol","h":"#method-2","p":385},{"i":398,"t":"After approximately 18 hours, the following implied growth rates were recorded: We can summarize our results in the following table: Alcohol percent Peak growth rate (h⁻¹) Percent of control Time to reach stationary phase 0% 0.75 100% 7 hours 4% 0.46 61% 9 hours 6% 0.27 36% 14 hours As expected, just the smallest addition of ethanol really cut down on our yeasts' ability to grow. At a 4% alcohol concentration, the maximum growth rate decreased by almost 40%!","s":"Results","u":"/experiments/yeast-in-ethanol","h":"#results","p":385},{"i":400,"t":"We encourage you to select alcohol concentrations outside of the expected range. At what point does yeast show no growth? Can you see anything interesting when your culture reaches the stationary phase? Hint: you may be able to observe a diauxic shift! Plenty of yeast strains are available at your local breweries. You can do the same experiment on different strains to see which yeasts are more tolerant than others. What concentrations of beers can they make?","s":"Recommendations","u":"/experiments/yeast-in-ethanol","h":"#recommendations","p":385},{"i":402,"t":"Prepare a sterile stock of 50g YPD / 1L distilled water. Aim to make 20 mL × the number of Pioreactors you are using, as each Pioreactor will require about 15 mL of media. Prepare 1 mL of each ethanol concentration you would like to use. Detailed calculations are found in the example above. Aim for an end ethanol concentration between 0-10%. Evenly divide the YPD stock into the vials you’d like to use (ie. 15 mL in each vial). Add the mililitre of ethanol solution into the respective vial. Mix with gentle shaking. Inoculate the stock with a very small amount of baker's yeast using best practices to avoid other contamination. Wait for the yeast granules to dissolve, aided by gentle rocking or stirring. Alternatively, a yeast stock solution can be made by diluting a small amount of yeast in 15 mL of YPD stock, then 1 drop of this stock solution can be added to your vials. Wipe the vials and place them in the Pioreactors. Visit pioreactor.local and start a new experiment. On the left menu, select the Pioreactors page. Add any additional Pioreactors that you would like to use (more information here). Select Manage all Pioreactors, and start Stirring activity and OD reading activity. Optional: you can turn on the Temperature automation activity and set it on Thermostat at an optimal temperature (ex. 30C). Confirm that everything looks normal (ex: receiving optical density signal). Back on the Pioreactors page, select Manage all Pioreactors and start Growth rate. It will take a minute for results to begin showing up. Optional: you can change the names of the Pioreactor in the UI to display the target temperature. Students can watch growth progress on the Overview page.","s":"Detailed procedure","u":"/experiments/yeast-in-ethanol","h":"#detailed-procedure","p":385},{"i":404,"t":"Alba-Lois, L., & Segal-Kischinevzky, C. (2010). Yeast fermentation and the making of beer and wine. Nature Education, 3(9), 17. Gray, W. D. (1941). Studies on the alcohol tolerance of yeasts. Journal of Bacteriology, 42(5), 561-574.","s":"References","u":"/experiments/yeast-in-ethanol","h":"#references","p":385},{"i":406,"t":"For those interested, you can use the command line to interact with the Pioreactors. This is called the command line interface (CLI). Log onto either the leader or worker and you can execute the following commands. Full options and up-to-date documentation are available with pio <command> --help.","s":"Command line interface","u":"/user-guide/cli","h":"","p":405},{"i":408,"t":"Interacting with the Pioreactor on the command line are through the pio tool. Available arguments are: pio logs will produce a stream of recent logs events. Logs are stored in /var/log/pioreactor.log. pio kill --name <job> --experiment <exp> or pio kill --all-jobs to end jobs. pio run <job> <options> will run the <job>. Each job may have specific command line arguments. pio version print the version of the PioreactorApp software. pio update app will update the software to the latest app version. pio plugins install <plugin name> will install a plugin pio plugins uninstall <plugin name> will uninstall a plugin pio plugins list will list the currently installed plugins pio blink will blink the Pioreactor's onboard LED. pio log -m <message> will log a message pio view-cache <cache> will print out the contents of the specified cache. pio clear-cache <cache> <key> will remove <key> from cache <cache>.","s":"Worker commands","u":"/user-guide/cli","h":"#worker-commands","p":405},{"i":410,"t":"The leader also has their own unique set of pio commands (these commands do not interact with the workers): pio db: open the sqlite3 CLI of the Pioreactor database. pio mqtt: tail the MQTT broker. pio update ui will update the UI software to the latest version and adding --app will upgrade the Pioreactor Python app (repo: pioreactor/pioreactor). pio update app will update the software to the latest version. pio cluster-status will report to the user each Pioreactor in the cluster, and metadata like status, IP, and state. pio workers has many subcommands for manager your cluster. For example: pio workers add <hostname>: add a Pioreactor to your cluster, with given (unique) name. Need a worker Pioreactor on the network first. See instructions here. pio workers discover will return a list of workers on the network (may be a superset of the current cluster.) Leader-only commands to control workers​ The leader computer interacts with the worker computers using the pios command. Unless otherwise noted, the pios will target all worker computers. Available pios commands on the leader computer are the following: pios kill --name <job> terminate the job <job> on the workers. Ex: pios kill --name dosing_control. pios run <job> on each worker, run the job <job> in the background. Job specific arguments can be specified after. Ex: pios run add_media --ml 1. Use -y to skip confirmation. pios update install the latest PioreactorApp code on each worker. pios sync-configs deploy the config.ini files to workers. pios install-plugin <plugin name> will install the plugin on each worker and the leader. pios reboot will reboot all workers, by default, in the cluster. See --units arg below. pios shutdown will shut down all workers, by default, in the cluster. See --units arg below. pios cp <filepath> will copy (and overwrite) filepath on the leader to all the workers. pios rm <filepath> will remove filepath on all the workers. tip In each of the above commands, specific workers can be invoked with --units (which can be used multiple times. Ex: pios run stirring --units pio1 --units pio2. tip -y will skip user confirmation of the command to run.","s":"Leader-only commands","u":"/user-guide/cli","h":"#leader-only-commands","p":405},{"i":413,"t":"Configuration of the Pioreactors is through configuration files, prefixed by .ini. There are two types of .ini files: a shared config.ini, which is the same across all units, and a unit-specific unit_config.ini file, which can have settings that overwrite those found in the shared config.ini. For example (and see image below), each unit will use the shared config.ini setting of target_rpm=500, unless an alternative setting is present in their specific unit_config.ini files (like target_rpm=400 found in unit1_config.ini) . This overriding lets you customize specific behavior per Pioreactor, without having to duplicate lots of configuration over and over again. Last-occurrence wins​ The config.ini can have duplicate entries (though it's not recommended), but only the last occurrence in the file will be used.","s":"How configuration works across Pioreactors","u":"/user-guide/configuration","h":"#how-configuration-works-across-pioreactors","p":411},{"i":415,"t":"At pioreactor.local, navigate to the Configuration page in the sidebar. Select the configuration file you wish to edit from the dropdown: Clicking [Save] will save the new configuration and will deploy the new configuration to the proper Pioreactor unit(s). Pioreactor also stores a history of changes to each configuration file. You can view previous versions of configuration files in the dropdown. Clicking [Revert] will save the displayed configuration file.","s":"Editing the configuration files from the web interface","u":"/user-guide/configuration","h":"#editing-the-configuration-files-from-the-web-interface","p":411},{"i":417,"t":"All the .ini files come from the leader unit. They are stored in /home/pioreactor/.pioreactor - one config.ini and a config_<unitName>.ini for each Pioreactor unit. The command pios sync-configs will deploy the .ini files to their correct unit. Editing the .ini files on the leader is correct workflow, as any edits on the worker units will be overwritten on the next pios sync-configs. One can programmatically, or by hand, edit the config_<unitName>.ini files to create varying parameters in an experiment. Running pios sync-configs will deploy the config files.","s":"Editing the configuration files from the command line","u":"/user-guide/configuration","h":"#editing-the-configuration-files-from-the-command-line","p":411},{"i":419,"t":"Sometimes it's desirable to make changes to the config.ini without having to boot the Pioreactor first. You can do this by plugging the microSD card into your computer, and adding a config.ini to the boot/ folder on it. This config.ini doesn't need to have all the fields, only the fields you wish to change. At start up, the Pioreactor will merge /boot/config.ini into the Pioreactor's config.ini, and then delete /boot/config.ini.","s":"Editing the config.ini before booting","u":"/user-guide/configuration","h":"#editing-the-configini-before-booting","p":411},{"i":421,"t":"If you need a reference config.ini, or to replace parts of yours, here's our default one that ships with the Raspberry Pi image. To use it, you'll need to make some changes, specifically to `cluster.leader` and `inventory`.","s":"Example config.ini","u":"/user-guide/configuration","h":"#example-configini","p":411},{"i":423,"t":"For more customization and control of your Pioreactor, you can access the Raspberry Pi's command line. From the command line, you can view more logs, control individual Pioreactors, and more.","s":"Accessing the Raspberry Pi","u":"/user-guide/accessing-raspberry-pi","h":"","p":422},{"i":425,"t":"There are two simple ways to access the Raspberry Pi from a Windows desktop.","s":"Access from Windows","u":"/user-guide/accessing-raspberry-pi","h":"#access-from-windows","p":422},{"i":427,"t":"Open the command prompt. Type ssh pioreactor@<insert unit name>.local. For example, to access on our Pioreactor named worker3, we typed ssh pioreactor@worker3.local. The default password is raspberry (see \"info\" below). If asked \"The authenticity of host...\", enter \"yes\". info When typing in the password, characters may not show up as you type - that's normal. This is a security feature. If successful, try entering pio blink - your Pioreactor's blue LED should starting blinking. See more commands here.","s":"1. Using the Command Prompt","u":"/user-guide/accessing-raspberry-pi","h":"#1-using-the-command-prompt","p":422},{"i":429,"t":"Start by installing the program PuTTY. Once downloaded, open PuTTY. Enter your Pioreactor's name as the hostname (if working with a cluster, enter your leader's hostname). Click \"Open\". If this is the first time to connect to the Raspberry Pi, you will have to accept its SSH certificate. On the next screen, use the username / password: pioreactor / raspberry. If successful, try entering pio blink - your Pioreactor's blue LED should starting blinking. See more commands here.","s":"2. Using PuTTY","u":"/user-guide/accessing-raspberry-pi","h":"#2-using-putty","p":422},{"i":431,"t":"Open the Terminal application. From the command line, enter ssh pioreactor@<name of pioreactor>.local. If this is the first time to connect to the Raspberry Pi, you will have to accept its SSH certificate. When prompted, enter the password raspberry. info When typing in the password, it may not show up as you type (this is a security feature) If successful, try entering pio blink - your Pioreactor's blue LED should starting blinking. See more commands here.","s":"Access from a Mac","u":"/user-guide/accessing-raspberry-pi","h":"#access-from-a-mac","p":422},{"i":433,"t":"You don't need my help. Try entering pio blink - your Pioreactor's blue LED should starting blinking. See more commands here.","s":"Access from Linux","u":"/user-guide/accessing-raspberry-pi","h":"#access-from-linux","p":422},{"i":435,"t":"If the above steps aren't working for your system, try the following: Instead if using the <unit name>.local, try using the IP address (if available). Example, ssh pioreactor@192.168.1.30 for a Raspberry Pi at IP address 192.168.1.30. Try power-cycling the Pioreactor.","s":"Troubleshooting","u":"/user-guide/accessing-raspberry-pi","h":"#troubleshooting","p":422},{"i":438,"t":"Depending on the purposes of your research, you may want to calibrate your Pioreactor against known samples and OD600 values. We've given you the option to do this through the command line, similar to how pump calibrations currently work. Calibrations using the UI are coming soon! OD600 calibrations are straightforward, and only require one vial, your sample of interest, and an accurate way to measure liquids. We recommend a micropipette of volume range 100 to 1000 uL. The calibration works by reading a dilution series. You will start with 10mL of your sample of interest cultivated in your media, at the highest density you expect to observe. During the calibration, you will specify and add an amount of your media to dilute your sample. To avoid overflowing, the program will prompt you to reduce the volume in your vial to 10mL at set intervals. Calibrations should be specific to your experiment setup. Any changes to your media, culture, or optical setup (i.e. changing IR intensity, replacing pieces, or changing the angle) will require a new calibration. If everything remains consistent, then we recommend running calibrations every 6 months, or whatever suits your purposes.","s":"Calibrating your OD600 readings","u":"/user-guide/calibrate-od600","h":"#calibrating-your-od600-readings","p":436},{"i":440,"t":"Connect to your Pioreactor by typing ssh pioreactor@<insert unit name>.local. For example, to calibrate on our Pioreactor named worker3, we typed ssh pioreactor@worker3.local. The default password is raspberry. To begin calibrations, type pio run od_calibration. Start off by inputting some metadata of your calibration. Provide a descriptive and unique name to make it easier to find your calibration again, if needed. Follow the rest of the questions. info One of your photodiodes will be located in the 45°, 90°, or 135° pocket on the vial holder. You will be prompted to confirm the angle of your PD cable. If this is incorrect, go to the Configuration tab on the Pioreactor UI and under od_config.photodiode_channel, change to your angle of choice, then restart your OD calibration. Following the questions, stirring and optical density reading will begin. A graph is generated as you calibrate so you can see your progress. Depending on your number of measurements, you may be prompted to reduce your vial volume to 10 mL. OPTIONAL: At this point, you may take the OD600 reading of your vial on a different instrument and input this OD600 value for the current measurement. Once you complete all your measurements, a calibration curve will appear over your graph. If you are satisfied with this, save your calibration. info By default, we fit the calibration curve with a polynomial. You can choose the degree of the polynomial if you wish, but we found that degree 4 works well for wide OD600 calibrations, and degree 1 (a linear model) works will for narrow calibrations near 0.","s":"Running the calibration","u":"/user-guide/calibrate-od600","h":"#running-the-calibration","p":436},{"i":442,"t":"Calibrations are applied automatically. That is, after performing a calibration, your future experiments that use optical density readings will use the post-calibration values and be displayed in the UI and saved to the database. If you wish to stop using calibrations, you can switch if off in the config.ini by setting adding use_calibations=0 under the [od_config] section.","s":"Using calibrations in your experiments","u":"/user-guide/calibrate-od600","h":"#using-calibrations-in-your-experiments","p":436},{"i":444,"t":"On the command line, you can display your current calibrations using pio run od_calibration display_current). This will display the calibration graphs and metadata for each angle (45°, 90°, and 135°). Setting a new calibration would replace the information shown here, and be applied to new experiments that use the given angle. To see a full list of all previous calibrations, use pio run od_calibration list.","s":"Viewing your previous calibrations","u":"/user-guide/calibrate-od600","h":"#viewing-your-previous-calibrations","p":436},{"i":446,"t":"If you wish to change your calibration to a previous version, use pio run od_calibrations change_current <name> where <name> is some previous calibration you've run (i.e from pio run od_calibration list).","s":"Changing a calibration","u":"/user-guide/calibrate-od600","h":"#changing-a-calibration","p":436},{"i":448,"t":"Pioreactor operation Optical density and LEDs Heating and Temperature control Mixing and stirring in the Pioreactor Can I plot the RPM in a chart in the UI? Raspberry Pi Hardware Dosing Data storage, access and recovery Networking","s":"Common questions","u":"/user-guide/common-questions","h":"","p":447},{"i":450,"t":"How can I restart my Pioreactor? Is pulling the power plug out safe?​ We suggest using the UI to reboot a Pioreactor: Pulling the plug is usually fine, but try to avoid doing it as much as possible. Can I still use the Pioreactor software without the hardware?​ Yes - the Pioreactor UI and software will still work. We provide a \"leader-only\" image that is designed to only host a cluster, and not be an active worker. The leader-only image, pioreactor_leader.zip , are available here. Why does the onboard blue LED keep flashing?​ There may be a problem. You can diagnose the problem by counting the number of flashes observed. What does the onboard button do?​ The button on the Pioreactor HAT sends a signal to the web UI to display a \"hello\" message. This is useful to know which Pioreactor in a cluster you are interacting with. The button also will republish the state of the Pioreactor. The button can be reprogrammed, too. How do I change the date or time on the Pioreactor?​ SSH into your Pioreactor, and run: sudo date --set \"Thu Nov 2 09:46:50 EDT 2023\"","s":"Pioreactor operation","u":"/user-guide/common-questions","h":"#pioreactor-operation","p":447},{"i":452,"t":"How does optical density work on the Pioreactor?​ The Pioreactor uses turbidity to measure optical density (other systems, like spectrophotometers, use attenuation). Specifically, the Pioreactor uses scattering of light. The system will shine infrared light into the culture, and measure the amount of light that is scattered off cells. The scattering has a good linear range (see below for more), and higher saturation point than attenuation for cultures of 20ml volume. If you have an instrument that measures OD600 or some other measurement of optical density, and you wish to calibrate to that, the Pioreactor has a routine to perform a calibration and record in the instruments units. See docs here. What are the units of Pioreactor's optical density​ The uncalibrated optical densities reported the UI and recorded in the database are have an arbitrary unit, and are per Pioreactor (so they can't be compared to each other). However, the normalized optical density, generated after starting the activity Growth rate in the UI, is comparable, which is why we suggest using it for inferences (especially if you haven't calibrated to some OD600 machine). Read more about our optical density measurements here. How can I change the frequency (rate) of optical density measurements?​ In the configuration, you can edit the parameter samples_per_second to adjust the how often the Pioreactor takes an optical density snapshot. Note that this parameter is the inverse of \"duration between readings\". For example, if you wish to record a measurement every 60 seconds, then samples_per_second=0.01666667 (which is 1/60). tip If you put a large gap between readings, like 1 reading / 60 seconds, then we also suggest turning off the downsampling on the UI's charts (it's on by default to avoid plotting thousands of points). To do this, SSH into your leader, and we'll edit the following files: nano /var/www/pioreactorui/contrib/charts/05_od.yaml And change the field down_sample from true to false. Do the same for the following files: nano /var/www/pioreactorui/contrib/charts/01_implied_growth_rate.yaml nano /var/www/pioreactorui/contrib/charts/04_normalized_od.yaml Why does the intensity for LED A turn on & off during an experiment?​ You may have noticed that the LED labelled A turns on & off every 5 seconds or so. This is (normally) the channel for the infrared (IR) LED, which is used in the optical density measurements. We only take reading every 5 seconds (the default), we don't need the IR LED on all the time. The Pioreactor will only turn on LED when needed. This preserves the strength of the LED over longer periods of time. For more advanced use cases, it also allows other optical measurements to take place without the IR LED interfering with them. Why does my optical density flatten, or even decrease? What is a saturation point?​ For some experiments, especially when using a scatter angle of 135°, you may notice that the optical density starts to flatten, and even decrease, when you know the culture should still be growing. This is not a property of the culture, but occurs because the culture is getting too dense, and light is now being interrupted before it reaches the photodiodes. Prior to this point, called the saturation point, the relationship between culture density and optical density is nearly linear. But after this point, there is a flattening, even negative, relationship between culture density and optical density. For all analysis, we recommend only studying when the culture is in the linear regime. You can mitigate the problem by choosing a smaller scatter angle (like 90° or 45°), diluting the culture using an automation like the turbidostat, or using a lower concentration of nutrient(s) in the media. Read more about Pioreactor's optical system here. What does the effect of the scatter angle have on optical density?​ The scatter angle is the angle between the IR LED and a photodiode. This angle can be 45°, 90°, or 135° (although 180° is possible, we don't consider it here). What is there to consider when choosing an angle. In general, the trend is shorter angles => less sensitive at low densities, but higher saturation point. By default, we suggest 45° as a good trade off between sensitivity and saturation. You can mix angles, and the Pioreactor's internal algorithm will still combine them into a single growth rate. Read more about Pioreactor's optical system here. Can I use my own 5mm LEDs and photodiodes for optical density?​ Of course! The only two requirements are that the spectrum of the LED overlaps with the spectrum of the photodiode, and that the LED light won't be absorbed by media/culture, nor damage the media/culture. Thus, the often-used 600nm light source works in the Pioreactor. None of our internal algorithms or analytics are dependent on the wavelength of light chosen. When you are using additional LEDs outside of the optical density LED & photodiode pair, you may worry that your additional LEDs will interfere with the optical density measurement. This won't happen, as we turn off all non-optical density LEDs before taking an optical density measurement. Is optical density the same as turbidity?​ Turbidity is a measure of optical density, like how decibels are a measurement of sound intensity. Similarly, absorbance is a measure of optical density.","s":"Optical density and LEDs","u":"/user-guide/common-questions","h":"#optical-density-and-leds","p":447},{"i":454,"t":"Why does the Pioreactor only provide a temperature reading every few minutes?​ We made a design choice early on to make preparation as error-free as possible. This involved thinking about sensors being in situ (in place), versus the sensors being on the outside of the vial. The temperature sensor in the Pioreactor is outside the vial, which means less chance of contamination, but there's a tradeoff (as you could guess): we have to rely on an estimation algorithm that requires a gew minutes to gather data on. We think this is a fair trade-off, as high frequency temperature readings are not that important in an experiment that lasts 12 hours or more. Why does the Pioreactor's heating keep shutting off?​ If you find that the Pioreactor's heating is shutting off, typically with an accompanying error and flashing blue light, then likely the temperature is becoming too high for safe handling. We restrict the onboard PCB's temperature to be no higher than 63℃. Temperature's higher than this can deform the plastic, and possibly cause burns. If the Pioreactor detects a temperature near or above this value, the software will shut off the heating, and possible the entire Raspberry Pi in extreme cases. To avoid this occurring, we suggest not setting the target temperature too high - not more than 20℃ above ambient temperature. Also, reducing the Kd parameter in [temperature_automation.stable] section in the config.ini would help. How does heating work on the Pioreactor?​ The Pioreactor has an onboard PCB, called the heating PCB, that sits below the glass vial. On the PCB are resistors that convert current from PWM outputs into heat. By varying the duty cycle of the PWM, we vary the amount of energy converted to heat.","s":"Heating and Temperature control","u":"/user-guide/common-questions","h":"#heating-and-temperature-control","p":447},{"i":456,"t":"How is mixing / stirring performed in the Pioreactor?​ Stirring is performed with a micro stir bar inside the vial, controlled by a pair of magnets spinning below the vial. The rotation speed, RPM, of the stir bar can be controlled using the Pioreactor software. This stirring is also how aeration is done. Can I use my own stir bar?​ Of course! The maximum length of a stir bar is 20mm. Keep the height low as to not interfere with the optics. (The provided stir bar is 3mm high). Try using other stir bar shapes / designs! The magnets rubs against the plastic screws above them, causing the stirring performance to be degraded / stop. How do I fix this?​ Dis-attach the top faceplate. Under the faceplate, slightly unscrew each of the four metal screws. This will add more space between the magnets and the plastic screws. How can I increase the strength of the magnetic force applied to the stirbar?​ For Pioreactor 20ml v1.0: Try to reduce the distance between the stirring magnets and the stir bar by carefully raising the stirring fan a small amount. Going even further, you can remove the 4mm screws in the bottom of the vial holder (but find another way to secure the PCB), thereby be able to bring the magnets even closer. How can I improve mixing and aeration?​ If the standard mixing and aeration with the stir bar is not enough for your application, you can do a few things, (in increasing order of complication, not necessarily effectiveness): If the tubes in the cap are submerged during operation, this is reduce the transfer of air. Pull them up from the top of the cap to keep them out of the liquid. Even more effective: shorten them with scissors. Increase the RPM of the stirring. This will increase the surface area exposed to the air. Be warned though: too high of an RPM will cause either a large enough vortex to interfere with the optical systems, or will causing the stir bar to fall out of sync. Add a baffle to the vial cap. A simple cylinder that rests into the liquid causes disturbance in the rotating liquid that both mixing and aeration are significantly improved. A tube can be removed from the cap, and a autoclavable rod can be inserted such that it enters the media, but won't interfere with the optics. Adding external aeration to your Pioreactor. In the simplest case, using an air pump.","s":"Mixing and stirring in the Pioreactor","u":"/user-guide/common-questions","h":"#mixing-and-stirring-in-the-pioreactor","p":447},{"i":458,"t":"Yes, follow the instructions here.","s":"Can I plot the RPM in a chart in the UI?","u":"/user-guide/common-questions","h":"#can-i-plot-the-rpm-in-a-chart-in-the-ui","p":447},{"i":460,"t":"What Raspberry Pi hardware can I use? I see Raspberry Pi 1, 2, 3, 4, 5, A, B, +, Zero - it's confusing!​ We've designed the hardware and software to be compatible with any Raspberry Pi that has onboard Wifi and a 40 pin header. That includes (at the time of writing): Raspberry Pi 3 Model B & B+ Raspberry Pi 3 Model A+ Raspberry Pi 4 Model B ³ Raspberry Pi 5 Model B Raspberry Pi Zero W (with headers) ¹ Raspberry Pi Zero 2 (with headers) Raspberry Pi 400 ² Although you can use any above, we like the Raspberry Pi 3 Model A+, and Raspberry Pi Zero 2 because of their low power consumption, slim build, and low price. Both have the necessary CPU power and memory for the Pioreactor workload, and are generally easy to source. However, they don't have ethernet connections! So talk to your team about if you need to use ethernet or wifi. If you need ethernet, we like the model RPi 3B. ¹ Raspberry Pi Zero W is on the list above, and is very low cost compared to the others. They can absolutely be used for Pioreactors as workers - we don't recommend them to be your leader (note sure what these terms mean? Here's an introduction to leader and workers). As workers, Raspberry Pi Zero W perform just fine, but will respond slower to commands. Note that this does not include the Raspberry Pi Zero 2 W model, which is fine for all roles. ² The Raspberry Pi 400 has its 40 pin header exposed in a different orientation, so your Pioreactor won't be able to sit on top like for other RPi versions. Take a look at this forum post to see how another user used the Raspberry Pi 400 with their Pioreactor. ³ Note that you don't need a lot of RAM for the Pioreactor, so we recommend getting the lower RAM option RPi 4s (1GB or 2GB) to save some money. However, 4GB and 8GB are fine, too. What microSD cards do you recommend?​ At least 16GB. We like 16GB or 32GB SanDisk Edge or Samsung microSD cards for their longevity, but any good quality, class 10 SD card will do. What power supply unit (PSU) do I need?​ If you look at the power rating, it should be about 5 V and at least 2.25 A, or above 12 W. We really like the official Raspberry Pi PSUs, available at most places you can purchase Raspberry Pis. Do I need any cooling for the Raspberry Pi?​ Nope, you shouldn't, unless you are connecting an external monitor. However, extra heat sinks are never a bad idea! Could a Raspberry Pi-compatible board work, like Rock Pi 4?​ Maybe? We haven't tested them, but so long as i) the GPIO pins are identical, and ii) Raspberry Pi OS can be installed, it should work. Why are the Raspberry Pi LEDs/USB/etc. turned off?​ We turn off the \"activity\" LED (usually the green one) to save some power for the Pioreactor's peripherals. You can turn these back on by editing the /boot/config.txt file on the RPi. What is the username/password for the Raspberry Pi?​ When setting up your Raspberry Pi with the Pioreactor software, you would have chosen a password. Try the recommended username: pioreactor, and password: raspberry. Can I use the desktop interface (with a display) with the Pioreactor?​ Not currently. Our software is based of the \"headless\" operating-system, which doesn't have display output.","s":"Raspberry Pi Hardware","u":"/user-guide/common-questions","h":"#raspberry-pi-hardware","p":447},{"i":462,"t":"Why does the Media card in the UI not update when I run a dosing command?​ The Media card will only update when an Dosing Automation is active (even the Silent automation). Why is it done this way? Often, you don't want volumes to be recorded there: during cleaning, during testing, etc. Often you only want volumes associated with the experiment to be there. note All dosing events ares recorded to the database however, and with a record of when the event occurred, and source of action. This data is available in the \"Export data\" web page, under Dosing event log.","s":"Dosing","u":"/user-guide/common-questions","h":"#dosing","p":447},{"i":464,"t":"💡 For any important project, we suggest manually exporting or backing up critical data multiple different places. This doesn't just apply to using the Pioreactor, but is good advice in general. Where are logs stored?​ For the logs that you see in the Log Table in the Experiment Overview page, these can be download on the Download experiment data page in the Pioreactor web interface. Other logs are also available, including dosing event and algorithm change-logs. More granular logs per Pioreactor are available in /var/log/pioreactor.log on the Raspberry Pis. How do I access raw experiment data?​ The Download experiment data page in the Pioreactor web interface provides CSV exports of common datasets from a pre-selected experiment. All data eventually lands in a SQLite3 database on the leader Pioreactor, by default located in /home/pioreactor/.pioreactor/storage/pioreactor.sqlite. This can be download using a tool like scp. To access the SQLite3 database from the command line, try pio db. My microSD card is corrupted - what can I do?​ Unfortunately, the microSD card becoming corrupted or damaged is an infrequent but possible risk with using Raspberry Pis. If the microSD card was inside a non-leader Pioreactor, it's best to try to reformat the microSD card and start fresh (i.e. reinstall the Pioreactor software and reintroduce it to the cluster). This is usually okay as no critical data is stored locally in workers, only log files and hardware calibrations will be lost. If the microSD was inside the leader Raspberry Pi, this is a bigger problem. Likely any running experiment will have to be restarted. Fortunately, if you have more than one Pioreactor in your cluster, then the leader's SQLite database has been periodically backing itself up to other Pioreactors in the cluster every few days. Using the command line, check other Pioreactors' /home/pioreactor/.pioreactor/storage directory for the latest backup named pioreactor.sqlite.backup (should be from within the past few days hours). You can use this database to restart a new leader.","s":"Data storage, access and recovery","u":"/user-guide/common-questions","h":"#data-storage-access-and-recovery","p":447},{"i":466,"t":"How do I change/edit the network the Pioreactor on?​ With modern Raspberry Pis, Can I use Ethernet cable connections instead of Wifi connections?​ Yes, so long as the Raspberry Pi's are connected to the same network and discoverable, this should work. Even mixing Ethernet and Wifi is fine. How can I determine the Pioreactor's IP address? Or the MAC address?​ Depending on your access to the Pioreactor, there are a few ways: In the UI's Inventory page. If you can't access the Pioreactor's UI or SSH in: the software will write the IP address to the /boot directory on the SD card. After the Pioreactor's blue LED has blinked, you can unplug the Pioreactor, remove the SD card, and place the SD card in another computer. Navigate to the card, and in the directory you should see a file called ip. Open this file, and the IP address should be there. Place the SD card back into the Pioreactor and plug it back in. I'm using a local access point, but I'd like to install plugins, update software, etc.​ To install a plugin​ On a computer that is connected to the internet, download the .whl file from the plugins webpage on PyPI. Then, connect that computer to your Pioreactor's local access point's network. To each Pioreactor you wish to install the plugin on, transfer the .whl file to the Pioreactor (using SFTP or FTP). Then, run pio plugins install <plugin-name> <path/to/local/.whl> To upgrade the Pioreactor software​ See steps here. If I have multiple Pioreactor leaders on my network, what leader does http://pioreactor.local point to?​ If there are multiple leaders on the same network, then each will override the other's pioreactor.local alias, and the alias will be unreliable. You can either access the leaders by their hostnames: http://<leader hostname>.local, or you can change the alias in the config.ini, too, by editing domain_alias under section [ui] (changing this requires a restart of the machine).","s":"Networking","u":"/user-guide/common-questions","h":"#networking","p":447},{"i":468,"t":"Pioreactors are able to be used as individual units, or in concert with other Pioreactors. In either case, a Pioreactor needs to be assigned as a leader. The leader unit controls other Pioreactors (and that may include itself), stores the database, hosts the web interface, and is the interface between users and the hardware. A leader will communicate and control all the workers (non-leader Pioreactors) in the inventory. info When you set up your first Pioreactor using our software installation guide, your Pioreactor was set up to be a leader already. You only need one leader in a Pioreactor cluster.","s":"Creating a Pioreactor cluster","u":"/user-guide/create-cluster","h":"","p":467},{"i":470,"t":"After installing the worker image onto your additional Pioreactor (see the instructions here), visit the Inventory page. On the Inventory page, you can search for and add worker Pioreactors to your cluster. Click \"Add new Pioreactor\" at the top right corner of this tab. In the popup, add the name of your worker and click \"Add Pioreactor\". Once a new Pioreactor is added, you may need to refresh the page to see the new worker in the cluster. This Inventory tab will display metadata pertaining to each of your Pioreactors. You can use this page to identify a Pioreactor (causes the blue LED on the HAT to blink), unassign a Pioreactor from any experiment, reboot a Pioreactor, or remove it from your cluster. This page also provides a summary of which Pioreactors are assigned to which experiment, as highlighted in yellow in the image below.","s":"Adding Pioreactors to your cluster","u":"/user-guide/create-cluster","h":"#adding-pioreactors-to-your-cluster","p":467},{"i":472,"t":"Workers can be active (available for running activities and cultures), or inactive. Inactive Pioreactors can still be assigned to experiments, but won't response to commands to run activities or participate in experiment profiles. Turning a worker to inactive will halt all it's activities.","s":"Active and inactive","u":"/user-guide/create-cluster","h":"#active-and-inactive","p":467},{"i":474,"t":"A cluster can be made up of a single Pioreactor, or can be scaled to as many Pioreactors as you have. This gives us a few different possible topologies of what your cluster of Pioreactor(s) might look like. Single Pioreactor​ The simplest topology is when you have a single Pioreactor, and so by default the Pioreactor is both the leader and the only worker. Cluster, and leader is a worker​ When you have multiple Pioreactors, you can nominate one to be the leader, and retain it as a worker, too: Cluster, and leader is not a worker​ You can also choose not to have the leader be a worker. This is useful if you have a spare Raspberry Pi without the Pioreactor hardware, or the number of Pioreactors grows large and you wish to keep one out of the inventory to focus on being a leader only.","s":"Possible cluster topologies","u":"/user-guide/create-cluster","h":"#possible-cluster-topologies","p":467},{"i":476,"t":"Can I change the name of a worker?​ Yes, so long as that worker isn't the leader. Note: this doesn't change historical data. Remove the worker from your cluster using the Inventory page. SSH into the worker (it should still be on your network, even if not part of the cluster). Run sudo hostnamectl set-hostname <new-worker-name> && sudo reboot After a moment, the worker will turn back on with the new name. You can then use the Inventory page to add the worker again.","s":"Common questions","u":"/user-guide/create-cluster","h":"#common-questions","p":467},{"i":478,"t":"When a Pioreactor successfully boots, the onboard blue LED will flash quickly for 2 seconds, and then stop. However, there are times when the Pioreactor encounters an error, and will use the LED to alert to you that something is wrong. By counting the number of short flashes (per cycle), you can diagnose what might be wrong. Number of flashes Error 1 Can't connect to network 2 Can't connect to leader 3 SD card is almost full 4 Stirring RPM is 0 5 ADC input is very high 6 Heating PCB is above 60 ℃ 7 Voltage problem 8 Webserver offline","s":"Blue LED flashing & error codes","u":"/user-guide/error-codes","h":"","p":477},{"i":480,"t":"If your blue LED is constantly on, it suggests either an hardware error, or that your Pioreactor is missing it's config.ini. Try a reboot, and if it persists, SSH in and check for the file ~/.pioreactor/config.ini. If that file is missing, it's either a worker that hasn't been connected to a cluster, or some part of the installation has gone wrong.","s":"The blue LED is constantly on?","u":"/user-guide/error-codes","h":"#the-blue-led-is-constantly-on","p":477},{"i":482,"t":"When pairing the Pioreactor with dosing pumps, there are new capabilities and experiments you can run. The Pioreactor is pre-programmed with the following dosing automations. In the below automations, values highlighted like so are configurable. Silent Chemostat Turbidostat PID Morbidostat Fed batch","s":"Dosing automations","u":"/user-guide/dosing-automations","h":"","p":481},{"i":484,"t":"Requires: None The silent automation is the simplest automation: doing nothing. The automation will still \"wake up\" every duration minutes, but does nothing.","s":"Silent","u":"/user-guide/dosing-automations","h":"#silent","p":481},{"i":486,"t":"Requires: 2 peristaltic pumps: one media pump one waste pump 2 liquid containers with luer attachments one labelled \"waste\" one labelled \"media\" The chemostat automation is the second simplest dosing automation. Every duration minutes, the media and waste pumps run and exchange volume (mL) of liquid inside the Pioreactor. Initially, the culture is growing and consuming nutrients and energy. Eventually, a nutrient will become scarce and will stall growing. Upon a pump refresh, this growth-limiting nutrient becomes abundant once again, and the culture can grow, up until consuming all of it again and stalling growth. Thus, the bioreactor enters into a nutrient near-equilibrium (hence the term \"chemostat\", for \"chemical-static\"). However, more long-term, because the culture is under an evolutionary pressure to grow, adaptions will occur that will improve the acquisition or utilization of the growth-limiting nutrient.","s":"Chemostat","u":"/user-guide/dosing-automations","h":"#chemostat","p":481},{"i":488,"t":"Requires: 2 peristaltic pumps: one media pump one waste pump 2 liquid containers with luer attachments one labelled \"waste\" one labelled \"media\" A turbidostat (\"turbidity-static\") tries to keep the turbidity (the optical density, or OD), constant over time. This is usually accomplished by taking frequent measurements of the turbidity (every 30 seconds), and performing a set media/waste pump cycle if the optical density (or normalized optical density) exceeds a target OD (or target nOD). The amount exchanged is the volume parameter (mL). For very fast growing cultures, we recommend a volume between 1.0 ml and 2.0 ml. This automation will always dose the volume parameter, even if it's not enough for the OD to drop below the target OD. If that happens, then OD > target OD, and so the automation will trigger after the next check (30 seconds).","s":"Turbidostat","u":"/user-guide/dosing-automations","h":"#turbidostat","p":481},{"i":490,"t":"Requires: 3 peristaltic pumps: one media pump one waste pump one alt media pump 3 liquid containers with luer attachments one labelled \"waste\" one labelled \"media\" one labelled \"alt media\" By introducing another pump (labelled \"alt media\"), another dimension of experiments opens up. We can exploit the short-time scale of adaption in microbes to evolve the culture from thriving in the original media to thriving in the alternative media, or some point in between the two. Think of it as slowly shifting the environment between the two media stocks so that the microbes are under constant evolutionary pressure. This is where the name morbidostat is from: \"morbid-static\". In the Pioreactor software, the transition between environments is controlled by observing the growth rate, and artificially keeping it suppressed (set to be target growth rate) by dynamically adjusting the ratio between the original media and the alternative media when a pump cycle is run. A pump cycle is run every duration minutes. Another parameter is the target OD, which should be low to keep the culture in a state of nutrient abundance (so that the primary evolutionary pressure is the alternative media adaptation).","s":"PID Morbidostat","u":"/user-guide/dosing-automations","h":"#pid-morbidostat","p":481},{"i":492,"t":"Requires: 1 peristaltic pump A source and sink, with the pump in-between. This automation moves a preset amount of volume every duration minutes using a pump. You choose the start and end points of the tube! info How does the vial maintain a constant volume throughout operation? When liquid is added, say 1ml, the volume rises an additional 1ml. Then 1ml of liquid is removed via efflux, but then the efflux pump runs again for an additional few seconds. The efflux pump is run for an additional few seconds to eliminate any volume deltas (for example, if the volume added is greater than the volume removed due to pumping errors). Otherwise, the deltas accumulate and the vial can overflow. This additional step helps guarantee that that volume of liquid never exceeds the end of the efflux tube.","s":"Fed batch","u":"/user-guide/dosing-automations","h":"#fed-batch","p":481},{"i":495,"t":"tip We're here to help: we can offer email or live support, just email us at hello@pioreactor.com. Here's how we suggest your workflow be. Starting with your leader Pioreactor, make note of the name of it. The next steps will turn off all data collection, so do this outside of any running experiments. SSH into the leader, and create a new file with: nano ~/export_data.sh Paste the code linked here into the editor. crtl-x to exit the editor. Run this export script with bash export_data.sh. This creates an export file with all your experiment data, config files, Python plugins, profiles, etc. Exporting will take time proportional to how large your database is. Once the export file is finished being created, make note of the filename of the export. Locally, on the command line (or with FileZilla), download the file. You can do: # this is run on your local computer, i.e. the one you SSH from. scp pioreactor@<leader name>.local:/home/pioreactor/<filename of export> . Optional: do this for each Pioreactor worker in your cluster. Exporting workers will save data like calibrations, but we suggest you re-calibrate after anyways. Almost all important data, like historical experiments and logs, are stored on the leader, so you may be okay with just transferring leader data and wiping workers. It's up to you. Happy to chat further at hello@pioreactor.com. With the export file(s) local, you may now proceed with re-imaging your Pioreactors, by following the same steps here. Important: choose the same Pioreactor hostnames!","s":"Export your data","u":"/user-guide/export-import-existing-data","h":"#export-your-data","p":493},{"i":497,"t":"Once your new Pioreactor leader is running (check that you can access the UI at http://pioreactor.local), we'll upload the export with: # this is run on your local computer scp <filename of export> pioreactor@<leader name>.local:/home/pioreactor/ You may receive an error: host key verification failed. Open the known_hosts file in your .ssh folder and delete the line containing your <leader name>. When prompted, Are you sure you want to continue connecting? enter yes. Enter password raspberry and continue. SSH into the leader, and create a new file with: nano ~/import_data.sh Paste the code linked here into the editor. crtl-x to exit the editor. Run this export script with bash import_data.sh <filename of export>. The Pioreactor will update itself, and then perform a restart. Once the Pioreactor is back online, you should see your old experiments in the UI. Optional: If you exported your worker data, you can do the same thing. You're done!","s":"Import your data to a new, fresh, Pioreactor","u":"/user-guide/export-import-existing-data","h":"#import-your-data-to-a-new-fresh-pioreactor","p":493},{"i":500,"t":"Experiment profiles are another way to automatically control your Pioreactor(s). Think of them as \"scripts\" (in the \"movie script\" sense) that you can write, and the Pioreactor will perform. For example, you can use experiment profiles to automatically start stirring and start temperature control when an experiment begins, and then automatically turn off stirring and temperature control hours later. They can be used to update activity settings, without you needing to be around. We think of them as \"clicking in the UI, but headless\".","s":"What are experiment profiles?","u":"/user-guide/experiment-profiles","h":"#what-are-experiment-profiles","p":498},{"i":502,"t":"In your UI, visit Profiles page on the left-hand sidebar. Here, you can choose an experiment profile to run, start it, stop it (if running), and edit an existing or create a new profile. There's also a \"dry-run\" option, which won't actually execute any actions, but instead will log the action that would have occurred. This is useful to testing a profile first.","s":"How do I use experiment profiles?","u":"/user-guide/experiment-profiles","h":"#how-do-i-use-experiment-profiles","p":498},{"i":504,"t":"Experiment profiles are written as a YAML file (rhymes with \"camel\"). A YAML file is a structured way to describe data, and we use that to define our experiments. You can browse experiment profile examples below.","s":"What do they look like?","u":"/user-guide/experiment-profiles","h":"#what-do-they-look-like","p":498},{"i":506,"t":"See examples of experiment profiles here.","s":"Examples","u":"/user-guide/experiment-profiles","h":"#examples","p":498},{"i":508,"t":"Below is a schema for experiment profiles. We also do a run-time check # Main structure of the experiment profile experiment_profile_name: <string> # Name of the experiment profile # Metadata section (optional) metadata: author: <string> # Author of the experiment profile description: <string> # Description of the experiment profile # Plugins section (optional) plugins: - name: <string> # Name of the plugin min_version: <string> # Minimum required version of the plugin # Common jobs section (optional) # Jobs that are common for all Pioreactors common: jobs: <job_name>: actions: - type: <string> # Type of action: \"start\", \"pause\", \"resume\", \"stop\", \"update\", or \"log\" hours_elapsed: <float> # Time when the action is scheduled (in hours after experiment start) # Options for the action (optional) # If type is 'log', a 'message' parameter is required here options: <option_name>: <value> # Arguments for the action (optional) arguments: <list> # Pioreactors section (optional) # Jobs that are specific to some Pioreactors pioreactors: <pioreactor_unit_name>: # Optional label for the Pioreactor label: <string> jobs: <job_name>: actions: - type: <string> # Type of action: \"start\", \"pause\", \"resume\", \"stop\", or \"update\" hours_elapsed: <float> # Time when the action is scheduled (in hours after experiment start) # Optional 'if' directive for conditional execution of actions if: <string> # Can be an expression # Options for the action (optional) # Values can be expressions, denoted with ${{ }} options: <option_name>: <value>","s":"Experiment profiles schema","u":"/user-guide/experiment-profiles-schema","h":"","p":507},{"i":510,"t":"See examples of experiment profiles here.","s":"Examples","u":"/user-guide/experiment-profiles-schema","h":"#examples","p":507},{"i":513,"t":"Experiment profiles can be managed in the UI at http://pioreactor.local/experiment-profiles. See video below for a demonstration.","s":"Using the UI","u":"/user-guide/create-edit-experiment-profiles","h":"#using-the-ui","p":511},{"i":515,"t":"All profiles are stored on the leader's disk under ~/.pioreactor/experiment_profiles/. You can create and edit profiles in this directory, as well.","s":"On the command line","u":"/user-guide/create-edit-experiment-profiles","h":"#on-the-command-line","p":511},{"i":518,"t":"When writing a profile, note that the hours_elapsed field refers to when the experiment profile started, and not when the experiment started.","s":"hours_elapsed refers to the profile start time","u":"/user-guide/create-edit-experiment-profiles","h":"#hours_elapsed-refers-to-the-profile-start-time","p":511},{"i":520,"t":"The if directive can be included in any action to conditionally execute it or not. The if statement is evaluated when the action is to be executed (i.e., when elapsed_hours has passed). The if directive is a general boolean expression, and to common operators can be used: and or not True and False ( and ) Also included are numbers (floats), and strings (examples later). The comparison operators are: == >= and <= > and < The operators addition +, subtraction -, multiplication *, and division / are allowed on floats, as well. The power of if comes when you combine it with expressions, see below:","s":"How the if directive works","u":"/user-guide/create-edit-experiment-profiles","h":"#how-the-if-directive-works","p":511},{"i":522,"t":"Expressions are the method used to get is dynamic data, provided from jobs, during execution of profiles. For example, the following: pio1::stirring::target_rpm will fetch the target_rpm from pio1's stirring job at the time the action is to be executed. To use this in an example: stirring: ... - type: update hours_elapsed: 6.0 if: pio1::stirring::target_rpm >= 500 options: target_rpm: 400 will check, after 6 hours, if the target_rpm is above 500, and if true, will update the target RPM to 400. You can also compare against strings. For example, to stop a job if the temperature automation running is equal to thermostat, use: temperature_control: ... - type: stop hours_elapsed: 6.0 if: pio1::temperature_control::automation_name == thermostat Where do these dynamic values come from? Each job has published_settings that can be referenced (refer to the job's source code to all published_settings for a job, or they are published in MQTT). Some published settings have are actually nested json blobs, but we need either numbers or strings to compare in our boolean expression. You can index these json blobs in the boolean expression using ., for example: temperature_automation: ... - type: update hours_elapsed: 6.0 if: pio1::temperature_control::temperature.temperature <= 30 options: target_temperature: 32 We use temperature.temperature because the temperature published setting is a json blob that looks like the following, and we wish to reference the \"temperature\" field in the blob: { \"temperature\": <float>, \"timestamp\": <ISO 8601 timestamp> }","s":"How expressions work","u":"/user-guide/create-edit-experiment-profiles","h":"#how-expressions-work","p":511},{"i":524,"t":"Similar to an if directive using dynamic data, options can also have dynamic data (see notes above for syntax, too). However, to distinguish between a string and an expression, an expression must be wrapped in ${{ ... }}. For example, consider the following update action: pioreactors: worker1: jobs: stirring: actions: - type: start hours_elapsed: 0 options: target_rpm: 500 - type: update hours_elapsed: 12 options: target_rpm: ${{ worker1:stirring:target_rpm + 50 }} This will update the value of target_rpm to whatever its current value is (after 1 hour), and add 50 to it. You can use the any pioreactor and any job in an expression - you aren't limited to the job your editing. For example, the update below will dynamically set the target_rpm to a function of optical density. pioreactors: worker1: jobs: stirring: actions: - type: start hours_elapsed: 0 options: target_rpm: 500 - type: update hours_elapsed: 12 options: target_rpm: ${{ worker1:stirring:target_rpm + worker1:od_reading:od1.od * 10 }}","s":"Expressions in options","u":"/user-guide/create-edit-experiment-profiles","h":"#expressions-in-options","p":511},{"i":526,"t":"Expressions can reference individual Pioreactors, for example worker1:stirring:target_rpm, but what if you want to specify all Pioreactors in an expression? This is useful for using expressions in the common block. The syntax for this is to use the following ::<job_name>:setting For example, to conditionally change the stirring RPM in all Pioreactors, and to update it: common: jobs: stirring: actions: - type: update hours_elapsed: 6 if: ${{ ::stirring:target_rpm <= 500 }} options: target_rpm: 500 You can also use this syntax in options: common: jobs: stirring: actions: - type: update hours_elapsed: 6 if: ${{ ::stirring:target_rpm <= 500 }} options: target_rpm: ${{ ::stirring:target_rpm + 10 * ::od_reading:od1.od }}","s":"Expressions in the common block","u":"/user-guide/create-edit-experiment-profiles","h":"#expressions-in-the-common-block","p":511},{"i":528,"t":"The repeat directive is the most powerful action, as it allows you loop actions over and over again to check for a condition change, update based on state, etc. The repeat action requires two new necessary fields: actions: a list of actions (start, stop, update, etc.) that you want to repeat. The field hours_elapsed refers to the start of the loop, not when the profile starts. repeat_every_hours: this is a float describing how long, in hours, the loop should last for. For example, repeat an action every 2 hours, or generally: repeat a sequence of actions every X hours. Your repeat action should look like, for example: - type: repeat hours_elapsed: 6.0 # when to start the looping, 6 hours repeat_every_hours: 0.5 # perform the actions every 30 minutes actions: - type: update hours_elapsed: 0.0 ... - type: update hours_elapsed: 0.1 ... Finally, there is more control using the other optional fields: max_hours: this controls how long the loop should run for. For example, if repeat_every_hours is 0.5 (or 30 minutes), and max_hours is 6, then the loop will repeat 12 times before exiting. while: this is an expression, like if, that runs at the start of each loop, including the first. For example, the following profile will run media until the OD is less than 3.0. We also remove waste so we don't overflow the vial. This is a really coarse turbidostat, and is just for demonstration - don't use this: You can also use the if directive to skip running the entire repeat action, too. add_media: actions: - type: repeat hours_elapsed: 6.0 repeat_every_hours: 0.0025 # every 9 seconds while: ${{ worker1:od_reading:od1.od > 3.0 }} actions: - type: start options: volume: 1 remove_waste: actions: - type: repeat hours_elapsed: 6.0 repeat_every_hours: 0.0025 # every 9 seconds while: ${{ worker1:od_reading:od1.od > 3.0 }} actions: - type: start options: volume: 1.5","s":"The repeat action","u":"/user-guide/create-edit-experiment-profiles","h":"#the-repeat-action","p":511},{"i":530,"t":"A common task is to start the thermostat, and you may want to do something like: # wrong, this won't work ❌ common: jobs: thermostat: actions: - type: start hours_elapsed: 0.0 options: target_temperature: 30 However, to start (and stop) automations (which the thermostat is), you actually need to use the controllers: # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat target_temperature: 30 Likewise, to stop a automation, you need to stop the controller: # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat target_temperature: 30 - type: stop hours_elapsed: 12.0 How do you update target_temperature, see below.","s":"Start/stop controllers instead of automations","u":"/user-guide/create-edit-experiment-profiles","h":"#startstop-controllers-instead-of-automations","p":511},{"i":532,"t":"A setting like target_temperature or volume is attached to the automation, not a controller, so you need to update the automation: # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat target_temperature: 30 - type: stop hours_elapsed: 12.0 temperature_automation: # this is thermostat - type: update hours_elapsed: 1.0 options: target_temperature: 32 - type: update hours_elapsed: 2.0 options: target_temperature: 34","s":"Update automations instead of controllers","u":"/user-guide/create-edit-experiment-profiles","h":"#update-automations-instead-of-controllers","p":511},{"i":534,"t":"Check your YAML syntax with a tool like: https://www.yamllint.com/ Note that indentation matters! For example, these mean different things, and only the second one is correct: # wrong ❌ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat # this should be indented to align with options target_temperature: 30 # this should be indented to align with options # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat # lined up! target_temperature: 30","s":"YAML syntax check, and indentation problems","u":"/user-guide/create-edit-experiment-profiles","h":"#yaml-syntax-check-and-indentation-problems","p":511},{"i":536,"t":"This is likely because you are using - where you shouldn't: # wrong ❌ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: - automation_name: thermostat # don't put - here - target_temperature: 30 # don't put - here # correct ✅ common: jobs: temperature_control: actions: - type: start hours_elapsed: 0.0 options: automation_name: thermostat # don't put - here target_temperature: 30 # don't put - here","s":"Expected `object`, got `array` - at ` ... .options`","u":"/user-guide/create-edit-experiment-profiles","h":"#expected-object-got-array---at---options","p":511},{"i":538,"t":"Some applications require more power to your Pioreactor if it is using lots of peripherals. This may include using more powerful pumps, more powerful external LEDs, etc. Or, if you see warning messages that reference under voltage or throttling, you probably are asking the Pioreactor to do too much given its default 5V power supply. You can supply a higher voltage / amp power to the peripherals using the barrel jack connection. The barrel jack connection allows for power supply units of up to 18V to the PWM channels 1 through 4 (PWM channel 5, used for onboard heating, is not effected, and always tied to the 5V rail). Please make sure your barrel jack connector is positive center. Look for a symbol like the following, or confirm in some other manner Finally, to enable the PWM channels to use the new auxiliary power supply, you need to move the shunt connector to the position closest to the LED outputs. (If the shunt connector is not present, the PWM rail is powered by the RPi's power supply, minus a diode drop. It's recommend to replace the shunt, however.) note When changing the default power supply, any stirring calibration and pump calibrations will need to be updated. Also, the initial_duty_cycle under stirring in the configuration may need to change. caution Be mindful that the default stirring motor provided with the Pioreactor has a maximum voltage rating of 12V.","s":"Supplying more power to the PWM channels","u":"/user-guide/external-power","h":"","p":537},{"i":540,"t":"When using multiple of Pioreactor's peristaltic pumps, we recommend a 12V power supply, with at least 1 amp (this is the same as a 12W power supply). Our pumps use maximum 0.4A, and the stirring motor uses 0.1A.","s":"Power supply for using Pioreactor peristaltic pumps","u":"/user-guide/external-power","h":"#power-supply-for-using-pioreactor-peristaltic-pumps","p":537},{"i":542,"t":"positive center barrel size: 2.1mm I.D. x 5.5mm O.D. Maximum voltage: 18V","s":"More details on power supply","u":"/user-guide/external-power","h":"#more-details-on-power-supply","p":537},{"i":544,"t":"Hardware calibrations serve as a method to get accurate performance from your Pioreactor.","s":"Hardware calibrations","u":"/user-guide/hardware-calibrations","h":"","p":543},{"i":546,"t":"info You'll need the following: Pioreactor HAT Pioreactor sleeve Vial and stirbar Internally, the Pioreactor will vary the amount of voltage to apply to the stirring motor to reach the desired RPM, however, this can take a few minutes. We can significantly improve this by asking the Pioreactor to create a \"map\" between voltage and RPM beforehand. Then the Pioreactor only needs to perform a lookup in the map to hit the desired RPM. note This is optional, but can really help stirring performance. Creating a stirring calibration is also very easy, so we recommend it. Calibrating the stirring in the UI # Start by filling a Pioreactor vial about 3/4th with water, and place the stirbar inside. Close with lid. Place into the Pioreactor. From the web interface, in Pioreactors, find the Pioreactor you wish to calibrate. Click Calibrate. Click stirring. Click Start. The Pioreactor will increment the voltage applied to the motor, and record the RPM. After it's done, it will collect this data into a calibration curve, and store it locally. You're done! Your stirring RPM should be much more responsive now.","s":"Stirring calibration (optional)","u":"/user-guide/hardware-calibrations","h":"#stirring-calibration-optional","p":543},{"i":549,"t":"Calibrating a pump, like a low-volume peristaltic pump, is very important to accurately dispense or remove a target volume. There is no liquid feedback loop in the Pioreactor (unlike in the stirring & RPM relationship), so this calibration curve is important. There are three pumps on the Pioreactor: media, alt-media, and waste. You don't need to have all three available, and can calibrate them one at a time. For calibration, you'll need the following: A pump, with power connection to Pioreactor's PWM outputs An accurate weighing scale, with accuracy of 0.1g or better. Container of water tip Supplying external power? Make sure to plug in your external power before pump calibration! Calibrating the pumps # We'll perform this routine through your computer's command line. Need help accessing it? Enter ssh pioreactor@<insert unit name>.local. For example, to calibrate on our Pioreactor named worker3, we typed ssh pioreactor@worker3.local. The default password is raspberry. Enter pio run pump_calibration. Follow the prompts to calibrate your media, waste, and/or alternate media pumps. Calibrations can be performed depending on the frequency of your Pioreactor use.","s":"Pump calibration","u":"/user-guide/hardware-calibrations","h":"#pump-calibration","p":543},{"i":552,"t":"Starting in software version 23.12.11, you can edit your calibration, too. At the end of the calibration, your data is listed (or use pio run pump_calibration display to see the data again). Copy the json data (between { and }) into new json file on the Raspberry Pi, say ~/pump_data.json for example. Make any edits you wish to the data. Then you can \"rerun\" the calibration with data from that file: pio run pump_calbration -f ~/pump_data.json","s":"Made a mistake, or want to change some data?","u":"/user-guide/hardware-calibrations","h":"#made-a-mistake-or-want-to-change-some-data","p":543},{"i":554,"t":"Choose from the guides below:","s":"Getting started guides","u":"/user-guide/getting-started","h":"","p":553},{"i":556,"t":"✨New Pioreactor 20ml v1.1 Pioreactor 20ml v1.0","s":"Pioreactor 20ml assembly","u":"/user-guide/getting-started","h":"","p":553},{"i":560,"t":"✨New Pioreactor 20ml v1.0 → v1.1 upgrade kit Temperature Expansion Kit Adding peristaltic pumps Adding more LEDs","s":"Upgrade kits and accessories","u":"/user-guide/getting-started","h":"","p":553},{"i":566,"t":"Software installation","s":"Software guides","u":"/user-guide/getting-started","h":"","p":553},{"i":569,"t":"Normally, the external hardware will have two terminals, corresponding to positive and ground. The positive terminal may be marked by a dot, or \"+\" symbol, or be colored red. Make note of this terminal. The PWM outputs on the Pioreactor are 0.100\" (2.54mm) pitch connectors, with the positive pin closer to the onboard button (also marked on the edge on the underneath of the HAT circuit board). Simple Dupont female square head fit just fine in them (example). The only problem with using these connectors is that they are not locked in-place, and can slip out of the connection. The nice connectors we use for LEDs, the stirring motor and our pumps are TE Connectivity AMP connectors 487526-1. These also require a specific socket connector.","s":"Hardware connection assembly","u":"/user-guide/hardware-connection-assembly","h":"","p":568},{"i":571,"t":"Experiment data can be exported using the Export data tab on the Pioreactor site. You can retrieve datasets from any previous experiments, including from all experiments simultaneously using the <All experiments> option at the bottom of the list. Select your experiment from the drop down menu. Select the datasets you would like to download. Click the Export button to download the raw data as .csv files. Each dataset on the list will export as its own .csv file. note Is a dataset not available in the list? Is there a specific data point you'd like but can't find? Feel free to ask about it on our forums.","s":"Exporting data","u":"/user-guide/export-data","h":"","p":570},{"i":573,"t":"When exporting datasets, most csv files will include a single metric against a time series. If you'd like to compare many datasets using a single time series, we recommend export of the Pioreactor Unit Activity dataset. This dataset summarizes all activities from one Pioreactor against a single time series to make working with data easier. The dataset will follow a running timeseries (column A) and include metrics for OD, temperature, stirring, LED updates and dosing. Consider this example where we turned on temperature and stirring: Temperature and stirring datasets are exported on separate .csv files and follow their unique time series. In comparison, the Pioreactor Unit dataset compiles both against the same time series, making it much more accessible:","s":"Pioreactor Unit Activity Data","u":"/user-guide/export-data","h":"#pioreactor-unit-activity-data","p":570},{"i":575,"t":"note This article isn't intended as a crash course in Python, or Pioreactor software, but some helpful ways to write small scripts for your Pioreactor. If interested in learning more, check out the developer docs for detailed information. For some testing and playing purposes, it's really easy to get started writing scripts to automate parts of your Pioreactor. For this tutorial, you'll need to be able to SSH into your Raspberry Pi.","s":"Writing Pioreactor scripts with Python","u":"/user-guide/intro-python-scripting","h":"","p":574},{"i":577,"t":"SSHing means to connect to a computer remotely, and interact with its command line. In our case, we wish to interact with the Raspberry Pi remotely. SSH software depends on your operating system: Windows users: use the Command Prompt, or install PuTTY, or install the Secure Shell App for Google Chrome. macOS users: open up the terminal app: command+space, search for \"terminal\". linux users: y'all don't need my help :) We need to connect to the Raspberry Pi: hostname: your Pioreactor's name (see web interface) also-known-as your Raspberry Pi's hostname. user: pioreactor password: the one you used when you installed the Pioreactor, by default it's raspberry. One your online, you can have some fun and type pio blink to have your Pioreactor blink!","s":"1. SSHing into your Raspberry Pi","u":"/user-guide/intro-python-scripting","h":"#1-sshing-into-your-raspberry-pi","p":574},{"i":579,"t":"We'll start with something simple: writing a script to turn on the Pioreactor's stirring. To create a file called script_test.py and edit it on the Raspberry Pi command line, type nano script_test.py. You'll be shown an editor. Let's enter the following Python code: import time from pioreactor.background_jobs.stirring import start_stirring stirrer = start_stirring(target_rpm=400) time.sleep(10) Hit crtl-x, and then Y to save our file.","s":"2. Writing our first script.","u":"/user-guide/intro-python-scripting","h":"#2-writing-our-first-script","p":574},{"i":581,"t":"To run our script, type python3 script_test.py in the command line. If everything works correctly, your Pioreactor's stirring will start, and then finish after 10 seconds. You're a hacker now :) To make stirring run forever, let's edit the file again: nano script_test.py, and replace time.sleep(10) with: import time from pioreactor.background_jobs.stirring import start_stirring stirrer = start_stirring(target_rpm=400) stirrer.block_until_disconnected() Save the file with crtl-x, and then Y, and run the script again. Now, the job will run until you log off, or exit the program with ctrl-c. This is because block_until_disconnected will block to program at that line.","s":"3. Running our Python script","u":"/user-guide/intro-python-scripting","h":"#3-running-our-python-script","p":574},{"i":583,"t":"Let's add some more to our script. Let's say we also want to: turn on an LED in channel B, turn on optical density reading (with 90° photodiode in channel 1 and reference in channel 2). After 10 seconds, slow down the stirring RPM import time from pioreactor.background_jobs.stirring import start_stirring from pioreactor.background_jobs.od_reading import start_od_reading from pioreactor.actions.led_intensity import led_intensity led_intensity({'B': 50}) stirrer = start_stirring(target_rpm=400) od_reader = start_od_reading(\"90\", \"REF\") time.sleep(10) stirrer.set_target_rpm(300) stirrer.block_until_disconnected() You should see data coming into to your experiment overview in the web interface!","s":"4. Extending our script: more jobs, changing RPM, and adding lights.","u":"/user-guide/intro-python-scripting","h":"#4-extending-our-script-more-jobs-changing-rpm-and-adding-lights","p":574},{"i":585,"t":"Next, we'd like to start heating and keep our vial at a constant temperature. Recall that all temperature tasks are actually temperature automations. In this case, we require the thermostat temperature automation, invoked from a temperature controller: import time from pioreactor.background_jobs.stirring import start_stirring from pioreactor.background_jobs.od_reading import start_od_reading from pioreactor.actions.led_intensity import led_intensity from pioreactor.background_jobs.temperature_control import start_temperature_control led_intensity({'B': 50}) stirrer = start_stirring(target_rpm=400) od_reader = start_od_reading(\"90\", \"REF\") temp_controller = start_temperature_control(\"thermostat\", target_temperature=32) time.sleep(10) stirrer.set_target_rpm(300) stirrer.block_until_disconnected()","s":"5. Adding an automation","u":"/user-guide/intro-python-scripting","h":"#5-adding-an-automation","p":574},{"i":587,"t":"This is just a small example of scripts you can make. If you need to learn more, we suggest checking out the developer guide.","s":"Conclusion","u":"/user-guide/intro-python-scripting","h":"#conclusion","p":574},{"i":589,"t":"So far, we have worked with basic activities that you can directly set as a one time thing, typically at the beginning of your experiment (starting stirring, OD readings, etc.). For more advanced experiments, we introduce automations. Automations are preset functions that are automated, or performed by the Pioreactor without the need of your intervention. This is great for when you want to change the environment of your experiment in some way, whether periodically or at a given time — and you don't want to change your settings each time! Some examples: Every 15 minutes, you want to introduce new media and remove old media using pumps. When working with phototrophs (such as algae), you want to create “day/night” cycles by turning on/off your LEDs. Setting automations can be done so that the Pioreactor performs these tasks automatically. These automations can be found under Activities, when you Manage your Pioreactor.","s":"Introduction to automations","u":"/user-guide/intro-to-automations","h":"","p":588},{"i":591,"t":"When starting an automation, like a chemostat, it is ambiguous whether to start dosing (or checking whether to dose) immediately, or wait N minutes to start. Checking Skip first run will choose the latter: wait N minutes, and then begin.","s":"Skip first run?","u":"/user-guide/intro-to-automations","h":"#skip-first-run","p":588},{"i":593,"t":"The Pioreactor is an mostly open source, affordable, and extensible bioreactor platform. The goal is to enable biologists, educators, DIYers, biohackers, and enthusiasts to be able to reliably control and study the growth of microorganisms.","s":"Pioreactor user guide","u":"/user-guide/introduction","h":"","p":592},{"i":595,"t":"To start assembling your Pioreactor, check out our Getting Started guides.","s":"Need to assemble your Pioreactor?","u":"/user-guide/introduction","h":"#need-to-assemble-your-pioreactor","p":592},{"i":597,"t":"See the basic steps to operating your Pioreactor, or check out our repository of biology experiments.","s":"Help with your first experiment?","u":"/user-guide/introduction","h":"#help-with-your-first-experiment","p":592},{"i":599,"t":"If you are interested in the software internals, take a look at our developer guide.","s":"Developers","u":"/user-guide/introduction","h":"#developers","p":592},{"i":601,"t":"Check out the documentation (you're on it right now)! Ask a question on our community forums Contact us at support@pioreactor.com","s":"Looking for further help?","u":"/user-guide/introduction","h":"#looking-for-further-help","p":592},{"i":603,"t":"LED automations are ways to automatically control the 4 available LEDs in the Pioreactor. These LEDs can be used as a light source for photosynthetic microbes, influence the environment of the microbes, as additional sensors, or improve existing sensors.","s":"LED automations","u":"/user-guide/led-automations","h":"","p":602},{"i":605,"t":"Requires: None The silent automation is the simplest automation: doing nothing. The automation will still \"wake up\" every duration minutes, but does nothing.","s":"Silent","u":"/user-guide/led-automations","h":"#silent","p":602},{"i":607,"t":"Requires: up to 2 LEDs, in channels C and D. This automation will turn the LEDs in channels C & D on and off on a predetermined scheduale, specified by light_duration_minutes and dark_duration_minutes. The intensity of the LED is given by light_intensity. The LEDs start ON. Note: duration is permanently set to be 1 minute. The LEDs should go in pockets X2 and X3 on the Pioreactor.","s":"Light/Dark cycle","u":"/user-guide/led-automations","h":"#lightdark-cycle","p":602},{"i":610,"t":"You can run the pumps from the Pioreactor UI. These are NOT automations, but rather simple actions to use to set up an experiment, perform cleaning, or intervene in an experiment. Cycling​ Under the Dosing tab, you run the media pump or the alt-media pump and concurrently the waste pump. This is called cycling. By running the waste pump simultaneously, the vial will avoid overflow. You can cycle for a set duration of time. Cycling is good for cleaning pumps, priming tubes with media, or filling your vial with media. Specific control of pumps​ Under the Dosing tab, you can also run specific pumps (media, waste, and alt-media) for a specific duration, volumes (if calibrated), or continuously. The latter will run until the Stop button is pressed. caution Careful not to overflow your vial! The vial can hold 20ml, but stay well below this. Adjustments from manual changes​ Sometimes you may want to add or remove liquid from the vial manually. These changes can be recorded by using the Manual adjustments form under the Dosing tab. These do not run the pumps, but will log the adjustments. This is useful for recording adjustments into the database, and keeping metrics accurate.","s":"Dosing","u":"/user-guide/manual-dosing-leds","h":"#dosing","p":608},{"i":612,"t":"Under the LED tab, you can update specific intensities of the LEDs.","s":"LEDs","u":"/user-guide/manual-dosing-leds","h":"#leds","p":608},{"i":614,"t":"Navigate to the Overview page on the Pioreactor web interface. Here you can view live charts for growth rate, OD, normalized OD, and temperature. These overview graphs are used to monitor collected data during the experiment runtime.","s":"Monitoring your experiment","u":"/user-guide/monitor-experiment","h":"","p":613},{"i":616,"t":"Recent event logs are found along the right side of the main Overview page. These logs document any errors, processes, or updates for each Pioreactor.","s":"Event logs","u":"/user-guide/monitor-experiment","h":"#event-logs","p":613},{"i":618,"t":"To change the settings of activities after starting, navigate to the Pioreactors tab. Under Manage for a single Pioreactor or Manage all Pioreactors, click the Settings tab. Here you can change the settings of your activities (such as temperature, RPM, and dosing volume) without pausing or stopping the activity.","s":"Changing settings","u":"/user-guide/monitor-experiment","h":"#changing-settings","p":613},{"i":620,"t":"To locate a Pioreactor, click Identify for the corresponding Pioreactor on the Pioreactors page. This will cause the Pioreactor's onboard LED to blink a blue light. Conversely, you can also find a Pioreactor's name by pressing the white button on the Pioreactor. This causes a tag to come up on the interface for as long as you are holding the button down:","s":"Identifying Pioreactors in your cluster","u":"/user-guide/monitor-experiment","h":"#identifying-pioreactors-in-your-cluster","p":613},{"i":622,"t":"Keep an eye on the optical density graph in the Overview page. Initially, you can expect the the OD to be relatively stable. The following are some common issues:","s":"Troubleshooting","u":"/user-guide/monitor-experiment","h":"#troubleshooting","p":613},{"i":624,"t":"This type of noise is typically caused by bubbling in the media due to metabolism. Noise gradually gets worse as the culture grows, where more metabolism leads to more CO2 bubbles. Thus, you would notice noise build up gradually as the culture becomes larger. To reduce the noise made by bubbles, we recommend allowing more airflow by raising the tubing enough so they aren't submerged in your media.","s":"Gradual increase in noise in OD","u":"/user-guide/monitor-experiment","h":"#gradual-increase-in-noise-in-od","p":613},{"i":626,"t":"note Optical density can decrease early => growth rates can dip negative early on & this is an artifact of turbidity measurements! For variations in OD at the beginning, make sure that your stirbar is in the vial! This is a common mistake we experienced after several experiments.","s":"Initial noise in OD","u":"/user-guide/monitor-experiment","h":"#initial-noise-in-od","p":613},{"i":628,"t":"Random, large spikes in OD readings are indicative of solid debris in your vial. Remove the vial and inspect the media for any debris. You may need to remake your vials and start over. Be sure to thoroughly wash and autoclave your vials and rinse any pumps (if being used). If clumps are to be expected (and unavoidable), you can increase your stirring RPM if allowed in your experiment protocol. This will cause larger clumps to aggregate in the center of the vial, due to a mini \"vortex\" formed by stirring.","s":"Random spikes in OD","u":"/user-guide/monitor-experiment","h":"#random-spikes-in-od","p":613},{"i":630,"t":"If your target temperature is close to room temperature, it can be subject to fluctuations based on changes in room temperature. For example, we set our target to 26 degrees C, and worked in a room with no AC: Each Pioreactor had an increase in temperature since the target fell below ambient. Note that the leader unit Pioreactor in the cluster was more sensitive to increases in ambient temperature since it requires more processing power.","s":"Temperature fluctuations","u":"/user-guide/monitor-experiment","h":"#temperature-fluctuations","p":613},{"i":632,"t":"If none of these issues apply to your data, feel free to contact us at support@pioreactor.com or post to our forums for further assistance.","s":"Looking for further help?","u":"/user-guide/monitor-experiment","h":"#looking-for-further-help","p":613},{"i":634,"t":"Info You can expect the assembly to take approximately 20-30 minutes.","s":"Before you begin assembly","u":"/user-guide/hardware-setup-intro","h":"","p":633},{"i":640,"t":"info Previously, Raspberry Pis used a file called wpa_supplicant.conf to handle wifi network connections. This is not longer the case. Modern Raspberry Pi software, including the Pioreactor, doesn't use wpa_supplicant.conf at all. Instead, the tool nmcli replaces it. Don't follow tutorials that use wpa_supplicant.conf.","s":"Networking","u":"/user-guide/networking","h":"","p":639},{"i":642,"t":"The main \"entry point\" for networking on the Pioreactor (and Raspberry Pi's in general) is the tool nmcli. This controls discovering networks, connecting to them, and editing connections. For example, running nmcli con will diplay a list of possible networking connections, and connected ones in green.","s":"General networking tools","u":"/user-guide/networking","h":"#general-networking-tools","p":639},{"i":644,"t":"You can first discover all the visible networks with: sudo nmcli d wifi list If you see your network on the list, then run: sudo nmcli device wifi connect <ssid name> password <ssid password> ifname wlan0 (If you get a \"Can't find\" error, try running the above list command again.)","s":"Connecting to a wifi network using nmcli","u":"/user-guide/networking","h":"#connecting-to-a-wifi-network-using-nmcli","p":639},{"i":646,"t":"First, some terminology and understanding for us: a computer, like a Pi, has networking interfaces. For example, the onboard wifi on RPi’s is one such interface. The larger, model Bs, have an ethernet connector, which is another interface. Each interface can connect to 0 or 1 networks. In order to connect to multiple networks, you need a Raspberry Pi with multiple interfaces. You can add interfaces with devices like a USB wifi device. To see what your current interfaces are doing, use: nmcli device The right hand side shows your connected interfaces. For example, if have a ethernet connection to a router, you'll see an eth0 connection active. If you have an additional wifi hardware device attached to your Pi, you'll see wlan1. To connect to another wifi network using wlan1, use: sudo nmcli device wifi connect <ssid name> password <ssid password> ifname wlan1 If your leader is connected to multiple networks A and B, and you access the UI over network A, but your workers access over network B, the leader is in the position called a \"gateway\". You'll need to make some configuration changes to your cluster. Since the leader is attached to networks A and B, it has two IPs (use hostname -I to see all the ips), let's call them ipA and ipB respectively. Access the configuration in the UI. In the shared config.ini, edit the [mqtt] broker field to be equal to ipA. Also edit the leader_address to be ipB. In each of the workers (including the leader's config.ini, if it's a worker), add the following: [mqtt] broker=ipB You may need to restart your cluster for these to take full effect.","s":"Connecting to multiple networks","u":"/user-guide/networking","h":"#connecting-to-multiple-networks","p":639},{"i":648,"t":"Note that you can only have 1 network connection for each network interface. So if you have only 1 wifi device (by default, RPi's only have 1 wifi device on them -> only 1 wifi interface), the following will replace any existing wifi connection. sudo nmcli con up PioreactorAP Setting leader_address and MQTT broker in your config.ini​","s":"Starting the Pioreactor local access point using nmcli","u":"/user-guide/networking","h":"#starting-the-pioreactor-local-access-point-using-nmcli","p":639},{"i":650,"t":"To change the web UI port from the default of 80, following these instructions: SSH into your leader Pioreactor. We'll edit the lighttpd configuration first: sudo nano /etc/lighttpd/lighttpd.conf and find the line starting with server.port. Change this to something else (preferably not a value below 1024). Save and exit. Restart lighttpd with: sudo systemctl restart lighttpd.service You should be able to access the web UI only on http://leader name:new port, for example: http://leader.local:8080 In your configuration, under the [ui] section, change the port option from 80 to your new port value. Save. You may need to restart your cluster for this new port to propagate to all machines correctly.","s":"Changing web UI port from 80 to something else","u":"/user-guide/networking","h":"#changing-web-ui-port-from-80-to-something-else","p":639},{"i":652,"t":"This is a work-in-progress, but here's one example.","s":"Connecting to eduroam","u":"/user-guide/networking","h":"#connecting-to-eduroam","p":639},{"i":654,"t":"If you would like to expose the Pioreactor UI to view remotely, you can use a service like Ngrok to do so. caution This exposes your Pioreactor UI and therefore your Raspberry Pi over the internet. You should have a strong password on your Raspberry Pi leader, and use a strong password for basic-auth (below). We make our best security effort in our products, however we are not responsible for any damages as a result of exposing your Raspberry Pi online. The following are the steps to take: Sign up for Ngrok - the free plan is all we need. Make sure to confirm your account through your email. Download the app onto the Raspberry Pi: wget -O ngrok.tgz https://bin.equinox.io/c/bNyj1mQVY4c/ngrok-v3-stable-linux-arm.tgz Unzip: tar zxvf ngrok.tgz Make a new folder for the program: sudo mkdir /opt/ngrok Move ngrok file there: sudo mv ngrok /opt/ngrok Make a config folder: mkdir ~/.ngrok Fill in the following: nano ~/.ngrok/ngrok.yml. We advise changing the basic auth credentials below to something more secure authtoken: <add your ngrok auth token here, find in nrgok dashboard> tunnels: ui: proto: http addr: 80 inspect: false basic_auth: [\"pioreactor:vogue-awesome-brag\"] #change this schemes: - http ws: proto: http addr: 9001 inspect: false schemes: - http version: \"2\" region: us Run in background: nohup /opt/ngrok/ngrok start ui ws --config ~/.ngrok/ngrok.yml & Alternatively, if you wish to set this up as a service that will launch on start up, the following sudo systemctl enable ngrok At dashboard.ngrok.com, you'll see two urls. One of the unique urls should link to your Pioreactor dashboard (when asked for a name and password, use the user name and the password used in the config above). However, the UI will crash - this is expected. Continue on. The other url is added to your config.ini. While SSH'd into your leader, open the config.ini: nano ~/.pioreactor/config.ini And edit the following section (but put in your unique url) [mqtt] ... # this should not have any https:// infront: ws_url=<your url>.ngrok-free.app ws_protocol=wss ... Deploy your config with pios sync-configs, and refresh your UI that previously crashed. You're all done! You can now access the Pioreactor UI anywhere. The username and password are the same you added to your yaml file above.","s":"Ngrok","u":"/user-guide/ngrok-remote-access","h":"","p":653},{"i":657,"t":"The interaction of light within samples of suspended microorganisms will differ from light passing through concentrated solutions. Instead of being absorbed, light is scattered by the cells in suspension. This scattered light is measured as optical density (OD). As turbidity increases, more scattering occurs, resulting in a higher OD reading. tip Looking to calibrate for OD600 readings? Visit this page.","s":"Background on optical density","u":"/user-guide/od-normal-growth-rate","h":"#background-on-optical-density","p":655},{"i":659,"t":"Due to manufacturing variables such as differences in LED strength and sensitivity, the raw OD readings can't be compared against each other. Instead, we use the normalization technique described below: A series of initial OD readings are averaged to produce a reference value (denominator). New OD readings after the reference value are normalized using the following simple equation: latest ODreference OD=normalized OD\\frac{\\normalsize \\text{latest\\thickspace OD}}{\\normalsize \\text{reference\\thickspace OD}}=\\text{normalized\\thickspace OD}referenceODlatestOD​=normalizedOD For example: Pioreactor name Reference OD Latest OD Pioreactor1 0.030 0.033 Pioreactor2 0.010 0.015 It's difficult to compare raw OD readings since the starting values are different. However, if we normalize using the above equation: Pioreactor1​ 0.0330.030=1.1\\frac{\\small 0.033}{\\small 0.030}=1.10.0300.033​=1.1 Culture growth by 1.1x. Pioreactor2​ 0.0150.010=1.5\\frac{\\small 0.015}{\\small 0.010}=1.50.0100.015​=1.5 Culture growth by 1.5x. We can more accurately compare culture growth using these ratios as opposed to using the raw OD values. tip Because of the way we defined normalized optical density, it has the following easy interpretation: its the multiplicative amount the culture has changed by. So if the normalized OD is 2.0, the culture has doubled its initial concentration, i.e. doubled the population since the volume is fixed. This also works for traditional OD600 measurements: if your initial sample has OD600 equal to 0.45, then a normalized OD of 2.0 is the same as an OD600 of twice that, or 0.90. (Generally...).","s":"Normalization","u":"/user-guide/od-normal-growth-rate","h":"#normalization","p":655},{"i":661,"t":"While basic normalization accounts for initial OD differences, it does not consider the optical density of the media itself. For a more accurate growth rate calculation, you can blank your sample. Blanking your vials is recommended for experiments that begin with low OD readings (ex. inoculating small amounts of yeast). By blanking, you are able to observe the OD of only the microorganism of interest. As an example, let's consider the same data as above, but this time we have information on the blank ODs: Pioreactor name Blank OD (media) Reference OD (media with culture) Difference (reference - blank) Latest OD Pioreactor1 0.025 0.030 0.005 0.033 Pioreactor2 0.005 0.010 0.005 0.015 We can now subtract the blank values from the latest OD and reference OD values: latest OD−blank ODreference OD−blank OD=blanked normalized OD\\frac{\\normalsize \\text{latest\\thickspace OD}-\\text{blank\\thickspace OD}}{\\normalsize \\text{reference\\thickspace OD}-\\text{blank\\thickspace OD}}=\\text{blanked\\thickspace normalized\\thickspace OD}referenceOD−blankODlatestOD−blankOD​=blankednormalizedOD Pioreactor1​ 0.033−0.0250.030−0.025=1.6x\\frac{\\small 0.033-0.025}{\\small 0.030-0.025}=1.6x0.030−0.0250.033−0.025​=1.6x Culture growth by 1.6x. Pioreactor2​ 0.015−0.0050.010−0.005=2x\\frac{\\small 0.015-0.005}{\\small 0.010-0.005}=2x0.010−0.0050.015−0.005​=2x Culture growth by 2x. By accounting for the OD of the blank media, we are able to calculate a more accurate growth rate.","s":"Blanking","u":"/user-guide/od-normal-growth-rate","h":"#blanking","p":655},{"i":663,"t":"We inoculated two vials with a drop of re-hydrated yeast, and tracked their growth at temperatures 27°C and 35°C. The following normalized optical density chart was generated by the Pioreactor: From the normalized optical density, an implied growth rate graph is generated. The relationship between the implied growth rate, gr\\text{gr}gr and the normalized optical density, nOD\\text{nOD}nOD is exponential, defined by the following equation: nOD(t)=exp⁡(∫0tgr(s)ds)\\text{nOD}(t) = \\exp{ \\left( \\int_0^t \\text{gr}(s)ds \\right)}nOD(t)=exp(∫0t​gr(s)ds) We can rewrite this equation in terms of the growth rate: gr(t)=nOD′(t)nOD(t)\\text{gr}(t)= \\frac{ \\text{nOD}'(t)} {\\text{nOD}(t)}gr(t)=nOD(t)nOD′(t)​ which plainly states that the growth rate is the rate of change of the size of the culture, normalized by the size of the culture. This rate can give insight on the state of your culture under different external conditions. These graphs can be interpreted in 4 phases: The lag phase: No observed growth, but high cell activity. In this stage, cells are in a nutrient rich environment and are preparing for growth by synthesizing proteins and other necessary molecules. Exponential (or log) phase: Cells are now dividing and doubling in numbers after each generation time. Generation times are dependent on the species you are using for your experiment. Stationary phase: Eventually the growth of cells reaches a plateau as nutrients are used up and waste products accumulate. At this point, the number of dividing cells will equal the number of dying cells. Decline (or death) phase: As nutrients are depleted, cell growth slows while cell death increases. Here's how these phases would apply to our graphs, focusing on the 35°C vial: Some things to note: The lag phase can be detected easily in the growth rate graph, as the rate is stable and doesn't begin increasing until a bit after 6 PM. This is not easily determined in the nOD graph, since at this point the overall turbidity of the culture is low. The exponential phase occurs when the growth rate is high/increasing. When the culture reaches the stationary phase, growth rate drops to 0 since the culture is no longer growing in size. The turbidity is constant. The decline phase is not represented in the graphs above, as yeast remain in the stationary phase over many days.","s":"Growth rate","u":"/user-guide/od-normal-growth-rate","h":"#growth-rate","p":655},{"i":671,"t":"Pinch valves are useful for controlling gas into the Pioreactor by \"pinching\" a gas line closed (or keeping it open). This could used be for injecting gas periodically into the headspace, or acting as a bubbler by putting the injection tube directly into the culture. Below is a diagram of using a pinch valve to periodically provide CO₂ into the head space of the Pioreactor's vial: The pinch valve opens and closes, controlled by the Pioreactor, to allow gas from the CO₂ source into the headspace. The Pioreactor controls the pinch valve via the PWM channels and software (plugins). warning Keeping a pinch valve powered continuously for a long time can reach temperatures above 60℃!","s":"Pinch valves","u":"/user-guide/pinch-valves","h":"","p":670},{"i":673,"t":"Some options for pinch valves that will be useful for your application: Normally closed (NC) / normally open (NO). When no power is provided to the pinch valve, a normally closed pinch valve will force the tube to be closed. Conversely, a normally open pinch valve will keep the tube open when no power is provided. tip We suggest a normally closed valve most of the time, since if the Pioreactor loses power, or an experiment ends and power is turned off, we would like the tube to be closed to avoid losing gas. PWM: safest option is \"continuously\" (or \"continuous\"). This means that we can power the pinch valve continuously without it overheating, however it still may be hot to touch. Voltage: The Pioreactor normally operates at 5V, and there are pinch valves that work at this voltage. More common though are pinch valves that work at 12V. To use a 12V pinch valve, you'll need to supply 12V to the auxiliary power input on your Pioreactor. Tube size: this is dependent on your system.","s":"Pinch valve options","u":"/user-guide/pinch-valves","h":"#pinch-valve-options","p":670},{"i":675,"t":"To control the pinch valve, we suggest using the pioreactor relay plugin. This plugin will turn the PWM channel for the pinch valve (specified in your config.ini) on and off at your control. By default, it won't operating when OD readings are taken. You can install this plugin from the Pioreactor UI.","s":"Software","u":"/user-guide/pinch-valves","h":"#software","p":670},{"i":677,"t":"Takasago Fluidics have a quality product with lots of options. However, the distribution is from Japan, and is quite expensive though, and they require buying through a sales person. We've also designed a simple housing to attach it to our Pioreactor dosing platform.","s":"Recommended pinch valves","u":"/user-guide/pinch-valves","h":"#recommended-pinch-valves","p":670},{"i":679,"t":"For some use cases, you may want to create a local WiFi network just for your Pioreactors (this is called a local access point, or a hotspot). Why might you want to do this? If you want to get started right away, without dealing with exiting WiFi networks. If your usual WiFi network is restrictive (ex: doesn't allow Raspberry Pis, or requires IT support to host them). If you want to take the Pioreactor, or cluster of Pioreactors, out into the field where there is no network. The Pioreactor comes with the ability to create its own local access point, which other Pioreactors can connect to. See image below: info The built-in local access point is meant for small clusters of Pioreactors, and it's range and stability is limited. If you want a proper local access point, we suggest purchasing an inexpensive wifi router and using that (the router does not need to be connected to the internet - it will still create a wifi network you can connect Pioreactors to regardless).","s":"Local access points","u":"/user-guide/local-access-point","h":"","p":678},{"i":681,"t":"The Pioreactor has the necessary software and hardware to create the local access point. To start the access point: If starting with a new Pioreactor, during software set up: Leave the \"Configure wireless LAN\" unchecked. Continue with the instructions at Setting up your Raspberry Pi. After the SD card has been written to, remove the SD card from your computer, and immediately insert it back in. A boot (or bootfs) device should be present now that is your SD card. If asked to reformat the SD card, select NO. Select your country: -- Select --AfghanistanAland IslandsAlbaniaAlgeriaAmerican SamoaAndorraAngolaAnguillaAntarcticaAntigua And BarbudaArgentinaArmeniaArubaAustraliaAustriaAzerbaijanBahamasBahrainBangladeshBarbadosBelarusBelgiumBelizeBeninBermudaBhutanBoliviaBosnia And HerzegovinaBotswanaBouvet IslandBrazilBritish Indian Ocean TerritoryBrunei DarussalamBulgariaBurkina FasoBurundiCambodiaCameroonCanadaCape VerdeCayman IslandsCentral African RepublicChadChileChinaChristmas IslandCocos (Keeling) IslandsColombiaComorosCongoCongo, Democratic RepublicCook IslandsCosta RicaCote D'IvoireCroatiaCubaCyprusCzech RepublicDenmarkDjiboutiDominicaDominican RepublicEcuadorEgyptEl SalvadorEquatorial GuineaEritreaEstoniaEthiopiaFalkland Islands (Malvinas)Faroe IslandsFijiFinlandFranceFrench GuianaFrench PolynesiaFrench Southern TerritoriesGabonGambiaGeorgiaGermanyGhanaGibraltarGreeceGreenlandGrenadaGuadeloupeGuamGuatemalaGuernseyGuineaGuinea-BissauGuyanaHaitiHeard Island & Mcdonald IslandsHoly See (Vatican City State)HondurasHong KongHungaryIcelandIndiaIndonesiaIran}, Islamic Republic OfIraqIrelandIsle Of ManIsraelItalyJamaicaJapanJerseyJordanKazakhstanKenyaKiribatiKoreaKuwaitKyrgyzstanLao People's Democratic RepublicLatviaLebanonLesothoLiberiaLibyan Arab JamahiriyaLiechtensteinLithuaniaLuxembourgMacaoMacedoniaMadagascarMalawiMalaysiaMaldivesMaliMaltaMarshall IslandsMartiniqueMauritaniaMauritiusMayotteMexicoMicronesia}, Federated States OfMoldovaMonacoMongoliaMontenegroMontserratMoroccoMozambiqueMyanmarNamibiaNauruNepalNetherlandsNetherlands AntillesNew CaledoniaNew ZealandNicaraguaNigerNigeriaNiueNorfolk IslandNorthern Mariana IslandsNorwayOmanPakistanPalauPalestinian Territory}, OccupiedPanamaPapua New GuineaParaguayPeruPhilippinesPitcairnPolandPortugalPuerto RicoQatarReunionRomaniaRussian FederationRwandaSaint BarthelemySaint HelenaSaint Kitts And NevisSaint LuciaSaint MartinSaint Pierre And MiquelonSaint Vincent And GrenadinesSamoaSan MarinoSao Tome And PrincipeSaudi ArabiaSenegalSerbiaSeychellesSierra LeoneSingaporeSlovakiaSloveniaSolomon IslandsSomaliaSouth AfricaSouth Georgia And Sandwich Isl.SpainSri LankaSudanSurinameSvalbard And Jan MayenSwazilandSwedenSwitzerlandSyrian Arab RepublicTaiwanTajikistanTanzaniaThailandTimor-LesteTogoTokelauTongaTrinidad And TobagoTunisiaTurkeyTurkmenistanTurks And Caicos IslandsTuvaluUgandaUkraineUnited Arab EmiratesUnited KingdomUnited StatesUnited States Outlying IslandsUruguayUzbekistanVanuatuVenezuelaVietnamVirgin Islands}, BritishVirgin Islands}, U.S.Wallis And FutunaWestern SaharaYemenZambiaZimbabwe and download the specific local_acccess_point file: Download Drag/move the downloaded local_access_point file to the SD card directory. Eject the SD card safely, and continue with instructions at Setting up your Raspberry Pi. If starting from an existing Pioreactor: with the power off remove the SD card from the Pioreactor and insert it into a computer. Select your country: -- Select --AfghanistanAland IslandsAlbaniaAlgeriaAmerican SamoaAndorraAngolaAnguillaAntarcticaAntigua And BarbudaArgentinaArmeniaArubaAustraliaAustriaAzerbaijanBahamasBahrainBangladeshBarbadosBelarusBelgiumBelizeBeninBermudaBhutanBoliviaBosnia And HerzegovinaBotswanaBouvet IslandBrazilBritish Indian Ocean TerritoryBrunei DarussalamBulgariaBurkina FasoBurundiCambodiaCameroonCanadaCape VerdeCayman IslandsCentral African RepublicChadChileChinaChristmas IslandCocos (Keeling) IslandsColombiaComorosCongoCongo, Democratic RepublicCook IslandsCosta RicaCote D'IvoireCroatiaCubaCyprusCzech RepublicDenmarkDjiboutiDominicaDominican RepublicEcuadorEgyptEl SalvadorEquatorial GuineaEritreaEstoniaEthiopiaFalkland Islands (Malvinas)Faroe IslandsFijiFinlandFranceFrench GuianaFrench PolynesiaFrench Southern TerritoriesGabonGambiaGeorgiaGermanyGhanaGibraltarGreeceGreenlandGrenadaGuadeloupeGuamGuatemalaGuernseyGuineaGuinea-BissauGuyanaHaitiHeard Island & Mcdonald IslandsHoly See (Vatican City State)HondurasHong KongHungaryIcelandIndiaIndonesiaIran}, Islamic Republic OfIraqIrelandIsle Of ManIsraelItalyJamaicaJapanJerseyJordanKazakhstanKenyaKiribatiKoreaKuwaitKyrgyzstanLao People's Democratic RepublicLatviaLebanonLesothoLiberiaLibyan Arab JamahiriyaLiechtensteinLithuaniaLuxembourgMacaoMacedoniaMadagascarMalawiMalaysiaMaldivesMaliMaltaMarshall IslandsMartiniqueMauritaniaMauritiusMayotteMexicoMicronesia}, Federated States OfMoldovaMonacoMongoliaMontenegroMontserratMoroccoMozambiqueMyanmarNamibiaNauruNepalNetherlandsNetherlands AntillesNew CaledoniaNew ZealandNicaraguaNigerNigeriaNiueNorfolk IslandNorthern Mariana IslandsNorwayOmanPakistanPalauPalestinian Territory}, OccupiedPanamaPapua New GuineaParaguayPeruPhilippinesPitcairnPolandPortugalPuerto RicoQatarReunionRomaniaRussian FederationRwandaSaint BarthelemySaint HelenaSaint Kitts And NevisSaint LuciaSaint MartinSaint Pierre And MiquelonSaint Vincent And GrenadinesSamoaSan MarinoSao Tome And PrincipeSaudi ArabiaSenegalSerbiaSeychellesSierra LeoneSingaporeSlovakiaSloveniaSolomon IslandsSomaliaSouth AfricaSouth Georgia And Sandwich Isl.SpainSri LankaSudanSurinameSvalbard And Jan MayenSwazilandSwedenSwitzerlandSyrian Arab RepublicTaiwanTajikistanTanzaniaThailandTimor-LesteTogoTokelauTongaTrinidad And TobagoTunisiaTurkeyTurkmenistanTurks And Caicos IslandsTuvaluUgandaUkraineUnited Arab EmiratesUnited KingdomUnited StatesUnited States Outlying IslandsUruguayUzbekistanVanuatuVenezuelaVietnamVirgin Islands}, BritishVirgin Islands}, U.S.Wallis And FutunaWestern SaharaYemenZambiaZimbabwe and download the specific local_acccess_point file: Download Drag/move the downloaded local_access_point file to your SD card (called boot or bootfs). Eject the SD card safely, and put back into the Pioreactor.","s":"Starting a local access point","u":"/user-guide/local-access-point","h":"#starting-a-local-access-point","p":678},{"i":683,"t":"After plugging in the Pioreactor, the local access point will start and you should see a new network called pioreactor, with password raspberry. You should be able to connect to this new access point with any computer, phone, tablet, etc. Once connected, the usual urls should work: http://pioreactor.local will bring up the Pioreactor interface (having trouble? Not working? Try our troubleshooting steps below. info Without access to the internet, the Pioreactor will have the wrong internal time. You can change this using this method","s":"Access the local access point","u":"/user-guide/local-access-point","h":"#access-the-local-access-point","p":678},{"i":685,"t":"info Raspberry Pi 3B and Raspberry Pi Zero W have trouble connecting to these local access points. Follow instructions here. Other Pioreactors will need to be reconfigured to connect to this new access point. During set up in the Raspberry Pi Imager, using the ssid / wifi credentials: pioreactor and password raspberry in the wireless LAN section. Don't add the local_access_point file to these other Pioreactors - you only need to do that once. The maximum number of machines (Pioreactors and computers) that can be connected to a local access point on a Pioreactor is ~4-8. There is a possibility to add more, see issue here. This network may not be connected to the internet, so you won't be able to upgrade any software on the Pioreactors. See section below on how to add internet.","s":"Connecting more Pioreactors to your local access point","u":"/user-guide/local-access-point","h":"#connecting-more-pioreactors-to-your-local-access-point","p":678},{"i":687,"t":"If you are hosting the local access point on a Raspberry Pi that has an ethernet port (B models), you can plug this into a router that has access to the internet to provide internet to your entire cluster.","s":"Adding internet access to your local access point","u":"/user-guide/local-access-point","h":"#adding-internet-access-to-your-local-access-point","p":678},{"i":689,"t":"After SSH-ing into your Pioreactor, simply delete the local_access_point file in the /boot/firmware/ directory, and reboot.","s":"Turning off a local access point","u":"/user-guide/local-access-point","h":"#turning-off-a-local-access-point","p":678},{"i":691,"t":"In the config.ini, the SSID and password are editable under the section local_access_point. This requires a power-cycle to take effect.","s":"Changing SSID name or password for your local access point","u":"/user-guide/local-access-point","h":"#changing-ssid-name-or-password-for-your-local-access-point","p":678},{"i":694,"t":"Do you see the pioreactor network in the list of available wifi networks?​ If presented, use the option \"Use security key to connect\" (this is an alias for the password). Try power-cycling your Pioreactor The maximum number of machines (Pioreactors and computers) that can be connected to a local access point on a Pioreactor is ~4-8. There is a possibility to add more, see issue here. Alternatively, do you not see the pioreactor network in the list of available wifi networks?​ Try power-cycling the Raspberry Pi If you unplug the Pioreactor, and place the SD card back into your computer, do you see the local_access_point file? If not, try adding the file again, inserting the SD card in the Pioreactor, and restarting the Pioreactor.","s":"My computer can't connect to the local-access-point","u":"/user-guide/local-access-point","h":"#my-computer-cant-connect-to-the-local-access-point","p":678},{"i":696,"t":"Try http://<your_leaders_hostname>.local. Still not working? Try http://10.42.0.1)","s":"I'm on the network, but can't load the Pioreactor UI at http://pioreactor.local","u":"/user-guide/local-access-point","h":"#im-on-the-network-but-cant-load-the-pioreactor-ui-at-httppioreactorlocal","p":678},{"i":698,"t":"confirm that you are using the right wifi name and password in the Imager (default pioreactor and raspberry) The maximum number of access point clients (Pioreactors and computers) that can be connected to a local access point on a Pioreactor is ~4-8. There is a possibility to add more, see issue here.","s":"I can't connect a worker to my local access point","u":"/user-guide/local-access-point","h":"#i-cant-connect-a-worker-to-my-local-access-point","p":678},{"i":700,"t":"You can purchase an inexpensive wifi router and use that as the access point. Note that you don't need to connect this router to the internet - it will operate a network regardless. You can purchase a WIFI USB stick to improve the clients and range of your Pioreactor. For example, the Alfa AWUS036AC (take note to confirm your Raspberry Pi can has the correct USB connection).","s":"I'm pretty sure I'm at the limit of ~4-8 clients on my access point - what can I do?","u":"/user-guide/local-access-point","h":"#im-pretty-sure-im-at-the-limit-of-4-8-clients-on-my-access-point---what-can-i-do","p":678},{"i":708,"t":"Cleaning the vial​ It's recommend to clean your vial before every use. The vial and cap can be cleaned with soapy water. A useful accessory for cleaning is a small bottle brush / test tube brush. Rinse the vial to remove any soap residue. Choosing a volume for your culture​ We suggest using between 8ml to 16ml volume of liquid in the vial. tip Some things to consider when selecting a volume: a lower volume will provide more aeration per mL since the liquid-air interface is fixed. A lower volume will also be more responsive to changes in temperature, and be able to achieve a higher maximum temperature. But too low and the vortex caused by stirring may start interfering with the Pioreactor's optical system (a lower RPM can fix this though). Position of tubes in cap​ Keep at least 1 cap tube out of the liquid and well away from potential bubbles / foam that may occur. This will prevent gas pressure from building up. Something also to keep in mind: more tubes out of the liquid means more gas transfer with the ambient atmosphere. If using pumps with your Pioreactor, see the note below.","s":"1. Preparing the vial","u":"/user-guide/prepare-vial-for-cultures","h":"#1-preparing-the-vial","p":706},{"i":710,"t":"Prepare your media as your protocol suggests. For example: in the our experiments, we typically showcase yeast grown in YPD broth. To create YPD broth, mix YPD and water at a ratio of 50 grams YPD powder to 1 liter distilled water.","s":"2. Preparing media","u":"/user-guide/prepare-vial-for-cultures","h":"#2-preparing-media","p":706},{"i":712,"t":"Using heat​ Divide the mixture into the vials to the correct volume, and add the stir bar in the vial. The glassware vial, stir bar and vial cap that come with your Pioreactor are all fully autoclavable, and heat resistant up to 125℃. The luer lock ends can be covered with tin foil, or attached to air filters, or neither. Since the volume in the vial is so little, the autoclave only needs to be at its maximum temperature for a very short duration. tip Don't have an autoclave? A kitchen pressure cooker works just as well. Still don't have that? You can use a stove top or hotplate: heat on a medium-low heat until boiling, and let boil for a few minutes. However, an autoclave or a pressure cooker is a more effective sterilizer. tip \"Flick\" away any trapped liquid in the cap's tubes. Using sterile filtration​ Filtered media can be directly added to a sterilized glass vial, or via the (sterilized) male luer lock ports.","s":"3. Sterilization","u":"/user-guide/prepare-vial-for-cultures","h":"#3-sterilization","p":706},{"i":714,"t":"Ideally in a sterile environment, the vial's lid can be removed and the inoculant can be added. Alternatively, for additional sterility, a needle can be sent down a tube, without removing the cap at all. How much inoculant should you add? That depends on the concentration of your inoculant. From our experience, we create a dense culture/stock culture by adding some amount of culture to sterile media or water, and then inoculate our vials from this stock. For example, we add 0.5 grams of dried Baker's yeast to 15 mL of YPD broth, then store it in a fridge for further use. We recommend measuring with a micropipette. If you are using a dropper, hold it vertically for more accurate, consistent drops.","s":"4. Inoculation","u":"/user-guide/prepare-vial-for-cultures","h":"#4-inoculation","p":706},{"i":716,"t":"Keep the bottoms of the tubes in the cap from being submerged in your media to avoid creating a pressured environment. Adjust each luer lock end until the other end of the tube is above liquid level.","s":"5. Adjusting tube lengths (Optional)","u":"/user-guide/prepare-vial-for-cultures","h":"#5-adjusting-tube-lengths-optional","p":706},{"i":718,"t":"We recommend handling the vial with gloves, or handling only the cap. Minimize touching the glass as much as possible to avoid getting oils and fingerprints on the glass. Before placing in the Pioreactor sleeve, wiping the surface of the glass with a kimwipe is a great idea!","s":"6. Handling the glass","u":"/user-guide/prepare-vial-for-cultures","h":"#6-handling-the-glass","p":706},{"i":720,"t":"danger The outside of the glassware vial should be dry. If the vial is wet, even with single droplet, it can damage the electronics underneath. Place the glassware vial into the Pioreactor sleeve. Ensure that the vial is pressed all the way down and is touching the bottom of the vial holder. This ensures correct temperature regulation of the culture. Next, you can start your experiment in the browser.","s":"7. Positioning glassware in the Pioreactor sleeve","u":"/user-guide/prepare-vial-for-cultures","h":"#7-positioning-glassware-in-the-pioreactor-sleeve","p":706},{"i":722,"t":"Using pumps: influx and efflux.​ When using the Pioreactor with pumps, you'll be using the four luer lock tubes as influx and efflux. The tubes, which are identical lengths, can be moved up and down, and we suggest using this as a way to \"label\" tubes, and to control the maximum volume in the vial. This can be done before sterilization. Here's how: One tube can be pulled high up, so that about a millimeter is showing on the underside of the cap. This will be our air influx and efflux (recall that when liquid is added or removed, air needs to be removed or added respectively to not create a pressure difference). Two tubes can be pulled such they are aligned with the bottom rim of the cap. These two tubes will be the liquid influx tubes. For some operations, like a chemostat, you'll only be using one of these tubes, but some operations require more than one influx. The final tube is the liquid efflux tube. It will be positioned such that it controls the final amount of volume in the vial. Fill your vial to the desired final volume using water. Pull the final tube down such that its end just touches the top of the water when the cap is fully screwed on. It may take some minor adjustments to achieve this. info How does this maintain a constant volume throughout operation? When liquid is added, say 1ml, the volume rises an additional 1ml. Then 1ml of liquid is removed via efflux, but then the efflux pump runs again for an additional few seconds. The efflux pump is run for an additional few seconds to eliminate any volume differences or deltas (for example, if the volume added is greater than the volume removed due to pumping errors). Otherwise, the deltas accumulate and the vial can overflow. This additional step guarantees that that volume of liquid never exceeds the end of the efflux tube. During your experiment set up, the length of the tubes out of the cap can provide information about their \"roles\": longest tube is air exchange, shortest tube is efflux, and middle two tubes are influx.","s":"Extra","u":"/user-guide/prepare-vial-for-cultures","h":"#extra","p":706},{"i":725,"t":"The Pioreactor connects to your local network, and the UI is hosted locally on the Raspberry Pi. A priori, there's no access to view the UI from outside your local network (this is a good thing for security reasons). Let's change that. With some extra free services, we can safely connect to our Pioreactor cluster remotely. We've documented 2 ways to do this. Both require command-line access to the leader Pioreactor and some external services. Option 1: Ngrok. Remotely access your UI behind a simple username / password. Option 2: Tailscale. Spin up a simple VPN, and expose your UI to users of your VPN. Also allows for Pioreactors in different locations to be used together over the VPN.","s":"Introduction to remote access","u":"/user-guide/remote-access","h":"#introduction-to-remote-access","p":723},{"i":727,"t":"By allowing remote access to your Pioreactor, you are providing a possible vector for malicious folks to access the UI, and possibly your network. We've built the Pioreactor to minimize these holes, but there are two more additional changes you should make: To disallow users to upload files onto your server, enter the following into your leader: touch /home/pioreactor/.pioreactor/DISALLOW_UI_UPLOADS To disallow users to add plugins to your cluster, enter the following into your leader: touch /home/pioreactor/.pioreactor/DISALLOW_UI_INSTALLS We highly recommend doing both these actions. To remove these blocks, simply delete the files.","s":"Security","u":"/user-guide/remote-access","h":"#security","p":723},{"i":735,"t":"To get the best results and confirm your Pioreactor is working as expected, it's advisable to run a self-test on your Pioreactor after setting it up initially. The self-test routine can catch common errors that may compromise your data collection.","s":"Running a self-test","u":"/user-guide/running-self-test","h":"","p":734},{"i":737,"t":"Start on the Pioreactors page: Insert a closed vial with water and stir bar into the Pioreactor, and click \"Start\". The Pioreactor will start running tests against expected output and report back to you success and failures of those tests. Depending on the results of each test, you'll see success and failures: info The self-test routine is optional. Even with test failures, the Pioreactor is still operational (perhaps not where the test failed though!). We highly recommend a self-test at least after your initial setup.","s":"How to run the self-test routine","u":"/user-guide/running-self-test","h":"#how-to-run-the-self-test-routine","p":734},{"i":739,"t":"Pioreactor HAT is detected checks if the Pioreactor HAT is correctly placed on top of the Raspberry Pi. A non-trivial failure here suggests a problem connection between the HAT and the RPi, a failure with the i2c channel, or a failure with the RP2040 chip on the HAT. If Heating PCB is detected also fails, try disconnecting the Heater PCB flat-flex cable from the HAT (unlock and pull straight out), and trying the test again. Photodiodes are responsive to IR LED checks to ensure that the IR photodiode(s) have a linear relationship with the IR LED's output. The linear relationship is important. Common reasons why this test fails include: Not enough light is entering the PD position (see below for resolutions) The IR LED connected to the the wrong LED output. Make sure that the IR LED is identified correctly in the config.ini A loose (or absent) connection to the Pioreactor HAT, either in the photodiode(s) or the IR LED. The test will also report any valid IR LED & photodiode relationships in the dialog box. For example, IR ⇝ REF means that the REF photodiode has a linear relationship with the IR LED. Similarly, IR ⇝ 45 means the the photodiode in the 45° pocket has a linear relationship with the IR LED. The absence of a relationship here can tell you about what might be wrong. Tips: Try running this test again. Add a slight amount of turbid liquid (milk, culture, tea) to slightly increase the turbidity of the liquid inside. This increases the scatter of the liquid, and will help this test. If it continues to fail, contact us. No ambient IR light detected checks that the photodiodes are detecting a near-0 signal when the IR LED is completely off. This test may fail if a powerful IR signal is shining into or onto the Pioreactor's body (aka the Sun - don't put the Pioreactor in direct sunlight and avoid windows). Also make sure that the caps are on all the Pioreactor's LED pockets. Reference photodiode is the correct magnitude checks, if using the reference photodiode (REF), that the REF signal is less than 0.256 volts when the IR LED is at the level specified in the config.ini's [od_config].[ir_led_intensity] section. If this test fails, confirm that in your config.ini that REF is present for one of the channels under [od_config.photodiode_channel]. check the positioning of the REF photodiode (should be adjacent the the IR LED, snugly inserted, and with a cap). If still failing, try reducing the value in [od_config].[ir_led_intensity]. Reference photodiode is in the correct position checks, if using the reference photodiode (REF), that the REF cable is inserted into the correct photodiode position (channel 1 or 2). The correct position is provided in the config.ini's [od_config.photodiode_channel] section. Note: this is a flakey test, and can fail even when positioned correctly. The test compares the variances of the two signals (from photodiode channels 1 and 2), and the lower variance one is usually the REF. If this test fails, Is your vial in the Pioreactor? Does your vial have water and a stirbar in it? Confirm that in your config.ini that REF is present for one of the channels under [od_config.photodiode_channel]. Photodiode measures near zero signal for clear water checks that a non turbid liquid, like water, doesn't produce a signal (since there is no scatter). This is a new test, and may fail even if everything is okay. Check the following: confirm that your vial contains water (or any very clear liquid) and that your signal photodiode is positioned in 45°, 90°, or 135°. This test won't work for 180°. Heating PCB is detected checks that the heating PCB is correctly attached to the Pioreactor HAT. A non-trivial failure here suggests a problem when the i2c channel, a loose connection, or damage to the heating PCB. See notes for Pioreactor HAT is detected, too. Heating is responsive checks for a linear relationship between the temperature sensor and the PWM heating system. Stirring RPM is responsive checks for a linear relationship between PWM stirring system and the Hall sensor that measure's RPM. If this fails, check that the stirring power is connected correctly (and in the location specified in config.ini's [PWM] section). Another reason for failure is that the magnets are too far away from the base of the vial. See stirring troubleshooting. AUX power supply is appropriate value checks that the AUX power voltage is between 0V and 18V. If no AUX power is connected to the Pioreactor, the default voltage is 5V.","s":"Explanation of each test","u":"/user-guide/running-self-test","h":"#explanation-of-each-test","p":734},{"i":741,"t":"The heater in the Pioreactor wetware can be programmed to control the temperature of the vial in automated ways. Pioreactor is pre-programmed with the following temperature automations. In the below automations, values highlighted like so are configurable.","s":"Temperature automations","u":"/user-guide/temperature-automations","h":"","p":740},{"i":743,"t":"The Thermostat automation will try to maintain a target temperature using a feedback loop. You can select a target temperature (between ambient temperature and 50℃), and the automation will vary the onboard heater to maintain that temperature in the vial. At room temperature, the Pioreactor will be able to achieve up to about 43℃.","s":"Thermostat","u":"/user-guide/temperature-automations","h":"#thermostat","p":740},{"i":745,"t":"This automation is the simplest automation: do not apply any external heating. Reading and logging of temperature will still occur.","s":"Only record temperature","u":"/user-guide/temperature-automations","h":"#only-record-temperature","p":740},{"i":748,"t":"You can expect the setup process to take 10-15 minutes. If you encounter any problems, feel free to email us for support at hello@pioreactor.com. info Before you get started, you'll need to have the following: A Raspberry Pi (our list of recommended Raspberry Pis is here) A blank microSD card (our recommended microSD cards is here) A suitable power supply for the Raspberry Pi (our recommended power supply units are here) A computer with internet access and ability to read & write to a microSD card","s":"Before you begin","u":"/user-guide/software-set-up","h":"#before-you-begin","p":746},{"i":750,"t":"We'll start your blank microSD card. Download the Pioreactor leader & worker image file. info What is an image file? It's a file that contains all the required software preinstalled on it, including an operating system and our custom Pioreactor software. The image will be installed on the microSD card. Download the latest version of Raspberry Pi Imager for your operating system and install it. Open the newly-installed Raspberry Pi Imager. Click Choose Device, and \"No filtering\" at the top. Click Choose OS. Click on Use custom towards the bottom: Select the downloaded Pioreactor image from step 1. Insert your microSD card to your computer. After your microSD card is recognized by your computer, click Choose Storage and select it. Click Next. Click Edit settings: Check Set hostname. Input a unique name for this Pioreactor. Some names that we use for our first Pioreactor: pioreactor01, or leader, or pio01. Don't use pioreactor or raspberrypi. Check Set username and password. Enter the following: username: pioreactor. password: raspberry. Note: You can change the username and password later. Check Configure wireless LAN and enter your network name into SSID network name, WiFi password, and country. Or leave blank if using ethernet. tip If you are having difficulty connecting to a network, like at a university that may not easily allow Raspberry Pi's, there's a built-in solution for creating a local access point). Note that any tutorials that mention wpa_supplicant.conf are out of date. This has been deprecated by Raspberry Pis for a while. We have some further documentation on networking available here. Change timezone to your local timezone. Under the \"Services\" tab, check Enable SSH, and select Use password authentication. Your settings should look something like this: Click Save to save and exit the dialog box. Click \"Yes\" to begin writing. A prompt may appear asking for permission to write, accept it. Writing will take up to 5 minutes. Perfect time for a tea break. Once writing is complete, remove the microSD card, and place it into the Raspberry Pi. Your Raspberry Pi's power should be unplugged before inserting the microSD card. The microSD slot is located on the PWM side of the Pioreactor. Example for a Raspberry Pi A model: Plug power into your Raspberry Pi. LEDs onboard the Raspberry Pi may start to light up momentarily. After a few minutes, your Pioreactor HAT will briefly blink a blue LED, telling us it is ready. info Waited, but didn't see a blue LED blink, or maybe you missed it? Try pressing on the onboard button, near the side labelled \"PWM\", and pictured above. If this lights up the blue LED, you're good to move on. Still not working? Try power-cycling the Raspberry Pi, or email us at hello@pioreactor.com. After observing the blue LED flashing, navigate to http://pioreactor.local in a web browser to visit the web interface. If you are using local-access-point, looking for a pioreactor wifi network and then visit the link. (Not able to load http://pioreactor.local? Read Troubleshooting below). The Pioreactor is now ready for use! Follow this guide to set up your first experiment. If you're using a Pioreactor 20ml v1.0, edit your config.ini to [pioreactor] model=pioreactor_20ml version=1.0 and then reboot.","s":"Setting up your Raspberry Pi","u":"/user-guide/software-set-up","h":"#setting-up-your-raspberry-pi","p":746},{"i":752,"t":"Workers are additional Pioreactors that you can control from a single UI. Together, a leader and workers form a Pioreactor cluster. Step 1. Install the worker software​ Follow the same instructions above, but use a Pioreactor Worker image instead. All the settings are the same, including username and password, but choose a new hostname. See note below: note Choose a hostname that isn't currently being used in your cluster, ex: worker01, worker02, etc. Re-using old names is fine, so long as that worker isn't present in your cluster. Tip: if you plan to have many Pioreactors, use a leading zero in any numbers, like pio01, or worker01, etc. Below is a screenshot of example settings, your settings might be slightly different. If using a local-access-point on your leader Pioreactor, use the wifi ssid pioreactor and password raspberry. After the image is written to the microSD card, place the microSD card into the Raspberry Pi and power it on. The Pioreactor's blue LED will light up and stay on, indicating that it's ready to be connected. Move onto the next step. Step 2. Add worker to cluster using the UI​ Follow the instructions here to add your worker to your Pioreactor cluster. From the command line (Alternative)​ On the leader's command line, the command pio add-pioreactor <new name> will connect the new Pioreactor to the cluster. tip We recommend running a self-test on all Pioreactors after your initial setup to detect any hardware bugs at this point.","s":"Adding additional workers to your cluster","u":"/user-guide/software-set-up","h":"#adding-additional-workers-to-your-cluster","p":746},{"i":754,"t":"My leader Pioreactor never flashes the blue LED​ First, confirm that when you press the HAT button, the blue LED does not show up. If it does, you're good to go. It's likely that the installation failed (due to a settings issue), or there is a problem with the SD card. Double check the settings that you used and try reinstalling the image. Are you using a microSD card with a size larger than 32GB? You may need to reformat it to FAT32. To do this, in the Raspberry Pi Imager, first select \"Erase: format card as FAT32\" under \"Choose OS\". Then proceed with writing the image. My Pioreactor keeps flashing the blue LED​ On a successful start, the Pioreactor will flash its blue LED for about 2 seconds. If you observe the blue LED flashing for longer, something may be wrong. You can diagnose the problem by counting the number of flashes observed. My RPi won't connect to my WiFi.​ Some Raspberry Pis can't connect to Wifi natively, and some Raspberry Pis can only connect to 2.4GHz connections. See table below: If you are using the built-in WiFi in a Raspberry Pi3, a Pi3B+, or Pi Zero W, be aware that the signal strength from the tiny internal antenna may be weaker than other WiFi devices. Try moving your Pioreactor closer to the router as a test. If your network hidden? You will need to check hidden SSID in the configuration in the Raspberry Pi imager. To fix this, you'll need to restart the image installation from the Raspberry Pi Imager. Try power-cycling the Raspberry Pi (unplug and plug back in). If you are on a restrictive network (like at a university), and wish to avoid the network, creating a local access point may be a better option. You may have mis-typed your WiFi credentials. To fix this, you'll need to restart the image installation from the Raspberry Pi Imager. If connecting to a 5GHz WiFi connection, you need to supply a valid country code. See the list here: https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2/. It's possible your SD card is damaged. This can cause all sorts of problems (including failing to boot), not just WiFi issues. The most common cause of SD card failure is probably inserting or removing the SD card while the Pi is powered up. Check out some other possibilities here. I want to change the Pioreactor name on installation of leader​ Easiest solution is to start over. You can edit the name in the RPi Imager, and reflash the image onto the microSD card to remove all previous data. http://pioreactor.local in a web browser is not showing up​ In your browser's address bar, add the http:// in front of the url, like so: http://pioreactor.local. Try appending a backslash as well: http://pioreactor.local/. The UI is hosted on http, not https. Check if you are accessing http ://pioreactor.local, and not https ://pioreactor.local. Try accessing using the url http://<the name of your leader Pioreactor aka hostname>.local. If you know your Raspberry Pi's IP, try http://<IP address of your Raspberry Pi>. Here's information to determine the IP address. When pressing the button on the HAT, does the blue LED show up? If not, installation may have failed. Try installing the image again, and double check the settings. Try power-cycling the Raspberry Pi (unplug and plug back in). In your Raspberry Pi Imager settings, confirm that you clicked \"Set username and password\", and used the username pioreactor. If not, try reinstalling the image. Are you on an older Windows machine? You may need to install a DNS service, but also see workarounds here. Can I plug a monitor into the Raspberry Pi's HDMI port?​ Our current software turns off all external displays (for power and compute reasons), so any external monitor attached to the Pi won't work.","s":"Troubleshooting","u":"/user-guide/software-set-up","h":"#troubleshooting","p":746},{"i":757,"t":"To create a new experiment, click on the drop-down menu on the top of the left-hand bar. Click the \"New experiment\" button. On the next screen, enter your new experiment name. This name should be unique from prior experiment names. Enter optional metadata about your experiment; you can modify the description later, if necessary. Click \"Save\" when done.","s":"Creating an experiment","u":"/user-guide/set-up-an-experiment","h":"#creating-an-experiment","p":755},{"i":759,"t":"The Pioreactors tab will display any active and inactive Pioreactors assigned to the experiment. Click on \"Assign Pioreactors\" to assign pioreactors to the current experiment. Pioreactors that are assigned to another experiment will be unavailable, unless unassigned through the Inventory tab or through it's assigned experiment's Pioreactors tab.","s":"Assigning Pioreactors to your experiment","u":"/user-guide/set-up-an-experiment","h":"#assigning-pioreactors-to-your-experiment","p":755},{"i":761,"t":"When working with small amounts of a microorganism, or when using very turbid media, you can obtain more accurate growth rates by blanking the vial before inoculation. How to record a blank # Insert your sterile vial containing media into the Pioreactor before inoculating with your species of interest. On the website, click the Pioreactors tab on the left-hand menu, and choose one of the active Pioreactors. Select Calibrate, and under the Blanks tab, click Start. The Pioreactor will now record the optical density of the blank vial. Repeat for all the Pioreactors to be used. A notification will appear when a Pioreactor has finished blanking. You can now inoculate your vials and begin your experiment.","s":"(Optional) Blanking","u":"/user-guide/set-up-an-experiment","h":"#optional-blanking","p":755},{"i":764,"t":"tip When starting, it's useful to run a self test to confirm that your Pioreactors are all working as expected. How to run a self-test. On the Pioreactors page, you should see at least one Pioreactor under Active Pioreactors. You can start an activity using the \"Manage\" button. Once started, you can pause (and then resume) or stop jobs. Clicking the \"Manage all Pioreactors\" button will give you control to start and stop activities on all active Pioreactors. The typical sequence of activities to start is: Stirring Temperature automation, and selecting Thermostat Optical density After observing that the optical density looks normal on the Experiment Overview page, Growth rate Any other activities. Any of the automations can be started, or custom jobs you've added to your Pioreactor.","s":"Start activities from the Pioreactors page","u":"/user-guide/set-up-an-experiment","h":"#start-activities-from-the-pioreactors-page","p":755},{"i":766,"t":"If you'd like to change the settings of your activities after you start, navigate back to the Pioreactors tab. Under Manage for a single Pioreactor or Manage all Pioreactors, click the Settings tab. Here you can change the settings of your activities (such as temperature, RPM, and dosing volume) without pausing or stopping the activity. (Optional) If working with more than one Pioreactor in your cluster, it's useful to assign experiment-specific labels in these settings. These labels appear in the user interface, making progress checking and updating easier. The labels can be changed later. Click \"Assign\" when done. tip Use these labels to keep track of treatments on multiple Pioreactors. For example, labels '15C', '25C' and '35C' can be used to differentiate temperature treatments. These labels will be shown on graphs generated in the Overview page on the website. They can be changed in the UI later, too. Ending your experiment​ On the Overview, Pioreactors, and Profiles tabs, the option to Manage experiment is located in the top left corner. The option End experiment will stop all running activities and unassign all Pioreactors from the experiment. warning The option Delete experiment will do the same, while also deleting all experiment data. Note that you will not be able to export any data from a deleted experiment.","s":"Changing settings","u":"/user-guide/set-up-an-experiment","h":"#changing-settings","p":755},{"i":768,"t":"Unlike using Ngrok, this method does not expose your UI to the public internet. To access the UI remotely, you need to join an authenticated VPN. This greatly improves security, but adds a bit of additional work for users. info Tailscale is a really really cool service! You may find yourself using it for other projects, too. Sign up for an account at Tailscale. The free account is fine for now. Once signed up and logged in, visit the Tailscale admin. Install Tailscale on your computer. SSH into your leader Pioreactor. Install Tailscale for Raspberry Pi with the following: curl -fsSL https://tailscale.com/install.sh | sh. You don't need to install anything on the workers. Back in your Tailscale admin, you should see two machines: your computer and the leader Pioreactor. Make note of the ipv4 address for the leader - we will use it below. You should still be able to access http://pioreactor.local without any problems. In your config.ini, add your ipv4 address to the [mqtt] section: [mqtt] ... broker_address=<ipv4 address> ... If you have other Pioreactors in your cluster: you likely won't be adding those to tailscale (only adding the leader is necessary for remote access), so in each of the worker config files, add: [mqtt] broker_address=<leader name>.local And save. This means that your workers will connect \"locally\" (over the local network), but the UI will connect \"remotely\". Now, when you leave the local network, and if you have internet access, you can turn your VPN on and still access http://<ipv4 address>. Troubleshooting: try http://<hostname>, but confirm that magicDNS is on, too. You can use the Tailscale admin to add users to your VPN, too.","s":"Tailscale","u":"/user-guide/tailscale-remote-access","h":"","p":767},{"i":771,"t":"If your Pioreactor stops being responsive (and was previously working), For Raspberry Pi 3A model, is the Pi's green LED constantly on? there should be a short, perhaps caused by damage. Power off, and disconnect the heater PCB's flat-flex cable from the HAT (unlock, and pull straight out), and power on. Is the Pioreactor responsive now? Investigate the heater PCB for damage.","s":"My Pioreactor isn't responsive anymore","u":"/user-guide/troubleshooting-hardware","h":"#my-pioreactor-isnt-responsive-anymore","p":769},{"i":773,"t":"Is your HAT directly connected to the Raspberry Pi, or are you using a long cable to connect them? Long cables tend to degrade signals, which can cause communication problems between the HAT and RPi.","s":"I see a \"Pioreactor HAT must be present\" error, but the HAT is definitely attached.","u":"/user-guide/troubleshooting-hardware","h":"#i-see-a-pioreactor-hat-must-be-present-error-but-the-hat-is-definitely-attached","p":769},{"i":775,"t":"SSH into the Pioreactor that's causing problems. Run pio version -v. Does the firmware section say 0.0? If so, run sudo systemctl restart load_rp2040.service. Try pio version -v again. Continue below if firmware still says 0.0. Disconnect the heater PCB's flat-flex cable from the HAT (unlock, and pull straight out). Try pio version -v again. If this shows something other than 0.0 beside firmware, there could be a problem with your heater PCB. Email us at help@pioreactor.com. See section above.","s":"I see \"The internal ADC/DAC is not responding. Exiting.\"","u":"/user-guide/troubleshooting-hardware","h":"#i-see-the-internal-adcdac-is-not-responding-exiting","p":769},{"i":777,"t":"Check the connection between the 3\" flat-flex-cable and the HAT, and the connection on the heater PCB. It's possible that the connector could have been pulled out by accident.","s":"I see \"Heating PCB must be attached to Pioreactor HAT\" or Heating PCB must be present to measure RPM.\" errors.","u":"/user-guide/troubleshooting-hardware","h":"#i-see-heating-pcb-must-be-attached-to-pioreactor-hat-or-heating-pcb-must-be-present-to-measure-rpm-errors","p":769},{"i":779,"t":"See our stirring troubleshooting docs.","s":"I'm having trouble with Pioreactor's stirring.","u":"/user-guide/troubleshooting-hardware","h":"#im-having-trouble-with-pioreactors-stirring","p":769},{"i":781,"t":"You can improve your Pioreactor temperature sensing capabilities with the Temperature Expansion Kit. This kit allows for faster temperature response times, more granular temperature data, and increasing the maximum culture temperature. Below are instructions on how to assemble the new hardware to your existing Pioreactor. Step 0: before you begin # What's needed to upgrade your Pioreactor with the Pioreactor Expansion Kit: Pioreactor Temperature Expansion HAT 12mm nylon stand-offs thermowell Pt1000 probe A powered-off Pioreactor. A philips head screwdriver Step 1: Expose the Pioreactor HAT # Unplug all wires and cables attached to the Pioreactor HAT. Unscrew the four 6mm nylon screws on the top faceplate. Keep these screws nearby. Remove the top assembly. Keep this nearby. Step 2: Attach the new HAT # Place the new Temperature Expansion HAT onto the existing HAT, making sure the GPIO pins are lined up. It will fit snug, and you can apply pressure onto the corners of the boards. Tip: if the HAT is still hard to put on, you can screw in the 12mm standoffs to help force the new HAT down further. Finish placing the 12mm standoffs in. Place the Pioreactor top assembly back on, and screw back in the 6mm screws. Replug in the cables and wires into the original HAT. Normally: 90° -> PD channel 2 REF -> PD channel 1 IR -> LED channel A Stirring fan -> PWM 1 (unlabelled) Heater PCB flat-flex cable -> flat-flex connector (unlabelled) Step 3: Attach the Pt1000 # Attach the Pt1000 probe's connector to the new Temperature Expansion HAT. The connector only has one orientation that works. In your Pioreactor's vial, screw in the thermowell. info Make sure when the thermowell is straight when being screwed in (that is, perpendicular to the surface of the cap). It may be a tight squeeze. To help screw it in if it's difficult: Once a few threads are inserted, rotate the thermowell back and forwards a few times slowly to provide more clearance. You can use a pair of needle-nose pliers to hold secure the female end of the thermowell (i.e. one tip is inside the thermowell, and one outside), then twist the vial cap. If not already done so, screw in the Pt1000 into the thermowell. You're done the assembly! Next is to install the software. Power up the Pioreactor. Step 4: Install the software # 1. If you install the Kit across your entire Pioreactor cluster In your PioreactorUI, you can install the temperature-expansion-kit-plugin to all Pioreactors in your cluster. 2. If you installed the Kit on individual Pioreactors SSH into the individual Pioreactor, and type pio plugins install temperature-expansion-kit-plugin Important: in either case, Confirm in your configuration that the [temperature_automation.thermostat] values have been updated for the Pioreactors with the new hardware to be (exact values may vary slightly): Kp=0.017 Ki=0.0 Kd=4.0 You can also update the following configuration: [temperature_automation.config] # 50 or 60 only, depending on geographic location. This improves the accuracy. local_ac_hz=60","s":"Adding the Temperature Expansion Upgrade kit","u":"/user-guide/temperature-expansion-kit","h":"","p":780},{"i":789,"t":"First, get the file latest .whl file here onto any computer that can SSH into the Pioreactor. To get this .whl file onto a Pioreactor, use either scp, or FileZilla. Once the .whl file is on the Pioreactor, use pio plugin install temperature_expansion_kit_plugin --source <location of whl file>","s":"I don't have internet access - how can I install the plugin?","u":"/user-guide/temperature-expansion-kit","h":"#i-dont-have-internet-access---how-can-i-install-the-plugin","p":780},{"i":791,"t":"Try unplugging and plugging the probe back into the HAT. Try restarting the Pioreactor. If the error persists, contact us at hello@pioreactor.com","s":"I'm seeing \"Record null temperature. Is the Pt1000 probe connected?\" and the wire is connected.","u":"/user-guide/temperature-expansion-kit","h":"#im-seeing-record-null-temperature-is-the-pt1000-probe-connected-and-the-wire-is-connected","p":780},{"i":794,"t":"It is possible that your mDNS is being blocked or restricted. If possible, log into your router and enable settings that allow \"multicast\", or \"mDNS\", or \"IGMP proxing\". If you are using a the builtin local access point, this solution is not the correct one. Also, if you are able to provide a permanent IPv4 address to your leader, you can get a significant performance boost by setting the configuration some config parameters to the IPv4 address. [cluster.topology] # below is an example, your IPv4 may differ: leader_address=192.168.0.3 [mqtt] broker_address=192.168.0.3","s":"My Pioreactor activities start very slowly from the UI","u":"/user-guide/troubleshooting-networks","h":"#my-pioreactor-activities-start-very-slowly-from-the-ui","p":792},{"i":796,"t":"See our troubleshooting documentation here.","s":"I'm having trouble with the local access point","u":"/user-guide/troubleshooting-networks","h":"#im-having-trouble-with-the-local-access-point","p":792},{"i":799,"t":"Likely the fan's magnets are striking the 4mm screws above it. See this section if so.","s":"Stirring is making a grinding noise.","u":"/user-guide/troubleshooting-stirring","h":"#stirring-is-making-a-grinding-noise","p":797},{"i":801,"t":"First, with the stirring activity running, carefully examine if the fan below is spinning. If the fan is not spinning, Check to confirm that the fan's cable is in the right PMW channel. You can find the right PWM channel to use in the config.ini, under [PWM] (also check that it is not overwritten in the unit specific config.ini) Does the fan start to spin momentarily, but then stop? You may need to increase the target RPM in the UI. The lower limit of RPM is around 125. Target RPMs below 125 have a tendency to stall. Alternatively, increase the initial_duty_cycle by 10 units or so and try again. for Pioreactor 20ml 1.0: Visually inspect the top of the fan from the side. If you rotate the fan with a pen, is it touching (or nearly touching) the screws above it (see image below)? See this section if so. for Pioreactor 20ml 1.1: you may need to increase the distance between the fan and the vial holder. You can unscrew the M3 30mm screws slightly to increase the distance. Very gently wiggle the connection between the stirring wires and the HAT - does the fan start? It may be a bad connection. Contact us at support@pioreactor.com The fan may be damaged. Contact us at support@pioreactor.com If the fan is spinning: This issue may occur if the fan is positioned too far from the RPM sensors on the heater PCB above it. There should be no-to-very-little visible metal from the screw at the interface between the vial holder and the top faceplate's arms. See image below. Try pushing the fan only slightly higher up using a pen, pencil or thin rod. Avoid moving the fan too high up and hitting the vial holder's screws. Try moderately tightening the screws on the bottom of the top faceplate. Try lowering the initial_duty_cycle in the config.ini to a value like ~20. Are the two magnets still present on the fan? Visually inspect from the side, or unscrew the top faceplate from the vial holder to see better. The heater PCB may be damaged. Contact us at support@pioreactor.com. You can turn off the feedback loop by setting use_rpm=0 in the [stirring] section of your configuration. Set the initial_duty_cycle to some appropriate value (20 to 40), as well.","s":"UI is reporting \"Stirring RPM is 0\", or stirring self-test failed.","u":"/user-guide/troubleshooting-stirring","h":"#ui-is-reporting-stirring-rpm-is-0-or-stirring-self-test-failed","p":797},{"i":803,"t":"Detach the top faceplate. Under the faceplate, slightly unscrew each of the four metal screws. This action will create more space between the magnets and the plastic screws.","s":"The magnets rub against the plastic screws above them, causing the stirring performance to be degraded / stop.","u":"/user-guide/troubleshooting-stirring","h":"#the-magnets-rub-against-the-plastic-screws-above-them-causing-the-stirring-performance-to-be-degraded--stop","p":797},{"i":805,"t":"Check that the vial is pushed down all the way. Try moving the fan closer to the vial holder by gently tightening the screws on the bottom of the top faceplate. The liquid in the vial may be too viscous for the mixing to work.","s":"Stir bar is not spinning","u":"/user-guide/troubleshooting-stirring","h":"#stir-bar-is-not-spinning","p":797},{"i":807,"t":"Consider decreasing the value of Kp in the section stirring.pid in the config.ini by 50%. Are you trying to target a very low RPM? The lower limit of RPM is around 125. Target RPMs below 125 have a tendency to stall. Try performing a stirring calibration.","s":"Stirring is not able to keep a steady RPM","u":"/user-guide/troubleshooting-stirring","h":"#stirring-is-not-able-to-keep-a-steady-rpm","p":797},{"i":809,"t":"Consider reducing your target RPM. Check if the vial is pushed all the way down. From the side profile, check that no metal from the screws is showing ⇒ the vial is straight vertically. Try another stir bar design, like a cross shape.","s":"My stir bar keeps skipping. How can I reduce that?","u":"/user-guide/troubleshooting-stirring","h":"#my-stir-bar-keeps-skipping-how-can-i-reduce-that","p":797},{"i":811,"t":"This is likely caused by a short circuit in the fan's cable assembly. Remove the fan's power cable, and remove the plastic housing by applying pressure on the exposed metal tabs and gently pulling the wires out. Check for any stray wire strands and remove them. Carefully put the plastic housing back on until it clicks (red wire should be positioned closer to the GPIO pins), and try again.","s":"Raspberry Pi shuts off or restarts when stirring is turned on","u":"/user-guide/troubleshooting-stirring","h":"#raspberry-pi-shuts-off-or-restarts-when-stirring-is-turned-on","p":797},{"i":814,"t":"In your browser's address bar, add the http:// infront of the url, like so: http://pioreactor.local. The UI is hosted on http, not http_s_. Check if you are accessing http ://pioreactor.local, and not https ://pioreactor.local. Try accessing using the url http://<the permanent name of your Pioreactor aka hostname>.local If you know your Raspberry Pi's IP, try http://<IP address of your Raspberry Pi>. Here's information to determine the IP address Errors during installation: When pressing the button on the HAT, does the blue LED show up? If not, installation may have failed. See notes here. In your Raspberry Pi Imager settings, confirm that you clicked \"Set username and password\", and used the username pioreactor. If not, try reinstalling the image. Are you on an older Windows machine? You may need to install a DNS service, but also see workarounds here. Try SSHing in and restarting the webserver: sudo systemctl restart lighttpd.service && sudo systemctl status lighttpd.service.","s":"I'm not able to access http://pioreactor.local","u":"/user-guide/troubleshooting-ui","h":"#im-not-able-to-access-httppioreactorlocal","p":812},{"i":816,"t":"This error occurs because your UI can't connect to an internal system, MQTT, that is used for displaying data and actions. Likely you also weren't able to access the UI with http://pioreactor.local, but had to use an IP address as the url. To fix this: Navigate to the Configuration page in the side bar. Find the [mqtt] section, and change the broker_address configuration to your Pioreactor's IP. Ex: [mqtt] broker_address=192.168.0.10 Your IP may be different than the one above. Hit Save. Power-cycle the Pioreactor by rebooting it from the Inventory page. If you are using a remote access service, like ngrok or tailscale​ Likely you didn't fill out the ws parameter in the configuration correctly. See the remote access instructions again.","s":"I see \"Failed to connect to MQTT. ...\" in a pop-up - what can I do?","u":"/user-guide/troubleshooting-ui","h":"#i-see-failed-to-connect-to-mqtt--in-a-pop-up---what-can-i-do","p":812},{"i":818,"t":"Any of the following could solve your problem: Is there a green icon in the top-left of the Pioreactor card? If not, or it's grey, either the Pioreactor is powered off, or the monitor job is not running. If so, try power-cycling the Pioreactor. It's possible that the experiment has changed while the page has been left open - try refreshing the page and try again. If you had trouble accessing the UI (see question above), in your config.ini, change the leader_address field to whatever worked above, an IP for example. Possibly the web server is off. Try logging into your leader and typing sudo systemctl status lighttpd.service Do you also see a \"Failed to connect to MQTT. Is configuration for leader_address correct?\" error pop-up? If so, see question above. Try power-cycling the Pioreactor.","s":"When I click an action in the UI, I don't see any response. Or the button just spins and does nothing.","u":"/user-guide/troubleshooting-ui","h":"#when-i-click-an-action-in-the-ui-i-dont-see-any-response-or-the-button-just-spins-and-does-nothing","p":812},{"i":820,"t":"Brown-outs and restarts​ If you find that your Pioreactor is halting jobs (eg: the UI says lost and stirring/motors have stopped), or you find that your Pioreactor is restarting itself often, this could be due to brown-outs. Brown-outs are when your power supply is momentarily reduced to the point that the Raspberry Pi shuts down. When the power comes back up, the Raspberry Pi will start up again. This is most likely caused by: An inadequate power supply unit (PSU). You need to use a proper PSU (5V, at least 2.5 Amps), and certainly not a phone charger. We like the Raspberry Pi's official PSU. If you are running a lot of power: high temperature, stirring, pumping often, additional LEDs (or some combination) and you are experiencing brown-outs, we suggest adding an external power supply for the PWM outputs. You can view the PWM's voltage for a Pioreactor under Manage -> System -> Voltage on PWM rail. This should be near 5.0V. Pioreactor restarts when a PWM output is turned on​ If your Pioreactor restarts with a pump, stirring fan, etc. turns out, it's possible there is a short in the connectors. Email us at help@pioreactor.com","s":"Power and restarts","u":"/user-guide/troubleshooting-power","h":"","p":819},{"i":822,"t":"We publish new software occasionally that fixes bugs, adds new features, and improves performance. You can update your Pioreactor(s) to the latest software from the UI, or from the command line. We highly recommend keeping your Pioreactor software up to date!","s":"Updating the Pioreactor software","u":"/user-guide/updating-software","h":"","p":821},{"i":824,"t":"info To use this update method, you Raspberry Pi must be able to access the internet. Using a local access point, see method 2 below. When a new software version is released by our team, you will see a red \"badge\" in your UI's sidebar: Upon visiting the Updates page, you can see what version you have installed, and the latest version published by us. You can also read the changelog to see what improvements we've made in the latest releases. If you'd like to update, click on the \"Update to next release\" button. Updating software doesn't interrupt experiments or activities, but we suggest waiting until between experiments to update. Updating from the UI will update all the Pioreactors in your cluster. info The updating process will update to the next release, after your current version. So if your current version is 23.4.1, and there are two more recent releases, say 23.5.1 and 23.6.1, then the update process will update to 23.5.1. You can run the update process again to update to 23.6.1. We do this so that you will get changes folded in from each release we make. Installing previous versions or development versions​ You can install the bleeding-edge software from this page as well. Just select the development build in the drop down. Warning: this version may be unstable (and fun!) Similarly, from the command line, you can install specific versions. See pio update app --help for more.","s":"Method 1: Updating over the internet","u":"/user-guide/updating-software","h":"#method-1-updating-over-the-internet","p":821},{"i":826,"t":"Each time we release a new Pioreactor version, we create a bundle of the required files as a zip file. This zip file can be uploaded to your Pioreactor cluster via the UI. On the Releases page, download the release_xx.xx.xx.zip file for the version you want onto a computer with access to the Pioreactor web UI. In the web UI, visit Updates. In the drop down in the top right, select \"Update from zip file\". Select the zip file from step 1. Click update. Your browser does not support the video tag.","s":"Method 2: Update using a zip file and the UI","u":"/user-guide/updating-software","h":"#method-2-update-using-a-zip-file-and-the-ui","p":821},{"i":828,"t":"On the Releases page, download the release_xx.xx.xx.zip file for the version you want. We need a software tool up upload this release to the Pioreactor. You can use scp on the command line: scp <path to release archive> pioreactor@<leader hostname>.local:/home/pioreactor Skip to 8. below. or a tool like FileZilla. We'll continue with FileZilla below. Download and open FileZilla. Connect to the Pioreactor's local-access-point, pioreactor. Enter the following credentials in the top-right: host: pioreactor.local (or, your <leader hostname>.local or its IP address) username: pioreactor password: raspberry port: 22 Click Quickconnect. You should successfully connect to your Pioreactor's Raspberry Pi (and may need to accept a security pop-up). On the left-hand side is your computer's file system. Find the release_xx.xx.xx.zip file you downloaded earlier, and double click it to upload to the Raspberry Pi (that filesystem is on the right). You should see a successfully uploaded message, and the file should be present on the right-hand side now. You can close FileZilla. SSH into your Pioreactor. Now enter: pio update app --source release_xx.xx.xx.zip (Of course, replace the xx.xx.xx with your version). This will kick off a task to update your software. To update your workers, first we will distribute the release file to all workers: pios cp release_xx.xx.xx.zip -y Finally, run the following to update the software on the workers: pios update app --source release_xx.xx.xx.zip","s":"Method 3: Update using a zip file over scp or sftp","u":"/user-guide/updating-software","h":"#method-3-update-using-a-zip-file-over-scp-or-sftp","p":821},{"i":830,"t":"You can add your own LEDs to the Pioreactor. You might want to do this for the following reasons: Adding white LEDs (or red + blue LEDs) to turn grow algae Adding a while LED to illuminate the culture so you can easily see growth through the window Opto-genetic experiments to add LEDs to trigger expressions info You don't have to worry about your LED interfering with optical density measurements. When the OD Reading job is running, it forces all other LEDs off (setting intensity to 0%) before taking a reading.","s":"Using additional LEDs","u":"/user-guide/using-leds","h":"","p":829},{"i":833,"t":"The Pioreactor comes with a large set of functionality and behaviour to accomplish most projects. For example, continuous culturing, optical density reading, and stable temperatures are available out-of-the-box. However, the specifics and range of how people use bioreactors goes far beyond what we could ever cover. That's why Pioreactor has added a platform so that community members can make their own extensions and share them with others. We call these plugins. (Below is how to install plugins - if you are looking to create your own plugins, see here.) Installing plugins Automations installed via plugins Activities installed via plugins Uninstalling plugins Alternative: putting Python files in the the plugins folder","s":"Using community plugins","u":"/user-guide/using-community-plugins","h":"","p":832},{"i":835,"t":"From your Pioreactor's interface, the \"Plugins\" button on the left navigation bar will display all your currently installed plugins, and some recommended plugins. We also encourage you to explore our forums for more plugins created by the community. You can also use the \"Install plugin by name\" button in the top-right to install a plugin that is not featured on this page.","s":"Installing plugins","u":"/user-guide/using-community-plugins","h":"#installing-plugins","p":832},{"i":837,"t":"Some plugins add new automations to your Pioreactor. After installing, new dosing, LED, or temperature automations will be available in the list of automations available to you.","s":"Automations installed via plugins","u":"/user-guide/using-community-plugins","h":"#automations-installed-via-plugins","p":832},{"i":839,"t":"Some plugins add new activities to your Pioreactor. After installation, an activity's state and settings will show up on each Pioreactor's card. Below, we've installed the pioreactor-air-bubbler plugin: Managing on/off and settings are done just like any other job, in the Manage dialog:","s":"Activities installed via plugins","u":"/user-guide/using-community-plugins","h":"#activities-installed-via-plugins","p":832},{"i":841,"t":"You can uninstall plugins from the same page, too. These will remove the action on the Pioreactor's card, but won't delete the section in your config.ini. Also, if a SQL table was installed with the plugin, the table will not be deleted.","s":"Uninstalling plugins","u":"/user-guide/using-community-plugins","h":"#uninstalling-plugins","p":832},{"i":843,"t":"An alternative way to install a plugin is to place a Python file in the /home/pioreactor/.pioreactor/plugins directory on the Raspberry Pi. This is good for one-off scripts or plugins you are demoing or testing. See more about writing and distributing plugins.","s":"Alternative: putting Python files in the the plugins folder","u":"/user-guide/using-community-plugins","h":"#alternative-putting-python-files-in-the-the-plugins-folder","p":832},{"i":846,"t":"You can attach up to three peristaltic pumps to your Pioreactor, typically used for: adding fresh media to the vial, removing effluent from the vial, and adding an alternative media to the vial. First decide what you want your new pump to do: add media, remove waste, or add an alternative media. Pumps that are supplied by us will have a connector that connects to the PWM outputs on the Pioreactor hat. Which PWM you connect to is determined by your PWM settings in config.ini. In our case, if we were to use the pump as a media pump, we would connect the pump to PWM channel 2. Setting up the dosing platform # The dosing platform isn't needed, but helps organize your pumps. We sell them in our shop, but it's also open source - so you can 3D print your own! Set the dosing platform on a level surface. Place your Pioreactor in the platform, as shown. Note: a Raspberry Pi B model won't fit. Attach your two pumps' wires to media and waste PWMs on the Pioreactor (your config.ini has the PWM channels these should attach to, see section above). Vertically place each pump into the platform. Note the following: Check the orientation of the pump head: the tubes should be facing out. Each pump's wire should travel up one of the grooves in the side of the holder. The pump will feel snug in the holder. Do this for both pumps. The pumps should be have some gap between them and the Pioreactor, facing opposite directions, and not interfering with each other. Connecting the tubes # For both pumps, the tube that is closer to the Pioreactor's vial is the tube that will connect to the vial. Optional: If the pump→vial tubes seem too long, you can cut them to a preferable length. In the pictures shown, we cut the 9\" tube down to 6\". This reduces media waste and makes the platform more compact. For each pump, attach this tube to the Pioreactor's vial via the luer lock connection. You're done! Note the picture demonstrating the flow of liquid in and out of the Pioreactor's vial. caution When attaching tube ends that contain liquid to the vial, be careful of drops that might escape. We suggest taking the Pioreactor vial out of the vial holder when attaching tubes, to minimize the chance of a drop falling into the vial holder. After attaching, place back into the vial holder. tip If using your pumps for the first time, we suggest letting them run continuously for 10 minutes or so to \"loosen\" the tubing up and check for any problems. Here's how to do this: Unattach the end connected to the vial. Place both ends (source and sick) into a beaker of water, Use the Pioreactor UI to run them continuously.","s":"Viewing pump configuration in config.ini","u":"/user-guide/using-pumps","h":"#viewing-pump-configuration-in-configini","p":844},{"i":850,"t":"Read the calibration instructions for how to calibrate your pumps to move precise mL of liquid. Calibration is required for most dosing automations in the Pioreactor.","s":"Calibrating pumps","u":"/user-guide/using-pumps","h":"#calibrating-pumps","p":844},{"i":852,"t":"caution We strongly recommended you don't run peristaltic pumps continuously for hours at a time. By continuously, we mean \"always moving liquid\". The inner tubing has a lifetime and may wear out during operation, causing a leak. If you need to move liquid continuously for long periods of time, you need a different pump design.","s":"Using pumps in experiments","u":"/user-guide/using-pumps","h":"#using-pumps-in-experiments","p":844},{"i":854,"t":"To avoid contamination, pumps should be sterilized before and after use. Using heat​ You can disassemble the pump head, extract the tubing, and autoclave the tubing. (If it's your first time, make note of how the pumps are put back together) Put the tubing back in, reassemble the head, and your good to go. Using bleach and ethanol​ Create a 10% bleach dilution, or high concentration alcohol, in a container. Place the sink and source tubes of each pump you're sterilizing in the beaker. On the UI, in the Pioreactors tab, click Manage and go to the Dosing tab. Run continuously to cycle the disinfectant solution through each pump that you're using. Interrupt after sufficient cycling, at least 2 minutes. If finishing an experiment, repeat the above with water. If starting an experiment, you'll need to prime the pumps, see the next section. caution It's important to not keep harsh chemicals, like bleach, in the silicone tubing for long. Cleaning pumps should always end with flushing the tubes with water or something inert.","s":"Sterilizing the pumps before and after experiments","u":"/user-guide/using-pumps","h":"#sterilizing-the-pumps-before-and-after-experiments","p":844},{"i":856,"t":"You can attach the source of your media pump to your media bottle and \"prime\" it by running the media pump until media comes out. The sink end can be left in a bleach/ethanol container, or attached to a Pioreactor vial. Likewise, the waste pump can flushed with water, and then attached to the Pioreactor vial and waste bottle. tip Before attaching to media, waste, or vials for your experiments, you can spray the luer lock ends with ethanol. Be careful that no liquid that drips down into the Pioreactor vial holder.","s":"Preparing for experiments","u":"/user-guide/using-pumps","h":"#preparing-for-experiments","p":844},{"i":858,"t":"See documentation on how to run pumps manually from the UI.","s":"Running pumps from the web interface","u":"/user-guide/using-pumps","h":"#running-pumps-from-the-web-interface","p":844},{"i":860,"t":"pio run add_media --ml 3 or, if you wish to run continuously until interrupted (don't leave this running for hours, though). pio run add_media --continuously","s":"Running pumps from the command line","u":"/user-guide/using-pumps","h":"#running-pumps-from-the-command-line","p":844},{"i":862,"t":"Dosing automations, like turbidostats, chemostats, fed-batch, etc., are available to run once your pumps are attached and calibrated. These automations will programmatically add and remove media. Read more about automations.","s":"Programmatically run pumps using automations","u":"/user-guide/using-pumps","h":"#programmatically-run-pumps-using-automations","p":844},{"i":869,"t":"The Pioreactor HAT comes with a connector for the StemmaQT / Qwiic connector that can be used to attach additional hardware for your Pioreactor. See image below: info What is StemmaQT / Qwiic? It's simply a standardized physical connector, the JST SH, with electronic connections to 3.3V, GND and I²C. Many other hardware design companies, like Adafruit and SparkFun, implement StemmaQT / Qwiic on their boards, which expands the StemmaQT / Qwiic ecosystem.","s":"Using the StemmaQT/Qwicc connector","u":"/user-guide/using-stemma-qt","h":"","p":868},{"i":871,"t":"Suppose you are placing your Pioreactor in a CO₂ incubator, and want to record the CO₂ concentration of the incubator. The incubator does monitor the CO₂ concentration, but generally this isn't accessible to other tools. What you can do is purchase an external CO₂ sensor with StemmaQT / Qwiic connectors, like the SCD-40, and attach it to your Pioreactor. The Pioreactor can now read from the CO₂ sensor, and build logging, event-loops, plotting, etc. around the measurements. To read from the sensor, a plugin may be available for it, or you can write a simple Python script like so: note To run the script, you'll first need to install the Python library: sudo pip3 install adafruit-circuitpython-scd4x import sleep import board import adafruit_scd4x from pioreactor.pubsub import publish from pioreactor.whoami import get_unit_name, get_latest_experiment_name i2c = board.I2C() scd4x = adafruit_scd4x.SCD4X(i2c) exp = get_latest_experiment_name() unit = get_unit_name() scd4x.start_periodic_measurement() while True: if scd4x.data_ready: print(\"CO2: %d ppm\" % scd4x.CO2) publish(f\"pioreactor/{unit}/{exp}/scd4x/co2\", scd4x.CO2, retain=True) print(\"Temperature: %0.1f *C\" % scd4x.temperature) publish(f\"pioreactor/{unit}/{exp}/scd4x/temperature\", scd4x.temperature, retain=True) print(\"Humidity: %0.1f %%\" % scd4x.relative_humidity) publish(f\"pioreactor/{unit}/{exp}/scd4x/relative_humidity\", scd4x.relative_humidity, retain=True) print() time.sleep(1) Running this on your Pioreactor will publish the data to MQTT, and thus be available to any other bioreactor job. You could also turn this into a background job to make it even easier to use!","s":"Example","u":"/user-guide/using-stemma-qt","h":"#example","p":868},{"i":893,"t":"Writing your own custom automations is easy, but requires some knowledge of Python. If you're interested, see our documentation here.","s":"Writing your own 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6H6v2h2v-2z"></path></svg></span>Info</div><div class="admonitionContent_BuS1"><p>You can expect the assembly to take approximately 20-30 minutes.</p></div></div>
diff --git a/user-guide/20ml-v11-optics-assembly.html b/user-guide/20ml-v11-optics-assembly.html
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menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Wetware assembly</h1></header><div id="step-1-inserting-the-o-rings" style="padding:10px;margin:20px 0px 60px 0px;display:flex;flex-wrap:nowrap"><div id="mainImage" style="width:55%;float:left;margin-right:10px"><h2>Step 1: Inserting the O-rings<!-- -->  <a href="/user-guide/20ml-v11-wetware-assembly#step-1-inserting-the-o-rings">#</a></h2><img maxheight="240" src="/assets/images/oring-to-vial-holder-90296d009eb4636007070aef65daf76e.png"><div id="thumbnails" style="width:100%"><button class="highlightThumbnail_SKrZ"><img width="100px" src="/assets/images/oring-to-vial-holder-90296d009eb4636007070aef65daf76e.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/oring-groove-9c523d259dadca8b53bf3059033b3f9e.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/thin-oring-into-top-ed7b8690c3090fb835e616930ed45528.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/thick-oring-into-bottom-e3d67c4a373f992ae32a5c282d32dc13.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/vial-holders-with-orings-2e0dffab51055a06ae5f38f79a10b306.png"></button></div></div><section style="width:44%;float:left;margin-top:40px"><div class="theme-admonition theme-admonition-note admonition_xJq3 alert alert--secondary"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 14 16"><path fill-rule="evenodd" d="M6.3 5.69a.942.942 0 0 1-.28-.7c0-.28.09-.52.28-.7.19-.18.42-.28.7-.28.28 0 .52.09.7.28.18.19.28.42.28.7 0 .28-.09.52-.28.7a1 1 0 0 1-.7.3c-.28 0-.52-.11-.7-.3zM8 7.99c-.02-.25-.11-.48-.31-.69-.2-.19-.42-.3-.69-.31H6c-.27.02-.48.13-.69.31-.2.2-.3.44-.31.69h1v3c.02.27.11.5.31.69.2.2.42.31.69.31h1c.27 0 .48-.11.69-.31.2-.19.3-.42.31-.69H8V7.98v.01zM7 2.3c-3.14 0-5.7 2.54-5.7 5.68 0 3.14 2.56 5.7 5.7 5.7s5.7-2.55 5.7-5.7c0-3.15-2.56-5.69-5.7-5.69v.01zM7 .98c3.86 0 7 3.14 7 7s-3.14 7-7 7-7-3.12-7-7 3.14-7 7-7z"></path></svg></span>note</div><div class="admonitionContent_BuS1"><p>The vial holder of the v1.1 comes in two halves; a top vial holder and a bottom vial holder. Both have sections to insert O-rings for a more secure hold on your vials and increased protection against leaks. The <span style="background-color:rgb(220, 84, 183);border-radius:2px;color:#fff;padding:0.2rem">thinner O-ring (#024)</span> fits into the top piece. The <span style="background-color:rgb(255, 144, 36);border-radius:2px;color:#fff;padding:0.2rem">thicker O-ring (#121)</span> lines the bottom piece.</p></div></div><ol>
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From the command line, you can view more logs, control individual Pioreactors, and more.</p>
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aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Activities</h1></header><p>Below is a list of activities that come available with the Pioreactor. Additionally, you can add activities using plugins. <a href="/user-guide/using-community-plugins">Read more about using plugins</a>.</p>
diff --git a/user-guide/addition-hardware-pumps.html b/user-guide/addition-hardware-pumps.html
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href="/user-guide/export-import-existing-data">Export and import your data</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>More on peristaltic pumps</h1></header><p>The PWM output default to 5V (specifically, it&#x27;s tied to the power supply, so it may be 5.1V, 5.2V etc. See your power supply). You are able to use 12V pumps successfully even at 5V output. However, you can also use the <a href="https://docs.pioreactor.com/user-guide/external-power" target="_blank" rel="noopener noreferrer">AUX power connection to change the PWM output</a>.</p>
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cluster</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-leds">Using additional LEDs</a></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/experiment-profiles">Experiment Profiles</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/calibrate-od600">Standard curves for OD600 readings</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/configuration">Configuration via config.ini</a></li><li class="theme-doc-sidebar-item-link 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menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main 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Below is a list of our favourite plugins. Visit the <a href="/user-guide/using-community-plugins">guide on how to install plugins</a> into your Pioreactor.</p>
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cluster</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-leds">Using additional LEDs</a></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/experiment-profiles">Experiment Profiles</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link menu__link--active" aria-current="page" tabindex="0" href="/user-guide/calibrate-od600">Standard curves for OD600 readings</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/configuration">Configuration via config.ini</a></li><li 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Pioreactor software</a></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/temperature-expansion-kit">Upgrade kits</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-community-plugins">Using community plugins</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/available-plugins">List of available plugins</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Standard curves for OD600 readings</h1></header><h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="calibrating-your-od600-readings">Calibrating your OD600 readings<a href="#calibrating-your-od600-readings" class="hash-link" aria-label="Direct link to Calibrating your OD600 readings" title="Direct link to Calibrating your OD600 readings">​</a></h2>
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This is called the command line interface (CLI). Log onto either the <a href="/user-guide/create-cluster">leader or worker</a> and you can execute the following commands. Full options and up-to-date documentation are available with <code>pio &lt;command&gt; --help</code>.</p>
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class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Common questions</h1></header><div class="tableOfContentsInline_prmo"><ul class="table-of-contents"><li><a href="#pioreactor-operation">Pioreactor operation</a></li><li><a href="#optical-density-and-leds">Optical density and LEDs</a></li><li><a href="#heating-and-temperature-control">Heating and Temperature control</a></li><li><a href="#mixing-and-stirring-in-the-pioreactor">Mixing and stirring in the Pioreactor</a></li><li><a href="#raspberry-pi-hardware">Raspberry Pi Hardware</a></li><li><a href="#dosing">Dosing</a></li><li><a href="#data-storage-access-and-recovery">Data storage, access and recovery</a></li><li><a href="#networking">Networking</a></li></ul></div>
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href="/user-guide/software-set-up">Software installation</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/prepare-vial-for-cultures">Experiment basics</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/create-cluster">Extending your Pioreactor</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" 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class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Common questions</h1></header><div class="tableOfContentsInline_prmo"><ul class="table-of-contents"><li><a href="#pioreactor-operation">Pioreactor operation</a></li><li><a href="#optical-density-and-leds">Optical density and LEDs</a></li><li><a href="#heating-and-temperature-control">Heating and Temperature control</a></li><li><a href="#mixing-and-stirring-in-the-pioreactor">Mixing and stirring in the Pioreactor</a><ul><li><a href="#can-i-plot-the-rpm-in-a-chart-in-the-ui">Can I plot the RPM in a chart in the UI?</a></li></ul></li><li><a href="#raspberry-pi-hardware">Raspberry Pi Hardware</a></li><li><a href="#dosing">Dosing</a></li><li><a href="#data-storage-access-and-recovery">Data storage, access and recovery</a></li><li><a href="#networking">Networking</a></li></ul></div>
 <h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="pioreactor-operation">Pioreactor operation<a href="#pioreactor-operation" class="hash-link" aria-label="Direct link to Pioreactor operation" title="Direct link to Pioreactor operation">​</a></h2>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="how-can-i-restart-my-pioreactor-is-pulling-the-power-plug-out-safe">How can I restart my Pioreactor? Is pulling the power plug out safe?<a href="#how-can-i-restart-my-pioreactor-is-pulling-the-power-plug-out-safe" class="hash-link" aria-label="Direct link to How can I restart my Pioreactor? Is pulling the power plug out safe?" title="Direct link to How can I restart my Pioreactor? Is pulling the power plug out safe?">​</a></h4>
 <p>We suggest using the UI to reboot a Pioreactor:</p>
@@ -43,6 +43,7 @@ <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="what-are-the-units-of-p
 <p>The <em>uncalibrated</em> optical densities reported the UI and recorded in the database are have an arbitrary unit, and are per Pioreactor (so they can&#x27;t be compared to each other). However, the <em>normalized optical density</em>, generated after starting the activity <strong>Growth rate</strong> in the UI, is comparable, which is why we suggest using it for inferences (especially if you haven&#x27;t calibrated to some OD600 machine). Read more about our <a href="https://docs.pioreactor.com/user-guide/od-normal-growth-rate" target="_blank" rel="noopener noreferrer">optical density measurements here</a>.</p>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="how-can-i-change-the-frequency-rate-of-optical-density-measurements">How can I change the frequency (rate) of optical density measurements?<a href="#how-can-i-change-the-frequency-rate-of-optical-density-measurements" class="hash-link" aria-label="Direct link to How can I change the frequency (rate) of optical density measurements?" title="Direct link to How can I change the frequency (rate) of optical density measurements?">​</a></h4>
 <p>In the configuration, you can edit the parameter <code>samples_per_second</code> to adjust the how often the Pioreactor takes an optical density snapshot. Note that this parameter is the inverse of &quot;duration between readings&quot;. For example, if you wish to record a measurement every 60 seconds, then <code>samples_per_second=0.01666667</code> (which is 1/60).</p>
+<div class="theme-admonition theme-admonition-tip admonition_xJq3 alert alert--success"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 12 16"><path fill-rule="evenodd" d="M6.5 0C3.48 0 1 2.19 1 5c0 .92.55 2.25 1 3 1.34 2.25 1.78 2.78 2 4v1h5v-1c.22-1.22.66-1.75 2-4 .45-.75 1-2.08 1-3 0-2.81-2.48-5-5.5-5zm3.64 7.48c-.25.44-.47.8-.67 1.11-.86 1.41-1.25 2.06-1.45 3.23-.02.05-.02.11-.02.17H5c0-.06 0-.13-.02-.17-.2-1.17-.59-1.83-1.45-3.23-.2-.31-.42-.67-.67-1.11C2.44 6.78 2 5.65 2 5c0-2.2 2.02-4 4.5-4 1.22 0 2.36.42 3.22 1.19C10.55 2.94 11 3.94 11 5c0 .66-.44 1.78-.86 2.48zM4 14h5c-.23 1.14-1.3 2-2.5 2s-2.27-.86-2.5-2z"></path></svg></span>tip</div><div class="admonitionContent_BuS1"><p>If you put a large gap between readings, like 1 reading / 60 seconds, then we also suggest turning off the <em>downsampling</em> on the UI&#x27;s charts (it&#x27;s on by default to avoid plotting thousands of points). To do this, <a href="/user-guide/accessing-raspberry-pi">SSH</a> into your leader, and we&#x27;ll edit the following files:</p><div class="codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-text codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">nano /var/www/pioreactorui/contrib/charts/05_od.yaml</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div><p>And change the field <code>down_sample</code> from <code>true</code> to <code>false</code>. Do the same for the following files:</p><div class="codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-text codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">nano /var/www/pioreactorui/contrib/charts/01_implied_growth_rate.yaml</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div><div class="codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-text codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">nano /var/www/pioreactorui/contrib/charts/04_normalized_od.yaml</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div></div></div>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="why-does-the-intensity-for-led-a-turn-on--off-during-an-experiment">Why does the intensity for LED A turn on &amp; off during an experiment?<a href="#why-does-the-intensity-for-led-a-turn-on--off-during-an-experiment" class="hash-link" aria-label="Direct link to Why does the intensity for LED A turn on &amp; off during an experiment?" title="Direct link to Why does the intensity for LED A turn on &amp; off during an experiment?">​</a></h4>
 <p>You may have noticed that the LED labelled A turns on &amp; off every 5 seconds or so. This is (normally) the channel for the infrared (IR) LED, which is used in the optical density measurements. We only take reading every 5 seconds (the default), we don&#x27;t need the IR LED on all the time. The Pioreactor will only turn on LED when needed. This preserves the strength of the LED over longer periods of time. For more advanced use cases, it also allows other optical measurements to take place without the IR LED interfering with them.</p>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="why-does-my-optical-density-flatten-or-even-decrease-what-is-a-saturation-point">Why does my optical density flatten, or even decrease? What is a saturation point?<a href="#why-does-my-optical-density-flatten-or-even-decrease-what-is-a-saturation-point" class="hash-link" aria-label="Direct link to Why does my optical density flatten, or even decrease? What is a saturation point?" title="Direct link to Why does my optical density flatten, or even decrease? What is a saturation point?">​</a></h4>
@@ -53,7 +54,7 @@ <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="can-i-use-my-own-5mm-le
 <p>Of course! The only two requirements are that the spectrum of the LED overlaps with the spectrum of the photodiode, and that the LED light won&#x27;t be absorbed by media/culture, nor damage the media/culture. Thus, the often-used 600nm light source works in the Pioreactor. None of our internal algorithms or analytics are dependent on the wavelength of light chosen.</p>
 <p>When you are using additional LEDs outside of the optical density LED &amp; photodiode pair, you may worry that your additional LEDs will interfere with the optical density measurement. This won&#x27;t happen, as we turn off all non-optical density LEDs before taking an optical density measurement.</p>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="is-optical-density-the-same-as-turbidity">Is optical density the same as turbidity?<a href="#is-optical-density-the-same-as-turbidity" class="hash-link" aria-label="Direct link to Is optical density the same as turbidity?" title="Direct link to Is optical density the same as turbidity?">​</a></h4>
-<p>Turbidity is a measure of optical density, like how decibels are a measurement of sound intensity. Likewise, absorbance is a measure of optical density.</p>
+<p>Turbidity is a measure of optical density, like how decibels are a measurement of sound intensity. Similarly, absorbance is a measure of optical density.</p>
 <h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="heating-and-temperature-control">Heating and Temperature control<a href="#heating-and-temperature-control" class="hash-link" aria-label="Direct link to Heating and Temperature control" title="Direct link to Heating and Temperature control">​</a></h2>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="why-does-the-pioreactor-only-provide-a-temperature-reading-every-few-minutes">Why does the Pioreactor only provide a temperature reading every few minutes?<a href="#why-does-the-pioreactor-only-provide-a-temperature-reading-every-few-minutes" class="hash-link" aria-label="Direct link to Why does the Pioreactor only provide a temperature reading every few minutes?" title="Direct link to Why does the Pioreactor only provide a temperature reading every few minutes?">​</a></h4>
 <p>We made a design choice early on to make preparation as error-free as possible. This involved thinking about sensors being <em>in situ</em> (in place), versus the sensors being on the outside of the vial. The temperature sensor in the Pioreactor is outside the vial, which means less chance of contamination, but there&#x27;s a tradeoff (as you could guess): we have to rely on an estimation algorithm that requires a gew minutes to gather data on. We think this is a fair trade-off, as high frequency temperature readings are not that important in an experiment that lasts 12 hours or more.</p>
@@ -61,7 +62,7 @@ <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="why-does-the-pioreactor
 <p>If you find that the Pioreactor&#x27;s heating is shutting off, typically with an accompanying error and flashing blue light, then likely the temperature is becoming too high for safe handling. We restrict the onboard PCB&#x27;s temperature to be no higher than 63℃. Temperature&#x27;s higher than this can deform the plastic, and possibly cause burns. If the Pioreactor detects a temperature near or above this value, the software will shut off the heating, and possible the entire Raspberry Pi in extreme cases.</p>
 <p>To avoid this occurring, we suggest not setting the target temperature too high - not more than 20℃ above ambient temperature. Also, reducing the <code>Kd</code> parameter in <code>[temperature_automation.stable]</code> section in the config.ini would help.</p>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="how-does-heating-work-on-the-pioreactor">How does heating work on the Pioreactor?<a href="#how-does-heating-work-on-the-pioreactor" class="hash-link" aria-label="Direct link to How does heating work on the Pioreactor?" title="Direct link to How does heating work on the Pioreactor?">​</a></h4>
-<p>The Pioreactor has an onboard PCB, called the heating PCB, that sits below the glass vial. On the PCB are resistors that convert current from PWM outputs into heat. By varying the duty cycle of the PWM, we vary the amount of heat converted.</p>
+<p>The Pioreactor has an onboard PCB, called the heating PCB, that sits below the glass vial. On the PCB are resistors that convert current from PWM outputs into heat. By varying the duty cycle of the PWM, we vary the amount of energy converted to heat.</p>
 <h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="mixing-and-stirring-in-the-pioreactor">Mixing and stirring in the Pioreactor<a href="#mixing-and-stirring-in-the-pioreactor" class="hash-link" aria-label="Direct link to Mixing and stirring in the Pioreactor" title="Direct link to Mixing and stirring in the Pioreactor">​</a></h2>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="how-is-mixing--stirring-performed-in-the-pioreactor">How is mixing / stirring performed in the Pioreactor?<a href="#how-is-mixing--stirring-performed-in-the-pioreactor" class="hash-link" aria-label="Direct link to How is mixing / stirring performed in the Pioreactor?" title="Direct link to How is mixing / stirring performed in the Pioreactor?">​</a></h4>
 <p>Stirring is performed with a micro stir bar inside the vial, controlled by a pair of magnets spinning below the vial. The rotation speed, RPM, of the stir bar can be controlled using the Pioreactor software. This stirring is also how aeration is done.</p>
@@ -79,6 +80,8 @@ <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="how-can-i-improve-mixin
 <li>Add a <a href="https://www.printables.com/model/575292-baffle-for-pioreactor-vial-cap-a/files" target="_blank" rel="noopener noreferrer">baffle</a> to the vial cap. A simple cylinder that rests into the liquid causes disturbance in the rotating liquid that both mixing and aeration are significantly improved. A tube can be removed from the cap, and a autoclavable rod can be inserted such that it enters the media, but won&#x27;t interfere with the optics.</li>
 <li>Adding external aeration to your Pioreactor. In the simplest case, using an air pump.</li>
 </ol>
+<h3 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="can-i-plot-the-rpm-in-a-chart-in-the-ui">Can I plot the RPM in a chart in the UI?<a href="#can-i-plot-the-rpm-in-a-chart-in-the-ui" class="hash-link" aria-label="Direct link to Can I plot the RPM in a chart in the UI?" title="Direct link to Can I plot the RPM in a chart in the UI?">​</a></h3>
+<p>Yes, follow the instructions <a href="https://forum.pioreactor.com/t/creating-stirring-rpm-and-pwm-duty-cycle-charts-on-the-ui/339" target="_blank" rel="noopener noreferrer">here</a>.</p>
 <h2 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="raspberry-pi-hardware">Raspberry Pi Hardware<a href="#raspberry-pi-hardware" class="hash-link" aria-label="Direct link to Raspberry Pi Hardware" title="Direct link to Raspberry Pi Hardware">​</a></h2>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="what-raspberry-pi-hardware-can-i-use-i-see-raspberry-pi-1-2-3-4-5-a-b--zero---its-confusing">What Raspberry Pi hardware can I use? I see Raspberry Pi 1, 2, 3, 4, 5, A, B, +, Zero - it&#x27;s confusing!<a href="#what-raspberry-pi-hardware-can-i-use-i-see-raspberry-pi-1-2-3-4-5-a-b--zero---its-confusing" class="hash-link" aria-label="Direct link to What Raspberry Pi hardware can I use? I see Raspberry Pi 1, 2, 3, 4, 5, A, B, +, Zero - it&#x27;s confusing!" title="Direct link to What Raspberry Pi hardware can I use? I see Raspberry Pi 1, 2, 3, 4, 5, A, B, +, Zero - it&#x27;s confusing!">​</a></h4>
 <p>We&#x27;ve designed the hardware and software to be compatible with any Raspberry Pi that has onboard Wifi and a 40 pin header. That includes (at the time of writing):</p>
@@ -87,11 +90,12 @@ <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="what-raspberry-pi-hardw
 <li>Raspberry Pi 3 Model A+</li>
 <li>Raspberry Pi 4 Model B ³</li>
 <li>Raspberry Pi 5 Model B</li>
-<li>Raspberry Pi Zero W (with header) ¹</li>
-<li>Raspberry Pi Zero 2 W (with header)</li>
+<li>Raspberry Pi Zero W (with headers) ¹</li>
+<li>Raspberry Pi Zero 2 (with headers)</li>
 <li>Raspberry Pi 400 ²</li>
 </ul>
-<p>Although you can use any above, <strong>we like the Raspberry Pi 3 Model A+, and Raspberry Pi Zero 2 W</strong> because of their low power consumption, slim build, and low price. Both have the necessary CPU power and memory for the Pioreactor workload, and are generally easy to source. However, they don&#x27;t have ethernet connections! So talk to your team about if you need to use ethernet or wifi. If you need ethernet, we like the model 3B.</p>
+<p>Although you can use any above, <strong>we like the Raspberry Pi 3 Model A+, and Raspberry Pi Zero 2</strong> because of their low power consumption, slim build, and low price. Both have the necessary CPU power and memory for the Pioreactor workload, and are generally easy to source. However, they don&#x27;t have ethernet connections! So talk to your team about if you need to use ethernet or wifi. If you need ethernet, we like the model RPi
+3B.</p>
 <p>¹ <em>Raspberry Pi Zero W</em> is on the list above, and is very low cost compared to the others. They can absolutely be used for Pioreactors <em>as workers</em> - we don&#x27;t recommend them to be your <em>leader</em> (note sure what these terms mean? Here&#x27;s an introduction to <a href="/user-guide/create-cluster">leader and workers</a>). As workers, Raspberry Pi Zero W perform just fine, but will respond slower to commands. Note that this does not include the Raspberry Pi Zero <em>2</em> W model, which is fine for all roles.</p>
 <p>² The Raspberry Pi 400 has its 40 pin header exposed in a different orientation, so your Pioreactor won&#x27;t be able to sit on top like for other RPi versions. Take a <a href="https://forum.pioreactor.com/t/using-a-raspberry-pi-400/113/8" target="_blank" rel="noopener noreferrer">look at this forum post</a> to see how another user used the Raspberry Pi 400 with their Pioreactor.</p>
 <p>³ Note that you don&#x27;t need a lot of RAM for the Pioreactor, so we recommend getting the lower RAM option RPi 4s (1GB or 2GB) to save some money. However, 4GB and 8GB are fine, too.</p>
@@ -153,7 +157,7 @@ <h5 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="to-install-a-plugin">To
 <h5 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="to-upgrade-the-pioreactor-software">To upgrade the Pioreactor software<a href="#to-upgrade-the-pioreactor-software" class="hash-link" aria-label="Direct link to To upgrade the Pioreactor software" title="Direct link to To upgrade the Pioreactor software">​</a></h5>
 <p>See steps <a href="/user-guide/updating-software#method-2-update-using-a-zip-file-and-the-ui">here</a>.</p>
 <h4 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="if-i-have-multiple-pioreactor-leaders-on-my-network-what-leader-does-httppioreactorlocal-point-to">If I have multiple Pioreactor leaders on my network, what leader does <code>http://pioreactor.local</code> point to?<a href="#if-i-have-multiple-pioreactor-leaders-on-my-network-what-leader-does-httppioreactorlocal-point-to" class="hash-link" aria-label="Direct link to if-i-have-multiple-pioreactor-leaders-on-my-network-what-leader-does-httppioreactorlocal-point-to" title="Direct link to if-i-have-multiple-pioreactor-leaders-on-my-network-what-leader-does-httppioreactorlocal-point-to">​</a></h4>
-<p>If there are multiple leaders on the same network, then each will override the other&#x27;s <code>pioreactor.local</code> alias, and the alias will be unreliable. You can either access the leaders by their hostnames: <code>http://&lt;leader hostname&gt;.local</code>, or you can change the alias in the config.ini, too, by editing <code>domain_alias</code> under section <code>[ui]</code> (changing this requires a restart of the machine).</p></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/user-guide/troubleshooting-ui"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">User interface</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#pioreactor-operation" class="table-of-contents__link toc-highlight">Pioreactor operation</a></li><li><a href="#optical-density-and-leds" class="table-of-contents__link toc-highlight">Optical density and LEDs</a></li><li><a href="#heating-and-temperature-control" class="table-of-contents__link toc-highlight">Heating and Temperature control</a></li><li><a href="#mixing-and-stirring-in-the-pioreactor" class="table-of-contents__link toc-highlight">Mixing and stirring in the Pioreactor</a></li><li><a href="#raspberry-pi-hardware" class="table-of-contents__link toc-highlight">Raspberry Pi Hardware</a></li><li><a href="#dosing" class="table-of-contents__link toc-highlight">Dosing</a></li><li><a href="#data-storage-access-and-recovery" class="table-of-contents__link toc-highlight">Data storage, access and recovery</a></li><li><a href="#networking" class="table-of-contents__link toc-highlight">Networking</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer footer--dark"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Topics</div><ul class="footer__items clean-list"><li class="footer__item"><a class="footer__link-item" href="/user-guide/introduction">User Guide</a></li><li class="footer__item"><a class="footer__link-item" href="/developer-guide/introduction">Developer Guide</a></li><li class="footer__item"><a class="footer__link-item" href="/experiments/introduction">Experiments</a></li><li class="footer__item"><a href="https://github.com/Pioreactor/pioreactor/blob/master/CHANGELOG.md" target="_blank" rel="noopener noreferrer" class="footer__link-item">Changelog</a></li></ul></div><div class="col footer__col"><div class="footer__title">Community</div><ul class="footer__items clean-list"><li class="footer__item"><a href="https://forum.pioreactor.com/" target="_blank" rel="noopener noreferrer" class="footer__link-item">Community forums<svg width="13.5" height="13.5" aria-hidden="true" viewBox="0 0 24 24" class="iconExternalLink_nPIU"><path fill="currentColor" d="M21 13v10h-21v-19h12v2h-10v15h17v-8h2zm3-12h-10.988l4.035 4-6.977 7.07 2.828 2.828 6.977-7.07 4.125 4.172v-11z"></path></svg></a></li><li class="footer__item"><a href="https://twitter.com/pioreactor" target="_blank" rel="noopener noreferrer" class="footer__link-item">Twitter<svg width="13.5" height="13.5" aria-hidden="true" viewBox="0 0 24 24" class="iconExternalLink_nPIU"><path fill="currentColor" d="M21 13v10h-21v-19h12v2h-10v15h17v-8h2zm3-12h-10.988l4.035 4-6.977 7.07 2.828 2.828 6.977-7.07 4.125 4.172v-11z"></path></svg></a></li><li class="footer__item"><a href="https://github.com/pioreactor/" target="_blank" rel="noopener noreferrer" class="footer__link-item">GitHub<svg width="13.5" height="13.5" aria-hidden="true" viewBox="0 0 24 24" class="iconExternalLink_nPIU"><path fill="currentColor" d="M21 13v10h-21v-19h12v2h-10v15h17v-8h2zm3-12h-10.988l4.035 4-6.977 7.07 2.828 2.828 6.977-7.07 4.125 4.172v-11z"></path></svg></a></li></ul></div><div class="col footer__col"><div class="footer__title">Contributing to documentation</div><ul class="footer__items clean-list"><li class="footer__item">
+<p>If there are multiple leaders on the same network, then each will override the other&#x27;s <code>pioreactor.local</code> alias, and the alias will be unreliable. You can either access the leaders by their hostnames: <code>http://&lt;leader hostname&gt;.local</code>, or you can change the alias in the config.ini, too, by editing <code>domain_alias</code> under section <code>[ui]</code> (changing this requires a restart of the machine).</p></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/user-guide/troubleshooting-ui"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">User interface</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#pioreactor-operation" class="table-of-contents__link toc-highlight">Pioreactor operation</a></li><li><a href="#optical-density-and-leds" class="table-of-contents__link toc-highlight">Optical density and LEDs</a></li><li><a href="#heating-and-temperature-control" class="table-of-contents__link toc-highlight">Heating and Temperature control</a></li><li><a href="#mixing-and-stirring-in-the-pioreactor" class="table-of-contents__link toc-highlight">Mixing and stirring in the Pioreactor</a><ul><li><a href="#can-i-plot-the-rpm-in-a-chart-in-the-ui" class="table-of-contents__link toc-highlight">Can I plot the RPM in a chart in the UI?</a></li></ul></li><li><a href="#raspberry-pi-hardware" class="table-of-contents__link toc-highlight">Raspberry Pi Hardware</a></li><li><a href="#dosing" class="table-of-contents__link toc-highlight">Dosing</a></li><li><a href="#data-storage-access-and-recovery" class="table-of-contents__link toc-highlight">Data storage, access and recovery</a></li><li><a href="#networking" class="table-of-contents__link toc-highlight">Networking</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer footer--dark"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Topics</div><ul class="footer__items clean-list"><li class="footer__item"><a class="footer__link-item" href="/user-guide/introduction">User Guide</a></li><li class="footer__item"><a class="footer__link-item" href="/developer-guide/introduction">Developer Guide</a></li><li class="footer__item"><a class="footer__link-item" href="/experiments/introduction">Experiments</a></li><li class="footer__item"><a href="https://github.com/Pioreactor/pioreactor/blob/master/CHANGELOG.md" target="_blank" rel="noopener noreferrer" class="footer__link-item">Changelog</a></li></ul></div><div class="col footer__col"><div class="footer__title">Community</div><ul class="footer__items clean-list"><li class="footer__item"><a href="https://forum.pioreactor.com/" target="_blank" rel="noopener noreferrer" class="footer__link-item">Community forums<svg width="13.5" height="13.5" aria-hidden="true" viewBox="0 0 24 24" class="iconExternalLink_nPIU"><path fill="currentColor" d="M21 13v10h-21v-19h12v2h-10v15h17v-8h2zm3-12h-10.988l4.035 4-6.977 7.07 2.828 2.828 6.977-7.07 4.125 4.172v-11z"></path></svg></a></li><li class="footer__item"><a href="https://twitter.com/pioreactor" target="_blank" rel="noopener noreferrer" class="footer__link-item">Twitter<svg width="13.5" height="13.5" aria-hidden="true" viewBox="0 0 24 24" class="iconExternalLink_nPIU"><path fill="currentColor" d="M21 13v10h-21v-19h12v2h-10v15h17v-8h2zm3-12h-10.988l4.035 4-6.977 7.07 2.828 2.828 6.977-7.07 4.125 4.172v-11z"></path></svg></a></li><li class="footer__item"><a href="https://github.com/pioreactor/" target="_blank" rel="noopener noreferrer" class="footer__link-item">GitHub<svg width="13.5" height="13.5" aria-hidden="true" viewBox="0 0 24 24" class="iconExternalLink_nPIU"><path fill="currentColor" d="M21 13v10h-21v-19h12v2h-10v15h17v-8h2zm3-12h-10.988l4.035 4-6.977 7.07 2.828 2.828 6.977-7.07 4.125 4.172v-11z"></path></svg></a></li></ul></div><div class="col footer__col"><div class="footer__title">Contributing to documentation</div><ul class="footer__items clean-list"><li class="footer__item">
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diff --git a/user-guide/configuration.html b/user-guide/configuration.html
index 25e6c0773..15d7c179f 100644
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@@ -16,8 +16,8 @@
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href="/user-guide/software-set-up">Software installation</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/prepare-vial-for-cultures">Experiment basics</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret menu__link--active" aria-expanded="true" href="/user-guide/create-cluster">Extending your Pioreactor</a></div><ul style="display:block;overflow:visible;height:auto" class="menu__list"><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link menu__link--active" aria-current="page" tabindex="0" href="/user-guide/create-cluster">Creating a Pioreactor cluster</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-leds">Using additional LEDs</a></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/experiment-profiles">Experiment Profiles</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/calibrate-od600">Standard curves for OD600 readings</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/configuration">Configuration via config.ini</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-pumps">Using a peristaltic pump with your Pioreactor</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/hardware-calibrations">Hardware calibrations</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/external-power">Supplying more power to the PWM channels</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-stemma-qt">Using the StemmaQT/Qwicc connector</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" 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class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Creating a Pioreactor cluster</h1></header><p>Pioreactors are able to be used as individual units, or in concert with other Pioreactors. In either case, a Pioreactor needs to be assigned as a <em>leader</em>. The leader unit controls other Pioreactors (and that may include itself), stores the database, hosts the web interface, and is the interface between users and the hardware. A leader will communicate and control all the <em>workers</em> (non-leader Pioreactors) in the <em>inventory</em>.</p>
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questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Dosing automations</h1></header><p>When pairing the Pioreactor with dosing pumps, there are new capabilities and experiments you can run. The Pioreactor is pre-programmed with the following dosing automations. In the below automations, values highlighted <code>like so</code> are configurable.</p>
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codes</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/troubleshooting-hardware">Hardware and operation</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/troubleshooting-networks">Networking</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/troubleshooting-power">Power and restarts</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/troubleshooting-stirring">Stirring</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/troubleshooting-ui">User interface</a></li></ul></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Blue LED flashing &amp; error codes</h1></header><p>When a Pioreactor successfully boots, the onboard blue LED will flash quickly for 2 seconds, and then stop. However, there are times when the Pioreactor encounters an error, and will use the LED to alert to you that something is wrong. By counting the number of <em>short</em> flashes (per cycle), you can diagnose what might be wrong.</p>
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class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Experiment profiles schema</h1></header><p>Below is a schema for experiment profiles. We also do a run-time check</p>
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class="menu__link" tabindex="0" href="/user-guide/running-self-test">Running a self-test</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/create-cluster">Extending your Pioreactor</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Exporting data</h1></header><p>Experiment data can be exported using the <em>Export data</em> tab on the Pioreactor site.</p>
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class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Supplying more power to the PWM channels</h1></header><p>Some applications require more power to your Pioreactor if it is using lots of peripherals. This may include using more powerful pumps, more powerful external LEDs, etc. Or, if you see warning messages that reference under voltage or throttling, you probably are asking the Pioreactor to do too much given its default 5V power supply.</p>
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class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Hardware calibrations</h1></header><p>Hardware calibrations serve as a method to get accurate performance from your Pioreactor.</p>
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href="/user-guide/export-import-existing-data">Export and import your data</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Hardware connection assembly</h1></header><p>Normally, the external hardware will have two terminals, corresponding to positive and ground. The positive terminal may be marked by a dot, or &quot;+&quot; symbol, or be colored red. Make note of this terminal.</p>
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theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link menu__link--active" aria-current="page" tabindex="0" href="/user-guide/intro-python-scripting">Writing Pioreactor scripts with Python</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/export-import-existing-data">Export and import your data</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Writing Pioreactor scripts with Python</h1></header><div class="theme-admonition theme-admonition-note admonition_xJq3 alert alert--secondary"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 14 16"><path fill-rule="evenodd" d="M6.3 5.69a.942.942 0 0 1-.28-.7c0-.28.09-.52.28-.7.19-.18.42-.28.7-.28.28 0 .52.09.7.28.18.19.28.42.28.7 0 .28-.09.52-.28.7a1 1 0 0 1-.7.3c-.28 0-.52-.11-.7-.3zM8 7.99c-.02-.25-.11-.48-.31-.69-.2-.19-.42-.3-.69-.31H6c-.27.02-.48.13-.69.31-.2.2-.3.44-.31.69h1v3c.02.27.11.5.31.69.2.2.42.31.69.31h1c.27 0 .48-.11.69-.31.2-.19.3-.42.31-.69H8V7.98v.01zM7 2.3c-3.14 0-5.7 2.54-5.7 5.68 0 3.14 2.56 5.7 5.7 5.7s5.7-2.55 5.7-5.7c0-3.15-2.56-5.69-5.7-5.69v.01zM7 .98c3.86 0 7 3.14 7 7s-3.14 7-7 7-7-3.12-7-7 3.14-7 7-7z"></path></svg></span>note</div><div class="admonitionContent_BuS1"><p>This article isn&#x27;t intended as a crash course in Python, or Pioreactor software, but some helpful ways to write small scripts for your Pioreactor. If interested in learning more, check out the <a href="/developer-guide/introduction">developer docs</a> for detailed information.</p></div></div>
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questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Introduction to automations</h1></header><p>So far, we have worked with basic activities that you can directly set as a one time thing, typically at the beginning of your experiment (starting stirring, OD readings, etc.). For more advanced experiments, we introduce automations.</p>
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diff --git a/user-guide/led-automations.html b/user-guide/led-automations.html
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questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>LED automations</h1></header><p>LED automations are ways to automatically control the 4 available LEDs in the Pioreactor. These LEDs can be used as a light source for photosynthetic microbes, influence the environment of the microbes, as additional sensors, or improve existing sensors.</p>
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class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/remote-access">Remote access to your Pioreactors</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/networking">Networking</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link menu__link--active" aria-current="page" tabindex="0" href="/user-guide/local-access-point">Local access points</a></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/addition-hardware-pumps">Additional Hardware</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/intro-python-scripting">Writing Pioreactor scripts with Python</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/export-import-existing-data">Export and import your data</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Local access points</h1></header><p>For some use cases, you may want to create a local WiFi network just for your Pioreactors (this is called a local access point, or a hotspot). Why might you want to do this?</p>
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aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown 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markdown"><header><h1>Monitoring your experiment</h1></header><p>Navigate to the <em>Overview</em> page on the Pioreactor web interface. Here you can view live charts for growth rate, OD, normalized OD, and temperature. These overview graphs are used to monitor collected data during the experiment runtime.</p>
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class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Networking</h1></header><div class="theme-admonition theme-admonition-info admonition_xJq3 alert alert--info"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 14 16"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"></path></svg></span>info</div><div class="admonitionContent_BuS1"><p>Previously, Raspberry Pis used a file called <code>wpa_supplicant.conf</code> to handle wifi network connections. <strong>This is not longer the case</strong>. Modern Raspberry Pi software, including the Pioreactor, doesn&#x27;t use <code>wpa_supplicant.conf</code> at all. Instead, the tool <code>nmcli</code> replaces it. Don&#x27;t follow tutorials that use <code>wpa_supplicant.conf</code>.</p></div></div>
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your data</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Ngrok</h1></header><p>If you would like to expose the Pioreactor UI to view remotely, you can use a service like <a href="https://ngrok.com/" target="_blank" rel="noopener noreferrer">Ngrok</a> to do so.</p>
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class="menu__link menu__link--active" aria-current="page" tabindex="0" href="/user-guide/optics-assembly">Connect the optics system</a></li></ul></li></ul></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/software-set-up">Software installation</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/prepare-vial-for-cultures">Experiment basics</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/create-cluster">Extending your Pioreactor</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Connect the optics system</h1></header><div id="step-1-optic-cables-assembly" style="padding:10px;margin:20px 0px 60px 0px;display:flex;flex-wrap:nowrap"><div id="mainImage" style="width:55%;float:left;margin-right:10px"><h2>Step 1: Optic cables assembly<!-- -->  <a href="/user-guide/optics-assembly#step-1-optic-cables-assembly">#</a></h2><img maxheight="240" src="/assets/images/three_bulbs-706d6299dc47770176081db933965623.jpg"><div id="thumbnails" style="width:100%"><button class="highlightThumbnail_SKrZ"><img width="100px" 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href="/user-guide/export-import-existing-data">Export and import your data</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Pinch valves</h1></header><p>Pinch valves are useful for controlling gas into the Pioreactor by &quot;pinching&quot; a gas line closed (or keeping it open). This could used be for injecting gas periodically into the headspace, or acting as a bubbler by putting the injection tube directly into the culture. Below is a diagram of using a pinch valve to periodically provide CO₂ into the head space of the Pioreactor&#x27;s vial:</p>
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tabindex="0" href="/user-guide/activities">Activities</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/monitor-experiment">Monitoring your experiment</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/export-data">Exporting data</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/od-normal-growth-rate">Optical density, normalization, and growth rates</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/manual-dosing-leds">Dosing and LED updates</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link menu__link--active" aria-current="page" tabindex="0" href="/user-guide/running-self-test">Running a self-test</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/create-cluster">Extending your Pioreactor</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Running a self-test</h1></header><p>To get the best results and confirm your Pioreactor is working as expected, it&#x27;s advisable to run a self-test on your Pioreactor after setting it up initially. The self-test routine can catch common errors that may compromise your data collection.</p>
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To access the UI remotely, you need to join an authenticated VPN. This greatly improves security, but adds a bit of additional work for users.</p>
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questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Temperature automations</h1></header><p>The heater in the Pioreactor wetware can be programmed to control the temperature of the vial in automated ways. Pioreactor is pre-programmed with the following temperature automations. In the below automations, values highlighted <code>like so</code> are configurable.</p>
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href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Adding the Temperature Expansion Upgrade kit</h1></header><p>You can improve your Pioreactor temperature sensing capabilities with the Temperature Expansion Kit. This kit allows for faster temperature response times, more granular temperature data, and increasing the maximum culture temperature. Below are instructions on how to assemble the new hardware to your existing Pioreactor.</p>
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interface</a></li></ul></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Hardware and operation</h1></header><h3 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="my-pioreactor-isnt-responsive-anymore">My Pioreactor isn&#x27;t responsive anymore<a href="#my-pioreactor-isnt-responsive-anymore" class="hash-link" aria-label="Direct link to My Pioreactor isn&#x27;t responsive anymore" title="Direct link to My Pioreactor isn&#x27;t responsive anymore">​</a></h3>
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interface</a></li></ul></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Networking</h1></header><h3 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="my-pioreactor-activities-start-very-slowly-from-the-ui">My Pioreactor activities start very slowly from the UI<a href="#my-pioreactor-activities-start-very-slowly-from-the-ui" class="hash-link" aria-label="Direct link to My Pioreactor activities start very slowly from the UI" title="Direct link to My Pioreactor activities start very slowly from the UI">​</a></h3>
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diff --git a/user-guide/troubleshooting-stirring.html b/user-guide/troubleshooting-stirring.html
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href="/user-guide/software-set-up">Software installation</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/prepare-vial-for-cultures">Experiment basics</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret menu__link--active" aria-expanded="true" href="/user-guide/create-cluster">Extending your Pioreactor</a></div><ul style="display:block;overflow:visible;height:auto" class="menu__list"><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/create-cluster">Creating a Pioreactor cluster</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-leds">Using additional LEDs</a></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/experiment-profiles">Experiment Profiles</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/calibrate-od600">Standard curves for OD600 readings</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/configuration">Configuration via config.ini</a></li><li class="theme-doc-sidebar-item-link 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the Pioreactor software</a></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/temperature-expansion-kit">Upgrade kits</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-community-plugins">Using community plugins</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/available-plugins">List of available plugins</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Updating the Pioreactor software</h1></header><p>We publish new software occasionally that fixes bugs, adds new features, and improves performance. You can update your Pioreactor(s) to the latest software from the UI, or from the command line. <strong>We highly recommend keeping your Pioreactor software up to date!</strong></p>
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mainWrapper_z2l0"><div class="docsWrapper_hBAB"><button aria-label="Scroll back to top" class="clean-btn theme-back-to-top-button backToTopButton_sjWU" type="button"></button><div class="docRoot_UBD9"><aside class="theme-doc-sidebar-container docSidebarContainer_YfHR"><div class="sidebarViewport_aRkj"><div class="sidebar_njMd sidebarWithHideableNavbar_wUlq"><a tabindex="-1" class="sidebarLogo_isFc" href="/"><img src="/img/misc/colour-Docs-logo.png" alt="pioreactor" class="themedComponent_mlkZ themedComponent--light_NVdE"><img src="/img/misc/white-Docs-logo.png" alt="pioreactor" class="themedComponent_mlkZ themedComponent--dark_xIcU"></a><nav aria-label="Docs sidebar" class="menu thin-scrollbar menu_SIkG"><ul class="theme-doc-sidebar-menu menu__list"><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/introduction">Introduction</a></li><li class="theme-doc-sidebar-item-category 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href="/user-guide/software-set-up">Software installation</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/prepare-vial-for-cultures">Experiment basics</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret menu__link--active" aria-expanded="true" href="/user-guide/create-cluster">Extending your Pioreactor</a></div><ul style="display:block;overflow:visible;height:auto" class="menu__list"><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/create-cluster">Creating a Pioreactor cluster</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-leds">Using additional LEDs</a></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/experiment-profiles">Experiment Profiles</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/calibrate-od600">Standard curves for OD600 readings</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/configuration">Configuration via config.ini</a></li><li class="theme-doc-sidebar-item-link 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class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/temperature-expansion-kit">Upgrade kits</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link menu__link--active" aria-current="page" tabindex="0" href="/user-guide/using-community-plugins">Using community plugins</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/available-plugins">List of available plugins</a></li></ul></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Using community plugins</h1></header><p>The Pioreactor comes with a large set of functionality and behaviour to accomplish most projects. For example, continuous culturing, optical density reading, and stable temperatures are available out-of-the-box. However, the specifics and range of how people use bioreactors goes far beyond what we could ever cover. That&#x27;s why Pioreactor has added a platform so that community members can make their own extensions and share them with others. We call these <em>plugins.</em> (Below is how to install plugins - if you are looking to create your own plugins, see <a href="/developer-guide/plugin-as-python-package">here</a>.)</p>
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class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Using additional LEDs</h1></header><p>You can add your own LEDs to the Pioreactor. You might want to do this for the following reasons:</p>
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cluster</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/using-leds">Using additional LEDs</a></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-2 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" tabindex="0" href="/user-guide/experiment-profiles">Experiment Profiles</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/calibrate-od600">Standard curves for OD600 readings</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/user-guide/configuration">Configuration via config.ini</a></li><li class="theme-doc-sidebar-item-link 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class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Using a peristaltic pump with your Pioreactor</h1></header><h3 class="anchor anchorWithHideOnScrollNavbar_WYt5" id="viewing-pump-configuration-in-configini">Viewing pump configuration in config.ini<a href="#viewing-pump-configuration-in-configini" class="hash-link" aria-label="Direct link to Viewing pump configuration in config.ini" title="Direct link to Viewing pump configuration in config.ini">​</a></h3>
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class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><header><h1>Using the StemmaQT/Qwicc connector</h1></header><p>The Pioreactor HAT comes with a connector for the StemmaQT / Qwiic connector that can be used to attach additional hardware for your Pioreactor. See image below:</p>
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href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Building the vial holder</h1></header><div id="step-1-inserting-the-o-rings" style="padding:10px;margin:20px 0px 60px 0px;display:flex;flex-wrap:nowrap"><div id="mainImage" style="width:55%;float:left;margin-right:10px"><h2>Step 1: Inserting the O-rings<!-- -->  <a href="/user-guide/v11-upgrade-building-vial-holder#step-1-inserting-the-o-rings">#</a></h2><img maxheight="240" src="/assets/images/oring-to-vial-holder-90296d009eb4636007070aef65daf76e.png"><div id="thumbnails" style="width:100%"><button class="highlightThumbnail_SKrZ"><img width="100px" src="/assets/images/oring-to-vial-holder-90296d009eb4636007070aef65daf76e.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/oring-groove-9c523d259dadca8b53bf3059033b3f9e.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/thin-oring-into-top-ed7b8690c3090fb835e616930ed45528.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/thick-oring-into-bottom-e3d67c4a373f992ae32a5c282d32dc13.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/vial-holders-with-orings-2e0dffab51055a06ae5f38f79a10b306.png"></button></div></div><section style="width:44%;float:left;margin-top:40px"><div class="theme-admonition theme-admonition-info admonition_xJq3 alert alert--info"><div class="admonitionHeading_Gvgb"><span class="admonitionIcon_Rf37"><svg viewBox="0 0 14 16"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"></path></svg></span>info</div><div class="admonitionContent_BuS1"><p>The vial holder of the v1.1 now comes in two halves; a top vial holder and a bottom vial holder. Both have grooves to insert O-rings for a more secure hold on your vials and increased protection against leaks. The <span style="background-color:rgb(220, 84, 183);border-radius:2px;color:#fff;padding:0.2rem">thinner O-ring (#024)</span> fits into the top piece. The <span style="background-color:rgb(255, 144, 36);border-radius:2px;color:#fff;padding:0.2rem">thicker O-ring (#121)</span> lines the bottom piece.</p></div></div><ol>
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aria-expanded="false" href="/user-guide/create-cluster">Extending your Pioreactor</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Before you begin</h1></header><div id="step-1-upgrade-parts" style="padding:10px;margin:20px 0px 60px 0px;display:flex;flex-wrap:nowrap"><div id="mainImage" style="width:55%;float:left;margin-right:10px"><h2>Step 1: Upgrade parts<!-- -->  <a href="/user-guide/v11-upgrade-hardware-setup#step-1-upgrade-parts">#</a></h2><img maxheight="240" src="/assets/images/upgrade-parts-8bae6263090c0abcf781190f232a5c21.png"><div id="thumbnails" style="width:100%"><button class="highlightThumbnail_SKrZ"><img width="100px" src="/assets/images/upgrade-parts-8bae6263090c0abcf781190f232a5c21.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/old-pioreactor-0aead99ec34de067e3950e23b9a22ff4.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/screwdriver-d0fb9cfae69257e1df5d07450effbd1c.jpg"></button></div></div><section style="width:44%;float:left;margin-top:40px"><p>You will need:</p><ol>
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aria-expanded="false" href="/user-guide/create-cluster">Extending your Pioreactor</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Connecting the optics</h1></header><div id="step-1-insert-optic-cables-into-channels" style="padding:10px;margin:20px 0px 60px 0px;display:flex;flex-wrap:nowrap"><div id="mainImage" style="width:55%;float:left;margin-right:10px"><h2>Step 1: Insert optic cables into channels<!-- -->  <a href="/user-guide/v11-upgrade-optics-assembly#step-1-insert-optic-cables-into-channels">#</a></h2><img maxheight="240" src="/assets/images/led-and-pd-89131ca3d97ee8676cb0a22d6edcd422.jpg"><div id="thumbnails" style="width:100%"><button class="highlightThumbnail_SKrZ"><img width="100px" src="/assets/images/led-and-pd-89131ca3d97ee8676cb0a22d6edcd422.jpg"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/led-to-channel-a-c1a1684fe5903ea149a576194a0418d4.png"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/pds-to-channel-df758a9f28810fd33f0c2b3f9da7e913.png"></button></div></div><section style="width:44%;float:left;margin-top:40px"><ol>
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aria-expanded="false" href="/user-guide/create-cluster">Extending your Pioreactor</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" 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href="/user-guide/create-cluster">Extending your Pioreactor</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/intro-to-automations">Automations</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/accessing-raspberry-pi">Advanced</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/user-guide/error-codes">Troubleshooting</a></div></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-1 menu__list-item"><a class="menu__link" href="/user-guide/common-questions">Common questions</a></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col"><div class="docItemContainer_Djhp"><article><div class="theme-doc-markdown markdown"><header><h1>Wetware assembly</h1></header><div id="step-1-necessary-parts" style="padding:10px;margin:20px 0px 60px 0px;display:flex;flex-wrap:nowrap"><div id="mainImage" style="width:55%;float:left;margin-right:10px"><h2>Step 1: Necessary parts<!-- -->  <a href="/user-guide/wetware-assembly#step-1-necessary-parts">#</a></h2><img maxheight="240" src="/assets/images/square_nuts-48029c17ab44295d88d621b59ec986fb.jpg"><div id="thumbnails" style="width:100%"><button class="highlightThumbnail_SKrZ"><img width="100px" src="/assets/images/square_nuts-48029c17ab44295d88d621b59ec986fb.jpg"></button><button class="thumbnail_dvij"><img width="100px" src="/assets/images/heating_parts-c442edc62bce4898e0cbd9bf5e99d9fe.jpg"></button></div></div><section style="width:44%;float:left;margin-top:40px"><p>You will need:</p><ul>
diff --git a/user-guide/write-own-automations.html b/user-guide/write-own-automations.html
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