From 004c72573b9c836684c632f81e0c27fc369970b5 Mon Sep 17 00:00:00 2001 From: teresa-m Date: Mon, 27 Jan 2025 16:01:44 +0000 Subject: [PATCH 01/10] started GTA2025 event page --- events/2025-05-12-galaxy-academy-2025.md | 238 +++++++++++++++++++++++ 1 file changed, 238 insertions(+) create mode 100644 events/2025-05-12-galaxy-academy-2025.md diff --git a/events/2025-05-12-galaxy-academy-2025.md b/events/2025-05-12-galaxy-academy-2025.md new file mode 100644 index 00000000000000..60c826f97935ad --- /dev/null +++ b/events/2025-05-12-galaxy-academy-2025.md @@ -0,0 +1,238 @@ +--- +layout: event + +title: Galaxy Training Academy 2025 +description: | + The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day. + + + +cover-image: events/images/galaxy-academy-logo.png +cover-image-alt: logo for the Galaxy Academy event consisting of a laptop surrounded by illustrations of DNA molecules + +registration: + # link: + deadline: 2025-05-08 + open: false + +date_start: 2025-05-12 +date_end: 2025-05-16 + +cost: free +audience: Everyone who would like to get to know Galaxy and learn bioinformatics data analysis, whether you want to master a specific analysis or learn a new skill. +contact_email: academy@galaxyproject.org + +async: true +mode: online + +tags: +- microbiome +- single-cell +- proteomics +- introduction +- galaxy-interface +- assembly +- statistics + +contributions: + organisers: + - teresa-m + - natalie-wa + - annasyme + - delphine-l + - shiltemann + - dianichj + - dadrasarmin + instructors: + - ahmedhamidawan + - erxleben + - annasyme + - anuprulez + - abretaud + - bebatut + - bgruening + - clsiguret + - dannon + - dianichj + - deeptivarshney + - delphine-l + - elichad + - EngyNasr + - emmaustin20 + - GarethPrice-Aus + - igormakunin + - jdavcs + - lldelisle + - bernt-matthias + - foellmelanie + - meltemktn + - mschatz + - natalie-wa + - natefoo + - paulzierep + - pavanvidem + - plushz + - pratikdjagtap + - RZ9082 + - rlibouba + - SaimMomin12 + - stephanierobin + - subinamehta + - teresa-m + - timothygriffin + - tcollins2011 + - nomadscientist + - wm75 + funding: + - eurosciencegateway + - biont + - nfdi4plants + - deNBI + - by-covid + - elixir-europe + - mwk + - abromics + - ifb + + +location: + name: online + +infrastructure: + tiaas: true + servers: + - server: https://usegalaxy.eu + name: Galaxy EU + # tiaas_link: + - server: https://usegalaxy.org + name: Galaxy Main + - server: https://usegalaxy.org.au/ + name: Galaxy AU + + support: + platform: Slack + + +program: + - section: "Monday: Introduction" + description: You will start the the week onl your own time by watching videos and/or following the text-based tutorials provided in the program below. There are no live sessions, so you can determine your own schedule. A large team of instructors is available on Slack to answer your questions 24/7! Enjoy! + + + - section: "Galaxy introduction" + subsection: true + description: | + Kick off the week with a hands-on introduction to Galaxy, covering everything from basic navigation and data manipulation to reproducing published analyses, quality control, and mapping sequences to a reference genome. Whether you're new to Galaxy or looking to strengthen your skills, today's sessions will equip you with the foundational knowledge needed for more advanced topics. +# In the morning you can take part in the Icebreaker by joining us in the [Slack introduction channel](https://gtnsmrgsbord.slack.com/archives/C07NKAJ8THA). Or you can directly start with the tutorials. + +# **Need help with these tutorials?** Ask your questions via the [Slack introduction channel](https://gtnsmrgsbord.slack.com/archives/C07NKAJ8THA). + - section: Start to get to know Galaxy + subsection: true + tutorials: + - name: galaxy-intro-101 + topic: introduction + - name: history + topic: galaxy-interface + - name: collections + topic: galaxy-interface + - name: data-manipulation-olympics + topic: introduction + - name: galaxy-intro-ngs-data-managment + topic: introduction + - section: Quick start or fresh up your Galaxy knowledge + subsection: true + tutorials: + - name: galaxy-intro-short + topic: introduction + - section: "Fundamentals of Sequences analysis" + subsection: true + tutorials: + - name: quality-control + topic: sequence-analysis + - name: mapping + topic: sequence-analysis + + #- section: "Tuesday to Thursday: Choose your own Adventure!" + # tutorials: + # - type: custom + # name: Daily Icebreakers + # description: | + # **Tuesday:** For today's ice breaker, we would love to know one weird fact #that you know for no reason. + # **Wednesday:** We would love to hear where you find inspiration. Maybe you find inspirtaiton through nature or maybe you have a prominant role model in your life—we'd love to learn more about you! + # **Thursday:** if you could take any one movie prop from a movie set, what would it be? + + # Post your answers each day to Slack [#social](https://gtnsmrgsbord.slack.com/channels/social) channel. + + + - section: "Tuesday to Thursday: Pick a track" + subsection: true + description: | + Over the course of these three days, you can choose your preferred track and learn how to use Galaxy for data analysis in this research field. If you find multiple topics interesting, feel free to explore more than one track. Each track will guide you through the process, from basic to more advanced analyses, to accommodate learners of all levels. + + For assistance, you can access support through the Slack channel associated with each track module. Please note that while we strive to accommodate all time zones, responses to specific questions may take a bit longer depending on the availability of experts in your time zone. + tracks: # instead of tutorials, you can also define tracks, this will create a button per tracks that will lead to a different page + - title: Proteomics + link: events/tracks/gta2024-proteomics.md + #- title: Assembly + # link: events/tracks/gta2024-assembly.md + - title: Transcriptomics + link: events/tracks/gta2024-transcriptomics.md + - title: Single Cell + link: events/tracks/gta2024-single-cell.md + - title: Microbiome + link: events/tracks/gta2024-microbiome.md + #- title: Bacterial Genomics + # link: events/tracks/gta2024-bacterial-genomics.md + #- title: BY-COVID + # link: events/tracks/gta2024-bycovid.md + - title: Machine Learning + link: events/tracks/gta2024-ml.md + + - section: "Friday: Grab bag" + description: | + Can't get enough? Then please pick one of our FAIR tutorials below, or any of the tutorials of within one of the tracks. The trainers present on Slack will do their best to help you if you have a problem and answer questions, but they may not be expert in the topic you selected. + You can directly start with you prefered tutorial. + +#**Need help with these tutorials?** Ask your questions via the Slack Channel [#gta_friday-grab-bag](https://gtnsmrgsbord.slack.com/archives/C07N2A4HQ15). + - section: Fair training + subsection: true + tutorials: + - type: custom + name: Daily Icebreaker + description: | + **For the last ice breaker, we would love to know what the most interesting or exciting thing you learned this week is!!** + + Post your answer on Slack [#social](https://gtnsmrgsbord.slack.com/channels/social) channel + - type: custom + name: "[An overview of the RO-Crate concept and its implementations](https://gallantries.github.io/video-library/videos/ro-crates/intro/slides/)" + description: | + [ Lecture Video](https://gallantries.github.io/video-library/videos/ro-crates/intro/slides/) + - name: ro-crate-intro + topic: fair + - type: custom + name: "[Registering Galaxy workflows in WorkflowHub](https://gallantries.github.io/video-library/videos/ro-crates/workflowhub/tutorial/)" + description: | + [ Lecture Video](https://gallantries.github.io/video-library/videos/ro-crates/workflowhub/tutorial/) + - name: ro-crate-galaxy-best-practices + topic: fair + + +--- +# Welcome to the Galaxy Training Academy +Do you want to learn how to use Galaxy, a open source data analysis platform? Then you are at the right place. We offer here a **5-day Global Online and Asynchronous learning event**. + +**We will open registrations on the 3rd of March** + +## Do you want to join the GTA as an trainer? +Please fill our [form](https://docs.google.com/forms/d/e/1FAIpQLSf_DVEdf7n9MWJe7XLa3UTPGMNE9y-F8S-EHXRrZ-twNETYrg/viewform?usp=sf_link) to indicate in what capacity you would like to help. + +## Further information about the event +We provide you with training materials which you can study at your own pace and on your own time throughout the week. Don't worry, asynchronous does not mean that you are alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat** . + + +On the first day you can make yourself familiar with the Galaxy platform. In the next days you can follow different tracks, please go to the program tab for more information. + +You can set your own pace on your learning journey using our provided self-learning materials. Next to the program, you will find Slack channels you can join to exchange with the trainers and other participants during the event. Here you will also find help if you have qustions or run into an issue during the training. We try to cover all time zones with helpers for each topic, but please be patient if you do not get an immediat response. + +You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the setup tab. + +# **Certificates:** You can earn a certificate for the tracks you attended by answering a short questionnaire to verify your participation. From 5f5c59fc68da7078f34473a4e265cb34abfb61e5 Mon Sep 17 00:00:00 2001 From: teresa-m Date: Mon, 27 Jan 2025 17:32:39 +0000 Subject: [PATCH 02/10] added the first tracks without content to the program --- events/2025-05-12-galaxy-academy-2025.md | 14 +++++++------- events/tracks/gta2025-microbiome.md | 19 +++++++++++++++++++ events/tracks/gta2025-ml.md | 20 ++++++++++++++++++++ events/tracks/gta2025-proteomics.md | 20 ++++++++++++++++++++ events/tracks/gta2025-single-cell.md | 19 +++++++++++++++++++ events/tracks/gta2025-transcriptomics.md | 17 +++++++++++++++++ 6 files changed, 102 insertions(+), 7 deletions(-) create mode 100644 events/tracks/gta2025-microbiome.md create mode 100644 events/tracks/gta2025-ml.md create mode 100644 events/tracks/gta2025-proteomics.md create mode 100644 events/tracks/gta2025-single-cell.md create mode 100644 events/tracks/gta2025-transcriptomics.md diff --git a/events/2025-05-12-galaxy-academy-2025.md b/events/2025-05-12-galaxy-academy-2025.md index 60c826f97935ad..8f92806cc94df3 100644 --- a/events/2025-05-12-galaxy-academy-2025.md +++ b/events/2025-05-12-galaxy-academy-2025.md @@ -171,21 +171,21 @@ program: For assistance, you can access support through the Slack channel associated with each track module. Please note that while we strive to accommodate all time zones, responses to specific questions may take a bit longer depending on the availability of experts in your time zone. tracks: # instead of tutorials, you can also define tracks, this will create a button per tracks that will lead to a different page - title: Proteomics - link: events/tracks/gta2024-proteomics.md + link: events/tracks/gta2025-proteomics.md #- title: Assembly # link: events/tracks/gta2024-assembly.md - title: Transcriptomics - link: events/tracks/gta2024-transcriptomics.md + link: events/tracks/gta2025-transcriptomics.md - title: Single Cell - link: events/tracks/gta2024-single-cell.md + link: events/tracks/gta2025-single-cell.md - title: Microbiome - link: events/tracks/gta2024-microbiome.md + link: events/tracks/gta2025-microbiome.md #- title: Bacterial Genomics # link: events/tracks/gta2024-bacterial-genomics.md #- title: BY-COVID # link: events/tracks/gta2024-bycovid.md - title: Machine Learning - link: events/tracks/gta2024-ml.md + link: events/tracks/gta2025-ml.md - section: "Friday: Grab bag" description: | @@ -222,7 +222,7 @@ Do you want to learn how to use Galaxy, a open source data analysis platform? Th **We will open registrations on the 3rd of March** -## Do you want to join the GTA as an trainer? +## Do you want to join the GTA as a trainer? Please fill our [form](https://docs.google.com/forms/d/e/1FAIpQLSf_DVEdf7n9MWJe7XLa3UTPGMNE9y-F8S-EHXRrZ-twNETYrg/viewform?usp=sf_link) to indicate in what capacity you would like to help. ## Further information about the event @@ -235,4 +235,4 @@ You can set your own pace on your learning journey using our provided self-learn You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the setup tab. -# **Certificates:** You can earn a certificate for the tracks you attended by answering a short questionnaire to verify your participation. +**Certificates:** You will be able to obtain a certificates by the end to the event. more information are coming soon. \ No newline at end of file diff --git a/events/tracks/gta2025-microbiome.md b/events/tracks/gta2025-microbiome.md new file mode 100644 index 00000000000000..5f2bb47b17460a --- /dev/null +++ b/events/tracks/gta2025-microbiome.md @@ -0,0 +1,19 @@ +--- +layout: event-track + +title: Microbiome analysis +description: This track explains the capability to analyze microbiome data using Galaxy, covering essential tasks such as amplicon analysis and its visualization. It progresses to more advanced topics, including assembly and binning - the requirements for reconstructing Metagenome-Assembled Genomes (MAGs) from microbiome samples, and finally extends to complex analyses like metatranscriptome studies and pathogen detection. Start with the tutorial at your own pace. + +contributions: + organisers: + - paulzierep + - bebatut + + + +program: + - section: "Microbiome program" + description: | + Further information coming soon! + +--- diff --git a/events/tracks/gta2025-ml.md b/events/tracks/gta2025-ml.md new file mode 100644 index 00000000000000..8e0d5dbac9a2e8 --- /dev/null +++ b/events/tracks/gta2025-ml.md @@ -0,0 +1,20 @@ +--- +layout: event-track + +title: Machine Learning +description: This module will introduce you to the world of machine learning using Galaxy. Start with the tutorial at your own pace. + +contributions: + organisers: + - anuprulez + + + +program: + - section: "Machine Learning program" + description: | + Further information coming soon + + + +--- diff --git a/events/tracks/gta2025-proteomics.md b/events/tracks/gta2025-proteomics.md new file mode 100644 index 00000000000000..045a36c45b9b92 --- /dev/null +++ b/events/tracks/gta2025-proteomics.md @@ -0,0 +1,20 @@ +--- +layout: event-track + +title: Proteomics +description: Learn all about proteomics and how to analyze data in Galaxy. Start with the tutorial at your own pace. + +contributions: + organisers: + - pratikdjagtap + - foellmelanie + + + + +program: + - section: "Proteomics program" + description: | + Further information coming soon. + +--- diff --git a/events/tracks/gta2025-single-cell.md b/events/tracks/gta2025-single-cell.md new file mode 100644 index 00000000000000..62d2263810830e --- /dev/null +++ b/events/tracks/gta2025-single-cell.md @@ -0,0 +1,19 @@ +--- +layout: event-track + +title: Single Cell +description: Learn all about Sigle Cell on Galaxy. Start with the tutorial at your own pace. + +contributions: + organisers: + - pavanvidem + - nomadscientist + + + +program: + - section: "Single Cell program" + description: | + Further information coming soon. + +--- diff --git a/events/tracks/gta2025-transcriptomics.md b/events/tracks/gta2025-transcriptomics.md new file mode 100644 index 00000000000000..ba1290777aa8ae --- /dev/null +++ b/events/tracks/gta2025-transcriptomics.md @@ -0,0 +1,17 @@ +--- +layout: event-track + +title: Transcriptomics +description: Welcome to the transcriptomics track. Here you can learn how to map the raw RNA-seq sequencing data to a reference, preform an differential expression analysis, GO analysis. Further you can learn how to plot your processed data. Additionally you can also learn how to perform a differential Isofrom expression analysis, as well as how to annotate lncRNAs. If you want to learn more in the field of transciptomics please also have a look at the single cell track. Start with the tutorial at your own pace. + +contributions: + organisers: + - teresa-m + + + +program: + - section: "Transcriptomics program" + description: | + Further information coming soon +--- From c866989b4a5f3c5cfcbd9ffe39daa306e441dd6c Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Mon, 27 Jan 2025 12:43:07 -0500 Subject: [PATCH 03/10] Replace link to trainer application form --- events/2025-05-12-galaxy-academy-2025.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/events/2025-05-12-galaxy-academy-2025.md b/events/2025-05-12-galaxy-academy-2025.md index 8f92806cc94df3..49bf81bfb4f7ec 100644 --- a/events/2025-05-12-galaxy-academy-2025.md +++ b/events/2025-05-12-galaxy-academy-2025.md @@ -223,7 +223,7 @@ Do you want to learn how to use Galaxy, a open source data analysis platform? Th **We will open registrations on the 3rd of March** ## Do you want to join the GTA as a trainer? -Please fill our [form](https://docs.google.com/forms/d/e/1FAIpQLSf_DVEdf7n9MWJe7XLa3UTPGMNE9y-F8S-EHXRrZ-twNETYrg/viewform?usp=sf_link) to indicate in what capacity you would like to help. +Please fill our [form](https://forms.gle/V9QqSDNg2UmQaDHy8) to indicate in what capacity you would like to help. ## Further information about the event We provide you with training materials which you can study at your own pace and on your own time throughout the week. Don't worry, asynchronous does not mean that you are alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat** . @@ -235,4 +235,4 @@ You can set your own pace on your learning journey using our provided self-learn You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the setup tab. -**Certificates:** You will be able to obtain a certificates by the end to the event. more information are coming soon. \ No newline at end of file +**Certificates:** You will be able to obtain a certificates by the end to the event. more information are coming soon. From 00083cf9fd9263268e2b451cbc5e9ab59ef4339e Mon Sep 17 00:00:00 2001 From: teresa-m Date: Tue, 28 Jan 2025 16:42:25 +0000 Subject: [PATCH 04/10] updates main page --- events/2025-05-12-galaxy-academy-2025.md | 45 ++++++++++++++---------- 1 file changed, 26 insertions(+), 19 deletions(-) diff --git a/events/2025-05-12-galaxy-academy-2025.md b/events/2025-05-12-galaxy-academy-2025.md index 49bf81bfb4f7ec..2ee722b4725d09 100644 --- a/events/2025-05-12-galaxy-academy-2025.md +++ b/events/2025-05-12-galaxy-academy-2025.md @@ -3,9 +3,9 @@ layout: event title: Galaxy Training Academy 2025 description: | - The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day. + The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we offer a diverse selection of learning track for you. - +# cover-image: events/images/galaxy-academy-logo.png cover-image-alt: logo for the Galaxy Academy event consisting of a laptop surrounded by illustrations of DNA molecules @@ -36,10 +36,10 @@ tags: contributions: organisers: + - delphine-l - teresa-m - natalie-wa - annasyme - - delphine-l - shiltemann - dianichj - dadrasarmin @@ -88,7 +88,6 @@ contributions: - biont - nfdi4plants - deNBI - - by-covid - elixir-europe - mwk - abromics @@ -115,7 +114,7 @@ infrastructure: program: - section: "Monday: Introduction" - description: You will start the the week onl your own time by watching videos and/or following the text-based tutorials provided in the program below. There are no live sessions, so you can determine your own schedule. A large team of instructors is available on Slack to answer your questions 24/7! Enjoy! + description: You will start the the week on your own time by watching videos and/or following the text-based tutorials provided in the program below. There are no live sessions, so you can determine your own schedule. A large team of instructors is available on Slack to answer your questions 24/7! Enjoy! - section: "Galaxy introduction" @@ -168,7 +167,7 @@ program: description: | Over the course of these three days, you can choose your preferred track and learn how to use Galaxy for data analysis in this research field. If you find multiple topics interesting, feel free to explore more than one track. Each track will guide you through the process, from basic to more advanced analyses, to accommodate learners of all levels. - For assistance, you can access support through the Slack channel associated with each track module. Please note that while we strive to accommodate all time zones, responses to specific questions may take a bit longer depending on the availability of experts in your time zone. +# For assistance, you can access support through the Slack channel associated with each track module. Please note that while we strive to accommodate all time zones, responses to specific questions may take a bit longer depending on the availability of experts in your time zone. tracks: # instead of tutorials, you can also define tracks, this will create a button per tracks that will lead to a different page - title: Proteomics link: events/tracks/gta2025-proteomics.md @@ -196,12 +195,12 @@ program: - section: Fair training subsection: true tutorials: - - type: custom - name: Daily Icebreaker - description: | - **For the last ice breaker, we would love to know what the most interesting or exciting thing you learned this week is!!** + #- type: custom + # name: Daily Icebreaker + # description: | + # **For the last ice breaker, we would love to know what the most interesting or exciting thing you learned this week is!!** - Post your answer on Slack [#social](https://gtnsmrgsbord.slack.com/channels/social) channel + # Post your answer on Slack [#social](https://gtnsmrgsbord.slack.com/channels/social) channel - type: custom name: "[An overview of the RO-Crate concept and its implementations](https://gallantries.github.io/video-library/videos/ro-crates/intro/slides/)" description: | @@ -217,22 +216,30 @@ program: --- -# Welcome to the Galaxy Training Academy +# Welcome to the Galaxy Training Academy 2025 Do you want to learn how to use Galaxy, a open source data analysis platform? Then you are at the right place. We offer here a **5-day Global Online and Asynchronous learning event**. -**We will open registrations on the 3rd of March** +**We will open registrations on the 3rd of March.** ## Do you want to join the GTA as a trainer? Please fill our [form](https://forms.gle/V9QqSDNg2UmQaDHy8) to indicate in what capacity you would like to help. -## Further information about the event -We provide you with training materials which you can study at your own pace and on your own time throughout the week. Don't worry, asynchronous does not mean that you are alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat** . +## How will the event be run +The event is asynchronous which means you can set your own pace on your learning journey using our provided self-learning materials. You will start the event by your self at your own time. Don't worry, asynchronous does not mean that you are alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat**. +**How to participate** +First you will need to register. **We will open registrations on the 3rd of March.** +You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the setup tab. -On the first day you can make yourself familiar with the Galaxy platform. In the next days you can follow different tracks, please go to the program tab for more information. +**Content of the event** +We provide you with training materials which you can study at your own pace and on your own time throughout the week. Have a look at our [program](https://training.galaxyproject.org/training-material/). The program is still **under development**. -You can set your own pace on your learning journey using our provided self-learning materials. Next to the program, you will find Slack channels you can join to exchange with the trainers and other participants during the event. Here you will also find help if you have qustions or run into an issue during the training. We try to cover all time zones with helpers for each topic, but please be patient if you do not get an immediat response. +On the first day you can make yourself familiar with the Galaxy platform. In the next days you can follow different tracks, please go to the program tab for more information. On Friday we offer a ***Fair training*** program to you. -You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the setup tab. +**How to get help** +You will not be alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat**. Next to the program, you will find Slack channels you can join to exchange with the trainers and other participants during the event. Here you will also find help if you have questions or run into an issue during the training. We try to cover all time zones with helpers for each topic, but please be patient if you do not get an immediate response. + + +**Certificates** -**Certificates:** You will be able to obtain a certificates by the end to the event. more information are coming soon. +You will be able to obtain a certificates by the end to the event. more information are coming soon. From 60de4eb800dc33adeb639b8fabadb442ea533c71 Mon Sep 17 00:00:00 2001 From: teresa-m Date: Wed, 29 Jan 2025 10:30:21 +0000 Subject: [PATCH 05/10] added scott to the event page --- CONTRIBUTORS.yaml | 3 +++ events/2025-05-12-galaxy-academy-2025.md | 4 ++++ 2 files changed, 7 insertions(+) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 45bc23166faadc..3394e66afe4cc1 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -2316,6 +2316,9 @@ sbenateau: affiliations: - elixir-europe +scottcain: + name: Scott Cain + joined: 2025-01 sebastian-schaaf: name: Sebastian Schaaf diff --git a/events/2025-05-12-galaxy-academy-2025.md b/events/2025-05-12-galaxy-academy-2025.md index 2ee722b4725d09..1ce11fec5a5fbe 100644 --- a/events/2025-05-12-galaxy-academy-2025.md +++ b/events/2025-05-12-galaxy-academy-2025.md @@ -38,6 +38,7 @@ contributions: organisers: - delphine-l - teresa-m + - scottcain - natalie-wa - annasyme - shiltemann @@ -228,15 +229,18 @@ Please fill our [form](https://forms.gle/V9QqSDNg2UmQaDHy8) to indicate in what The event is asynchronous which means you can set your own pace on your learning journey using our provided self-learning materials. You will start the event by your self at your own time. Don't worry, asynchronous does not mean that you are alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat**. **How to participate** + First you will need to register. **We will open registrations on the 3rd of March.** You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the setup tab. **Content of the event** + We provide you with training materials which you can study at your own pace and on your own time throughout the week. Have a look at our [program](https://training.galaxyproject.org/training-material/). The program is still **under development**. On the first day you can make yourself familiar with the Galaxy platform. In the next days you can follow different tracks, please go to the program tab for more information. On Friday we offer a ***Fair training*** program to you. **How to get help** + You will not be alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat**. Next to the program, you will find Slack channels you can join to exchange with the trainers and other participants during the event. Here you will also find help if you have questions or run into an issue during the training. We try to cover all time zones with helpers for each topic, but please be patient if you do not get an immediate response. From 468cd4522e49174dd316860a6a4a5ec106fd3f76 Mon Sep 17 00:00:00 2001 From: teresa-m Date: Mon, 3 Feb 2025 17:34:46 +0000 Subject: [PATCH 06/10] added link to track programs of 2024 --- events/2025-05-12-galaxy-academy-2025.md | 22 +++++++++++++++------- events/tracks/gta2025-microbiome.md | 2 +- events/tracks/gta2025-ml.md | 2 +- events/tracks/gta2025-proteomics.md | 2 +- events/tracks/gta2025-single-cell.md | 4 +++- events/tracks/gta2025-transcriptomics.md | 4 +++- 6 files changed, 24 insertions(+), 12 deletions(-) diff --git a/events/2025-05-12-galaxy-academy-2025.md b/events/2025-05-12-galaxy-academy-2025.md index 1ce11fec5a5fbe..ec01376d724764 100644 --- a/events/2025-05-12-galaxy-academy-2025.md +++ b/events/2025-05-12-galaxy-academy-2025.md @@ -3,7 +3,7 @@ layout: event title: Galaxy Training Academy 2025 description: | - The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we offer a diverse selection of learning track for you. + The Galaxy Training Academy is a self-paced online training event for beginners as well as advanced learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we offer a diverse selection of learning track for you. # @@ -220,24 +220,32 @@ program: # Welcome to the Galaxy Training Academy 2025 Do you want to learn how to use Galaxy, a open source data analysis platform? Then you are at the right place. We offer here a **5-day Global Online and Asynchronous learning event**. -**We will open registrations on the 3rd of March.** +**Registrations will open on the 3rd of March.** ## Do you want to join the GTA as a trainer? Please fill our [form](https://forms.gle/V9QqSDNg2UmQaDHy8) to indicate in what capacity you would like to help. -## How will the event be run +## Do you want to participate as a learner? +In the following you will learn everything you need to know about the event. + +**Course format** + The event is asynchronous which means you can set your own pace on your learning journey using our provided self-learning materials. You will start the event by your self at your own time. Don't worry, asynchronous does not mean that you are alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat**. **How to participate** First you will need to register. **We will open registrations on the 3rd of March.** -You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the setup tab. +You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the [setup page](https://training.galaxyproject.org/training-material/events/2025-05-12-galaxy-academy-2025.html#setup). + + **Content of the event** -We provide you with training materials which you can study at your own pace and on your own time throughout the week. Have a look at our [program](https://training.galaxyproject.org/training-material/). The program is still **under development**. +We provide you with training materials which you can study at your own pace and on your own time throughout the week. Have a look at our [program](https://training.galaxyproject.org/training-material/events/2025-05-12-galaxy-academy-2025.html#program). The program is still **under development**. + + -On the first day you can make yourself familiar with the Galaxy platform. In the next days you can follow different tracks, please go to the program tab for more information. On Friday we offer a ***Fair training*** program to you. +On the first day you can make yourself familiar with the Galaxy platform. In the next days you can follow different tracks. Please go to the program tab for more information. On Friday we offer a ***Fair training*** program to you. **How to get help** @@ -246,4 +254,4 @@ You will not be alone! If you ever need help, you can contact one of our many tr **Certificates** -You will be able to obtain a certificates by the end to the event. more information are coming soon. +You will be able to obtain a certificates by the end to the event. More information are coming soon. diff --git a/events/tracks/gta2025-microbiome.md b/events/tracks/gta2025-microbiome.md index 5f2bb47b17460a..a68379d1542d1d 100644 --- a/events/tracks/gta2025-microbiome.md +++ b/events/tracks/gta2025-microbiome.md @@ -2,7 +2,7 @@ layout: event-track title: Microbiome analysis -description: This track explains the capability to analyze microbiome data using Galaxy, covering essential tasks such as amplicon analysis and its visualization. It progresses to more advanced topics, including assembly and binning - the requirements for reconstructing Metagenome-Assembled Genomes (MAGs) from microbiome samples, and finally extends to complex analyses like metatranscriptome studies and pathogen detection. Start with the tutorial at your own pace. +description: This track explains the capability to analyze microbiome data using Galaxy, covering essential tasks such as amplicon analysis and its visualization. It progresses to more advanced topics, including assembly and binning - the requirements for reconstructing Metagenome-Assembled Genomes (MAGs) from microbiome samples, and finally extends to complex analyses like metatranscriptome studies and pathogen detection. Start with the tutorial at your own pace. You can have a look at the program of the [GTA's 2024 Microbiome track](https://training.galaxyproject.org/training-material/events/tracks/gta2024-microbiome.html). contributions: organisers: diff --git a/events/tracks/gta2025-ml.md b/events/tracks/gta2025-ml.md index 8e0d5dbac9a2e8..f2687aedaba189 100644 --- a/events/tracks/gta2025-ml.md +++ b/events/tracks/gta2025-ml.md @@ -2,7 +2,7 @@ layout: event-track title: Machine Learning -description: This module will introduce you to the world of machine learning using Galaxy. Start with the tutorial at your own pace. +description: This module will introduce you to the world of machine learning using Galaxy. Start with the tutorial at your own pace. You can have a look at the program of the [GTA's 2024 Machine Learning track](https://training.galaxyproject.org/training-material/events/tracks/gta2024-ml.html). contributions: organisers: diff --git a/events/tracks/gta2025-proteomics.md b/events/tracks/gta2025-proteomics.md index 045a36c45b9b92..4002f887a0df3b 100644 --- a/events/tracks/gta2025-proteomics.md +++ b/events/tracks/gta2025-proteomics.md @@ -2,7 +2,7 @@ layout: event-track title: Proteomics -description: Learn all about proteomics and how to analyze data in Galaxy. Start with the tutorial at your own pace. +description: Learn all about proteomics and how to analyze data in Galaxy. Start with the tutorial at your own pace. You can have a look at the program of the [GTA's 2024 Proteomics track](https://training.galaxyproject.org/training-material/events/tracks/gta2024-proteomics.html). contributions: organisers: diff --git a/events/tracks/gta2025-single-cell.md b/events/tracks/gta2025-single-cell.md index 62d2263810830e..1574e8992163da 100644 --- a/events/tracks/gta2025-single-cell.md +++ b/events/tracks/gta2025-single-cell.md @@ -2,7 +2,9 @@ layout: event-track title: Single Cell -description: Learn all about Sigle Cell on Galaxy. Start with the tutorial at your own pace. +description: Learn all about Single Cell on Galaxy. Start with the tutorial at your own pace. You can have a look at the program of the [GTA's 2024 Single Cell track](https://training.galaxyproject.org/training-material/events/tracks/gta2024-single-cell.html). + + contributions: organisers: diff --git a/events/tracks/gta2025-transcriptomics.md b/events/tracks/gta2025-transcriptomics.md index ba1290777aa8ae..8d03154c25418e 100644 --- a/events/tracks/gta2025-transcriptomics.md +++ b/events/tracks/gta2025-transcriptomics.md @@ -2,7 +2,9 @@ layout: event-track title: Transcriptomics -description: Welcome to the transcriptomics track. Here you can learn how to map the raw RNA-seq sequencing data to a reference, preform an differential expression analysis, GO analysis. Further you can learn how to plot your processed data. Additionally you can also learn how to perform a differential Isofrom expression analysis, as well as how to annotate lncRNAs. If you want to learn more in the field of transciptomics please also have a look at the single cell track. Start with the tutorial at your own pace. +description: Welcome to the transcriptomics track. Here you can learn how to map the raw RNA-seq sequencing data to a reference, preform an differential expression analysis, GO analysis. Further you can learn how to plot your processed data. Additionally you can also learn how to perform a differential Isofrom expression analysis, as well as how to annotate lncRNAs. If you want to learn more in the field of transciptomics please also have a look at the single cell track. Start with the tutorial at your own pace. You can have a look at the program of the [GTA's 2024 transcriptomics track](https://training.galaxyproject.org/training-material/events/tracks/gta2024-transcriptomics.html). + + contributions: organisers: From f4b92a139326d8d0db005674f96d93e5d5d01360 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 10 Feb 2025 14:11:31 +0100 Subject: [PATCH 07/10] Update 2025-05-12-galaxy-academy-2025.md --- events/2025-05-12-galaxy-academy-2025.md | 44 ++++++++++++------------ 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/events/2025-05-12-galaxy-academy-2025.md b/events/2025-05-12-galaxy-academy-2025.md index ec01376d724764..5fc81161a1462f 100644 --- a/events/2025-05-12-galaxy-academy-2025.md +++ b/events/2025-05-12-galaxy-academy-2025.md @@ -3,7 +3,8 @@ layout: event title: Galaxy Training Academy 2025 description: | - The Galaxy Training Academy is a self-paced online training event for beginners as well as advanced learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we offer a diverse selection of learning track for you. + The Galaxy Training Academy is a self-paced online training event for beginners and advanced learners who want to improve their Galaxy data analysis skills. + Over the course of one week, we offer a diverse selection of learning track for you. # @@ -94,7 +95,6 @@ contributions: - abromics - ifb - location: name: online @@ -108,15 +108,14 @@ infrastructure: name: Galaxy Main - server: https://usegalaxy.org.au/ name: Galaxy AU - support: platform: Slack - program: - section: "Monday: Introduction" - description: You will start the the week on your own time by watching videos and/or following the text-based tutorials provided in the program below. There are no live sessions, so you can determine your own schedule. A large team of instructors is available on Slack to answer your questions 24/7! Enjoy! - + description: | + You will start the week on your local time by watching videos and/or following the text-based tutorials in the program below. There are no live sessions, so you can determine your schedule. + A large team of instructors is available on Slack to answer your questions 24/7! Enjoy! - section: "Galaxy introduction" subsection: true @@ -156,20 +155,19 @@ program: # - type: custom # name: Daily Icebreakers # description: | - # **Tuesday:** For today's ice breaker, we would love to know one weird fact #that you know for no reason. - # **Wednesday:** We would love to hear where you find inspiration. Maybe you find inspirtaiton through nature or maybe you have a prominant role model in your life—we'd love to learn more about you! - # **Thursday:** if you could take any one movie prop from a movie set, what would it be? + # **Tuesday:** For today's icebreaker, we would love to know one weird fact #that you know for no reason. + # **Wednesday:** We would love to hear where you find inspiration. Maybe you find inspiration through nature or maybe you have a prominent role model in your life—we'd love to learn more about you! + # **Thursday:** If you could take any one movie prop from a movie set, what would it be? # Post your answers each day to Slack [#social](https://gtnsmrgsbord.slack.com/channels/social) channel. - - section: "Tuesday to Thursday: Pick a track" subsection: true description: | Over the course of these three days, you can choose your preferred track and learn how to use Galaxy for data analysis in this research field. If you find multiple topics interesting, feel free to explore more than one track. Each track will guide you through the process, from basic to more advanced analyses, to accommodate learners of all levels. # For assistance, you can access support through the Slack channel associated with each track module. Please note that while we strive to accommodate all time zones, responses to specific questions may take a bit longer depending on the availability of experts in your time zone. - tracks: # instead of tutorials, you can also define tracks, this will create a button per tracks that will lead to a different page + tracks: # Instead of tutorials, you can also define tracks, this will create a button per track that will lead to a different page - title: Proteomics link: events/tracks/gta2025-proteomics.md #- title: Assembly @@ -189,8 +187,9 @@ program: - section: "Friday: Grab bag" description: | - Can't get enough? Then please pick one of our FAIR tutorials below, or any of the tutorials of within one of the tracks. The trainers present on Slack will do their best to help you if you have a problem and answer questions, but they may not be expert in the topic you selected. - You can directly start with you prefered tutorial. + Can't get enough? Then please pick one of our FAIR tutorials below or any of the tutorials within one of the tracks. The trainers present on Slack will do their best to help you + if you have a problem and answer questions, but they may not be experts in the topic you selected. + You can directly start with your preferred tutorial. #**Need help with these tutorials?** Ask your questions via the Slack Channel [#gta_friday-grab-bag](https://gtnsmrgsbord.slack.com/archives/C07N2A4HQ15). - section: Fair training @@ -199,7 +198,7 @@ program: #- type: custom # name: Daily Icebreaker # description: | - # **For the last ice breaker, we would love to know what the most interesting or exciting thing you learned this week is!!** + # **For the last icebreaker, we would love to know what the most interesting or exciting thing you learned this week is!!** # Post your answer on Slack [#social](https://gtnsmrgsbord.slack.com/channels/social) channel - type: custom @@ -218,24 +217,25 @@ program: --- # Welcome to the Galaxy Training Academy 2025 -Do you want to learn how to use Galaxy, a open source data analysis platform? Then you are at the right place. We offer here a **5-day Global Online and Asynchronous learning event**. +Do you want to learn how to use Galaxy, an open source data analysis platform? Then you are at the right place. We offer here a **5-day Global Online and Asynchronous learning event**. **Registrations will open on the 3rd of March.** ## Do you want to join the GTA as a trainer? -Please fill our [form](https://forms.gle/V9QqSDNg2UmQaDHy8) to indicate in what capacity you would like to help. +Please fill out our [form](https://forms.gle/V9QqSDNg2UmQaDHy8) to indicate in what capacity you would like to help. ## Do you want to participate as a learner? -In the following you will learn everything you need to know about the event. +In the following, you will learn everything you need to know about the event. **Course format** -The event is asynchronous which means you can set your own pace on your learning journey using our provided self-learning materials. You will start the event by your self at your own time. Don't worry, asynchronous does not mean that you are alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat**. +The event is asynchronous which means you can set your own pace on your learning journey using our provided self-learning materials. You will start the event by yourself at your preferred time. +Don't worry, asynchronous does not mean that you are alone! If you ever need help, you can contact one of our many trainers worldwide via **Slack chat**. **How to participate** -First you will need to register. **We will open registrations on the 3rd of March.** -You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the [setup page](https://training.galaxyproject.org/training-material/events/2025-05-12-galaxy-academy-2025.html#setup). +First, you will need to register. **We will open registrations on the 3rd of March.** +You only need a browser and an account on one of the Galaxy instances registered for this event. Please have a look at the [setup page](https://training.galaxyproject.org/training-material/events/2025-05-12-galaxy-academy-2025.html#setup). @@ -245,7 +245,7 @@ We provide you with training materials which you can study at your own pace and -On the first day you can make yourself familiar with the Galaxy platform. In the next days you can follow different tracks. Please go to the program tab for more information. On Friday we offer a ***Fair training*** program to you. +On the first day, you can make yourself familiar with the Galaxy platform. In the next days, you can follow different tracks. Please go to the program tab for more information. On Friday we offer a ***Fair training*** program to you. **How to get help** @@ -254,4 +254,4 @@ You will not be alone! If you ever need help, you can contact one of our many tr **Certificates** -You will be able to obtain a certificates by the end to the event. More information are coming soon. +You will be able to obtain a certificate by the end of the event. More information is coming soon. From 7919849db208ebd949ba8bdd2e44046f839a10aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 10 Feb 2025 14:12:07 +0100 Subject: [PATCH 08/10] Apply suggestions from code review --- events/tracks/gta2025-microbiome.md | 3 --- events/tracks/gta2025-ml.md | 5 ----- events/tracks/gta2025-single-cell.md | 4 ---- events/tracks/gta2025-transcriptomics.md | 4 ---- 4 files changed, 16 deletions(-) diff --git a/events/tracks/gta2025-microbiome.md b/events/tracks/gta2025-microbiome.md index a68379d1542d1d..4778cb2394a413 100644 --- a/events/tracks/gta2025-microbiome.md +++ b/events/tracks/gta2025-microbiome.md @@ -8,9 +8,6 @@ contributions: organisers: - paulzierep - bebatut - - - program: - section: "Microbiome program" description: | diff --git a/events/tracks/gta2025-ml.md b/events/tracks/gta2025-ml.md index f2687aedaba189..9793be464e32ef 100644 --- a/events/tracks/gta2025-ml.md +++ b/events/tracks/gta2025-ml.md @@ -8,13 +8,8 @@ contributions: organisers: - anuprulez - - program: - section: "Machine Learning program" description: | Further information coming soon - - - --- diff --git a/events/tracks/gta2025-single-cell.md b/events/tracks/gta2025-single-cell.md index 1574e8992163da..8942741d353410 100644 --- a/events/tracks/gta2025-single-cell.md +++ b/events/tracks/gta2025-single-cell.md @@ -4,15 +4,11 @@ layout: event-track title: Single Cell description: Learn all about Single Cell on Galaxy. Start with the tutorial at your own pace. You can have a look at the program of the [GTA's 2024 Single Cell track](https://training.galaxyproject.org/training-material/events/tracks/gta2024-single-cell.html). - - contributions: organisers: - pavanvidem - nomadscientist - - program: - section: "Single Cell program" description: | diff --git a/events/tracks/gta2025-transcriptomics.md b/events/tracks/gta2025-transcriptomics.md index 8d03154c25418e..04e6af1e28eff4 100644 --- a/events/tracks/gta2025-transcriptomics.md +++ b/events/tracks/gta2025-transcriptomics.md @@ -4,14 +4,10 @@ layout: event-track title: Transcriptomics description: Welcome to the transcriptomics track. Here you can learn how to map the raw RNA-seq sequencing data to a reference, preform an differential expression analysis, GO analysis. Further you can learn how to plot your processed data. Additionally you can also learn how to perform a differential Isofrom expression analysis, as well as how to annotate lncRNAs. If you want to learn more in the field of transciptomics please also have a look at the single cell track. Start with the tutorial at your own pace. You can have a look at the program of the [GTA's 2024 transcriptomics track](https://training.galaxyproject.org/training-material/events/tracks/gta2024-transcriptomics.html). - - contributions: organisers: - teresa-m - - program: - section: "Transcriptomics program" description: | From 1152bf830d7606287f5e92b9e88b25606afd42dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 10 Feb 2025 14:12:51 +0100 Subject: [PATCH 09/10] Update gta2025-proteomics.md --- events/tracks/gta2025-proteomics.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/events/tracks/gta2025-proteomics.md b/events/tracks/gta2025-proteomics.md index 4002f887a0df3b..29e2eafe007600 100644 --- a/events/tracks/gta2025-proteomics.md +++ b/events/tracks/gta2025-proteomics.md @@ -9,12 +9,9 @@ contributions: - pratikdjagtap - foellmelanie - - - program: - section: "Proteomics program" description: | - Further information coming soon. + Further information is coming soon. --- From ef2748bf8a0a55907027b74175bb2cdc37e125e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 10 Feb 2025 20:25:51 +0100 Subject: [PATCH 10/10] set TIaaS false --- events/2025-05-12-galaxy-academy-2025.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/events/2025-05-12-galaxy-academy-2025.md b/events/2025-05-12-galaxy-academy-2025.md index 5fc81161a1462f..02ba4ae65dd1cc 100644 --- a/events/2025-05-12-galaxy-academy-2025.md +++ b/events/2025-05-12-galaxy-academy-2025.md @@ -99,7 +99,7 @@ location: name: online infrastructure: - tiaas: true + tiaas: false servers: - server: https://usegalaxy.eu name: Galaxy EU