Merge pull request #20 from FinalSpark-np/good_practices

elab api

Author: ValentineDelevaux

neuroplatform-docs/np_core/db_usage.ipynb

@@ -352,6 +352,164 @@
    "source": [
     "door_df = db.door(start, stop)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# --------------------------------"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Getting metadata about your experiment\n",
+    "\n",
+    "Some information about your experiments are available with the following commands. They can be useful understand and study your results, don't hesitate to use them! \n",
+    "\n",
+    "If you need more information about those data, contact us on Discord or by email."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from neuroplatform import elab\n",
+    "\n",
+    "# Create the object elab()\n",
+    "metadata = elab()\n",
+    "metadata.check_server()  # This should print : 'The server works !' if everything is fine!\n",
+    "\n",
+    "# Choose the experiment you want to study : here for example we use 'fs410'\n",
+    "fs_name = \"fs410\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "1- Get the starting date of your experiment (the date when the organoids were put on the MEA) :"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "starting_date = metadata.get_start_date(fs_name)\n",
+    "print(starting_date)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "2- Get the cell batch (the cell batch with which the organoids of your experiment were generated) :"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cell_batch = metadata.get_cell_batch(fs_name)\n",
+    "print(cell_batch)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "3- Get the medium (the medium that was used on the MEA to keep the organoids alive) :"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "medium = metadata.get_medium(fs_name)\n",
+    "print(medium)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "4- Get the MEA (the name of the MEA on which your experiment is happening) :"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mea = metadata.get_mea(fs_name)\n",
+    "print(mea)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "5- Get the pump (the type of pump, the flux and the flux unit) :"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pump = metadata.get_pump(fs_name)\n",
+    "print(pump)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "6- Get the protocols (this gives indications about which version of MEA is used for this experiment) :"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "protocols = metadata.get_protocols(fs_name)\n",
+    "print(protocols)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "7- Get the death date (the date when the organoids were removed from the MEA) :"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "death_date = metadata.get_death_date(fs_name)\n",
+    "print(death_date)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {