diff --git a/.idea/.gitignore b/.idea/.gitignore
deleted file mode 100644
index 73f69e095..000000000
--- a/.idea/.gitignore
+++ /dev/null
@@ -1,8 +0,0 @@
-# Default ignored files
-/shelf/
-/workspace.xml
-# Datasource local storage ignored files
-/dataSources/
-/dataSources.local.xml
-# Editor-based HTTP Client requests
-/httpRequests/
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
new file mode 100644
index 000000000..74459b697
--- /dev/null
+++ b/.idea/inspectionProfiles/Project_Default.xml
@@ -0,0 +1,13 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="PyUnresolvedReferencesInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ignoredIdentifiers">
+        <list>
+          <option value="src.cobra.cobra" />
+          <option value="src.cobra.test.test_flux_analysis.test_user_defined_constraints.*" />
+        </list>
+      </option>
+    </inspection_tool>
+  </profile>
+</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
index 35415829b..5d64c867e 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
-  <component name="JavaScriptSettings">
-    <option name="languageLevel" value="ES6" />
-  </component>
   <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.7 (cobrapy)" project-jdk-type="Python SDK" />
+  <component name="PyCharmProfessionalAdvertiser">
+    <option name="shown" value="true" />
+  </component>
 </project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
index 189f24ab6..c8e807676 100644
--- a/.idea/modules.xml
+++ b/.idea/modules.xml
@@ -2,7 +2,7 @@
 <project version="4">
   <component name="ProjectModuleManager">
     <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/cobrapy-hemnant.iml" filepath="$PROJECT_DIR$/.idea/cobrapy-hemnant.iml" />
+      <module fileurl="file://$PROJECT_DIR$/.idea/cobrapy.iml" filepath="$PROJECT_DIR$/.idea/cobrapy.iml" />
     </modules>
   </component>
 </project>
\ No newline at end of file
diff --git a/documentation_builder/metadata.ipynb b/documentation_builder/metadata.ipynb
index 44dc1d291..ccf282d14 100644
--- a/documentation_builder/metadata.ipynb
+++ b/documentation_builder/metadata.ipynb
@@ -1,108 +1,299 @@
 {
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Metadata\n",
-    "\n",
-    "Metadata in the form of annotations, provenance or additional key:value pairs is an important asset for a model.\n",
-    "Such data can be handled via the `annotation` field on cobra objects"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {
-    "collapsed": false,
-    "deletable": true,
-    "editable": true,
-    "pycharm": {
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [
-    {
-     "ename": "ValueError",
-     "evalue": "time data '2020-08-26T23:28:20' does not match format '%Y-%m-%dT%H:%M:%S%z'",
-     "output_type": "error",
-     "traceback": [
-      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
-      "\u001B[0;31mValueError\u001B[0m                                Traceback (most recent call last)",
-      "\u001B[0;32m~/git/cobrapy-hemnant/src/cobra/core/metadata/history.py\u001B[0m in \u001B[0;36mvalidate_datetime\u001B[0;34m(datetime_str)\u001B[0m\n\u001B[1;32m    254\u001B[0m         \u001B[0;32mtry\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 255\u001B[0;31m             \u001B[0mdatetime\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mstrptime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdatetime_str\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0;34m\"%Y-%m-%dT%H:%M:%S%z\"\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    256\u001B[0m         \u001B[0;32mexcept\u001B[0m \u001B[0mValueError\u001B[0m \u001B[0;32mas\u001B[0m \u001B[0me\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;32m/usr/lib/python3.7/_strptime.py\u001B[0m in \u001B[0;36m_strptime_datetime\u001B[0;34m(cls, data_string, format)\u001B[0m\n\u001B[1;32m    576\u001B[0m     format string.\"\"\"\n\u001B[0;32m--> 577\u001B[0;31m     \u001B[0mtt\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mfraction\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mgmtoff_fraction\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0m_strptime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdata_string\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mformat\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    578\u001B[0m     \u001B[0mtzname\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mgmtoff\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mtt\u001B[0m\u001B[0;34m[\u001B[0m\u001B[0;34m-\u001B[0m\u001B[0;36m2\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m]\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;32m/usr/lib/python3.7/_strptime.py\u001B[0m in \u001B[0;36m_strptime\u001B[0;34m(data_string, format)\u001B[0m\n\u001B[1;32m    358\u001B[0m         raise ValueError(\"time data %r does not match format %r\" %\n\u001B[0;32m--> 359\u001B[0;31m                          (data_string, format))\n\u001B[0m\u001B[1;32m    360\u001B[0m     \u001B[0;32mif\u001B[0m \u001B[0mlen\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdata_string\u001B[0m\u001B[0;34m)\u001B[0m \u001B[0;34m!=\u001B[0m \u001B[0mfound\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mend\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;31mValueError\u001B[0m: time data '2020-08-26T23:28:20' does not match format '%Y-%m-%dT%H:%M:%S%z'",
-      "\nDuring handling of the above exception, another exception occurred:\n",
-      "\u001B[0;31mValueError\u001B[0m                                Traceback (most recent call last)",
-      "\u001B[0;32m~/git/cobrapy-hemnant/src/cobra/core/metadata/history.py\u001B[0m in \u001B[0;36mvalidate_datetime\u001B[0;34m(datetime_str)\u001B[0m\n\u001B[1;32m    269\u001B[0m                 \u001B[0;32mtry\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 270\u001B[0;31m                     \u001B[0mdatetime\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mstrptime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdate_p36\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0;34m\"%Y-%m-%dT%H:%M:%S%z\"\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    271\u001B[0m                 \u001B[0;32mexcept\u001B[0m \u001B[0mValueError\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;32m/usr/lib/python3.7/_strptime.py\u001B[0m in \u001B[0;36m_strptime_datetime\u001B[0;34m(cls, data_string, format)\u001B[0m\n\u001B[1;32m    576\u001B[0m     format string.\"\"\"\n\u001B[0;32m--> 577\u001B[0;31m     \u001B[0mtt\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mfraction\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mgmtoff_fraction\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0m_strptime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdata_string\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mformat\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    578\u001B[0m     \u001B[0mtzname\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mgmtoff\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mtt\u001B[0m\u001B[0;34m[\u001B[0m\u001B[0;34m-\u001B[0m\u001B[0;36m2\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m]\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;32m/usr/lib/python3.7/_strptime.py\u001B[0m in \u001B[0;36m_strptime\u001B[0;34m(data_string, format)\u001B[0m\n\u001B[1;32m    358\u001B[0m         raise ValueError(\"time data %r does not match format %r\" %\n\u001B[0;32m--> 359\u001B[0;31m                          (data_string, format))\n\u001B[0m\u001B[1;32m    360\u001B[0m     \u001B[0;32mif\u001B[0m \u001B[0mlen\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdata_string\u001B[0m\u001B[0;34m)\u001B[0m \u001B[0;34m!=\u001B[0m \u001B[0mfound\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mend\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;31mValueError\u001B[0m: time data '2020-08-26T23:28:20' does not match format '%Y-%m-%dT%H:%M:%S%z'",
-      "\nDuring handling of the above exception, another exception occurred:\n",
-      "\u001B[0;31mValueError\u001B[0m                                Traceback (most recent call last)",
-      "\u001B[0;32m<ipython-input-1-b9e186b1269a>\u001B[0m in \u001B[0;36m<module>\u001B[0;34m\u001B[0m\n\u001B[1;32m     11\u001B[0m metabolite.annotation.history = History(\n\u001B[1;32m     12\u001B[0m     \u001B[0mcreators\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0;34m[\u001B[0m\u001B[0mcreator\u001B[0m\u001B[0;34m]\u001B[0m\u001B[0;34m,\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 13\u001B[0;31m     \u001B[0mcreated_date\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0mHistoryDatetime\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mutcnow\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m,\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m     14\u001B[0m     \u001B[0mmodified_dates\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0;34m[\u001B[0m\u001B[0mHistoryDatetime\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mutcnow\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m]\u001B[0m\u001B[0;34m,\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m     15\u001B[0m )\n",
-      "\u001B[0;32m~/git/cobrapy-hemnant/src/cobra/core/metadata/history.py\u001B[0m in \u001B[0;36mutcnow\u001B[0;34m()\u001B[0m\n\u001B[1;32m    239\u001B[0m         \u001B[0mutcnow\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mdatetime\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mutcnow\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    240\u001B[0m         \u001B[0mvalue\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mutcnow\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mstrftime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m\"%Y-%m-%dT%H:%M:%S%z\"\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 241\u001B[0;31m         \u001B[0;32mreturn\u001B[0m \u001B[0mHistoryDatetime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mvalue\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    242\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    243\u001B[0m     \u001B[0;34m@\u001B[0m\u001B[0mstaticmethod\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;32m~/git/cobrapy-hemnant/src/cobra/core/metadata/history.py\u001B[0m in \u001B[0;36m__init__\u001B[0;34m(self, history_datetime)\u001B[0m\n\u001B[1;32m    207\u001B[0m     \u001B[0;32mdef\u001B[0m \u001B[0m__init__\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mself\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mhistory_datetime\u001B[0m\u001B[0;34m:\u001B[0m \u001B[0mstr\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;32mNone\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    208\u001B[0m         \u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m_datetime\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0;32mNone\u001B[0m  \u001B[0;31m# type: str\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 209\u001B[0;31m         \u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mdatetime\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mhistory_datetime\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    210\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    211\u001B[0m     \u001B[0;34m@\u001B[0m\u001B[0mproperty\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;32m~/git/cobrapy-hemnant/src/cobra/core/metadata/history.py\u001B[0m in \u001B[0;36mdatetime\u001B[0;34m(self, value)\u001B[0m\n\u001B[1;32m    215\u001B[0m     \u001B[0;34m@\u001B[0m\u001B[0mdatetime\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0msetter\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    216\u001B[0m     \u001B[0;32mdef\u001B[0m \u001B[0mdatetime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mself\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mvalue\u001B[0m\u001B[0;34m:\u001B[0m \u001B[0mstr\u001B[0m\u001B[0;34m)\u001B[0m \u001B[0;34m->\u001B[0m \u001B[0;32mNone\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 217\u001B[0;31m         \u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m_datetime\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mparse_datetime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mvalue\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    218\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    219\u001B[0m     \u001B[0;32mdef\u001B[0m \u001B[0mparse_datetime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mself\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mvalue\u001B[0m\u001B[0;34m:\u001B[0m \u001B[0mstr\u001B[0m\u001B[0;34m)\u001B[0m \u001B[0;34m->\u001B[0m \u001B[0mstr\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;32m~/git/cobrapy-hemnant/src/cobra/core/metadata/history.py\u001B[0m in \u001B[0;36mparse_datetime\u001B[0;34m(self, value)\u001B[0m\n\u001B[1;32m    223\u001B[0m             \u001B[0;32mreturn\u001B[0m \u001B[0mvalue\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mdatetime\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    224\u001B[0m         \u001B[0;32melif\u001B[0m \u001B[0misinstance\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mvalue\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mstr\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 225\u001B[0;31m             \u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mvalidate_datetime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mvalue\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    226\u001B[0m             \u001B[0;32mreturn\u001B[0m \u001B[0mvalue\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    227\u001B[0m         \u001B[0;32melif\u001B[0m \u001B[0misinstance\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mvalue\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mdatetime\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;32m~/git/cobrapy-hemnant/src/cobra/core/metadata/history.py\u001B[0m in \u001B[0;36mvalidate_datetime\u001B[0;34m(datetime_str)\u001B[0m\n\u001B[1;32m    270\u001B[0m                     \u001B[0mdatetime\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mstrptime\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdate_p36\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0;34m\"%Y-%m-%dT%H:%M:%S%z\"\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    271\u001B[0m                 \u001B[0;32mexcept\u001B[0m \u001B[0mValueError\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 272\u001B[0;31m                     \u001B[0;32mraise\u001B[0m \u001B[0mValueError\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mstr\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0me\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m    273\u001B[0m                 \u001B[0;32mreturn\u001B[0m \u001B[0;32mTrue\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m    274\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n",
-      "\u001B[0;31mValueError\u001B[0m: time data '2020-08-26T23:28:20' does not match format '%Y-%m-%dT%H:%M:%S%z'"
-     ]
+  "nbformat": 4,
+  "nbformat_minor": 0,
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.6.0"
+    },
+    "colab": {
+      "name": "metadata.ipynb",
+      "provenance": []
     }
-   ],
-   "source": [
-    "from cobra.core import Metabolite\n",
-    "from cobra.core.metadata import History, Creator, HistoryDatetime\n",
-    "\n",
-    "metabolite = Metabolite(id=\"glc\", name=\"D-glucose\")\n",
-    "creator = Creator(\n",
-    "    first_name=\"Max\",\n",
-    "    last_name=\"Mustermann\",\n",
-    "    organization_name=\"Muster University\",\n",
-    "    email=\"max.mustermann@cobrapy.org\"\n",
-    ")\n",
-    "metabolite.annotation.history = History(\n",
-    "    creators=[creator],\n",
-    "    created_date=HistoryDatetime.utcnow(),\n",
-    "    modified_dates=[HistoryDatetime.utcnow()],\n",
-    ")"
-   ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "outputs": [],
-   "source": [
-    "\n"
-   ],
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "bVgYSbcPLbwU",
+        "colab_type": "text"
+      },
+      "source": [
+        "# Metadata\n",
+        "\n",
+        "Metadata in the form of annotations, provenance or additional key:value pairs is an important asset for a model.\n",
+        "Such data can be handled via the `annotation` field on cobra objects"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "Rv-QKmAPM8PY",
+        "colab_type": "text"
+      },
+      "source": [
+        "# History\n",
+        "\n",
+        "History attribute, present in the `annotation` attribute of a COBRA component, stores the history of the component like creators, created date and modified date of that component."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "pycharm": {
+          "name": "#%%\n"
+        },
+        "id": "EsBAtYeHLbwc",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "from cobra.core import Metabolite\n",
+        "from cobra.core.metadata import History, Creator, HistoryDatetime\n",
+        "\n",
+        "metabolite = Metabolite(id=\"glc\", name=\"D-glucose\")\n"
+      ],
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "11wwIBGHWM66",
+        "colab_type": "text"
+      },
+      "source": [
+        "The dates have to be objects of `HistoryDateTime` class and creators that of `Creator` class. We can add then directly via constructor."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "Tmo3MUtpWn8K",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "history = History(\n",
+        "        creators=[\n",
+        "            Creator(\n",
+        "                first_name=\"Matthias\",\n",
+        "                last_name=\"Koenig\",\n",
+        "                organization_name=\"HU\",\n",
+        "                email=\"test@test.com\",\n",
+        "            ),\n",
+        "        ],\n",
+        "        created_date=HistoryDatetime(\"2020-06-26T02:34:30+05:30\"),\n",
+        "        modified_dates=[\n",
+        "            HistoryDatetime(\"2020-06-26T12:34:11+00:00\"),\n",
+        "            HistoryDatetime(\"2020-06-26T00:34:11+05:30\"),\n",
+        "        ],\n",
+        "    )\n",
+        "\n",
+        "metabolite.annotation.history = history"
+      ],
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "6EtjXs5FWsB2",
+        "colab_type": "text"
+      },
+      "source": [
+        "Or we can also add them by making object separtely and then adding in the history object."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "9tiNKucaW1nT",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "new_creator = Creator(\n",
+        "                first_name=\"Andreas\",\n",
+        "                last_name=\"Draeger\",\n",
+        "                organization_name=\"University of Tübingen\",\n",
+        "                email=\"test2@test2.com\",\n",
+        "            )\n",
+        "\n",
+        "metabolite.annotation.history.creators.append(new_creator)\n",
+        "modified_hdtime  = HistoryDatetime()\n",
+        "modified_hdtime.utcnow()\n",
+        "metabolite.annotation.history.modified_dates.append(modified_hdtime)"
+      ],
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "wXst9A76PuoJ",
+        "colab_type": "text"
+      },
+      "source": [
+        "# CVTerms\n",
+        "\n",
+        "CVTerms stands for Controlled Vocabulary Terms, are is used to store the external resources which are linked with the given COBRA component. We can make CVTerm's object either by passing the data directly from the constructor. We can also define the nested data for linked resources."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "whC9AASSQKnn",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "annotation_dict = {\n",
+        "    \"bqb_hasTaxon\": [{\"resources\": [\"http://identifiers.org/taxonomy/511145\"]}],\n",
+        "    \"bqm_is\": [\n",
+        "        {\n",
+        "            \"nested_data\": {\n",
+        "                \"bqb_isDescribedBy\": [\n",
+        "                    {\"resources\": [\"https://identifiers.org/pubmed/1111111\"]},\n",
+        "                    {\"resources\": [\"https://identifiers.org/eco/ECO:0000004\"]},\n",
+        "                ]\n",
+        "            },\n",
+        "            \"resources\": [\"http://identifiers.org/bigg.model/e_coli_core\"],\n",
+        "        }\n",
+        "    ],\n",
+        "}\n",
+        "\n",
+        "cvterms = CVTerms(annotation_dict)\n",
+        "metabolite.annotation.cvterms = cvterms\n",
+        "\n"
+      ],
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "-BP4wL2JXUlK",
+        "colab_type": "text"
+      },
+      "source": [
+        "Or we can also add data by making separate `CVTerm` objects and then adding them at a particular index (indexing is done for a single qualifier for adding alternative annotation)."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "DEyuH1cqXoar",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "cvterm1 = CVTerm(Qualifier.bqb_isDescribedBy, \"http://identifiers.org/doi/10.1128/ecosalplus.10.2.1\")\n",
+        "cvterm2 = CVTerm(Qualifier.bqb_isDescribedBy, \"http://identifiers.org/ncbigi/gi:16128336\")\n",
+        "\n",
+        "metabolite.annotation.cvterms.add_cvterm(cvterm1, 0)\n",
+        "metabolite.annotation.cvterms.add_cvterm(cvterm1, 1)"
+      ],
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "olUCYEdwSw6k",
+        "colab_type": "text"
+      },
+      "source": [
+        "# KeyValuePairs\n",
+        "\n",
+        "The KeyValuePair class is used for storing any type of key-value pair data, which is not suitable to store anywhere else in the model"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "ENKACjXES9k1",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "    entry1 = {\n",
+        "        \"id\": \"id1\",\n",
+        "        \"name\": \"abc_xyz\",\n",
+        "        \"key\": \"key1\",\n",
+        "        \"value\": \"45\",\n",
+        "        \"uri\": \"https://tinyurl.com/ybyr7b62\",\n",
+        "    }\n",
+        "    entry2 = KeyValueEntry.from_data({\n",
+        "        \"id\": \"id2\",\n",
+        "        \"name\": \"abc_xyz2\",\n",
+        "        \"key\": \"key2\",\n",
+        "        \"value\": \"48\",\n",
+        "        \"uri\": \"https://tinyurl2.com/ybyr7b62\",\n",
+        "    })\n",
+        "\n",
+        "    kvp = KeyValuePairs(entries=[entry1, entry2])\n",
+        "    metabolite.annotation.keyvaluepairs = kvp"
+      ],
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "Rl3UV44OTe4Q",
+        "colab_type": "text"
+      },
+      "source": [
+        "# Notes\n",
+        "The `notes` field under a COBRA component is used to store the notes data. Though it is not a right place to store key-value pairs, but earlier implementation has left many models where notes field have key-value pairs inside it. The current implementation contains a notes string as well as a notes dictionary, both synchronized with each other. One can only update values inside the notes dictioanry, adding new key-value pairs is restricted. Updating the dictionary will update the notes string also (only the key-value pair part). String manipulation, if required, will have to be done manually."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "psrA4ROmU4X6",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "notes_str = (\n",
+        "    '\\\n",
+        "<notes>\\n\\\n",
+        "  <body xmlns=\"http://www.w3.org/1999/xhtml\">\\n\\\n",
+        "    <div style=\"height: 60px; background-color: #09F;\">\\n\\\n",
+        "      <p> Key1 : Value 1 </p>\\n\\\n",
+        "      <p> Key2 : Value2 </p>\\n\\\n",
+        "      <div style=\"margin-left: auto; margin-right: auto; '\n",
+        "    'width: 970px;\">\\n\\\n",
+        "        <h1> A Heading </h1>\\n\\\n",
+        "        <div class=\"dc:title\"> e_coli_core - Escherichia coli '\n",
+        "    \"str. K-12 substr. MG1655 </div>\\n\\\n",
+        "      </div>\\n\\\n",
+        "      <p> Key3 : Value 3 </p>\\n\\\n",
+        "    </div>\\n\\\n",
+        "  </body>\\n\\\n",
+        "</notes>\"\n",
+        ")\n",
+        "\n",
+        "metabolite.notes = Notes(notes_str)\n",
+        "metabolite.notes[\"Key1\"] = \"New Value1\""
+      ],
+      "execution_count": null,
+      "outputs": []
     }
-   }
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.6.0"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 0
-}
\ No newline at end of file
+  ]
+}