update notebooks

minor cosmetic standardizations/changes to titles and intro
franciscozorrilla · Jan 9, 2024 · 644bb00 · 644bb00
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diff --git a/notebooks/1_fba.html b/notebooks/1_fba.html
@@ -14259,12 +14259,12 @@
 
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
-<h1 id="1.-Getting-Started">1. Getting Started<a class="anchor-link" href="#1.-Getting-Started">&#182;</a></h1>
+<h1 id="1.-Getting-started-with-GEMs-and-FBA">1. Getting started with GEMs and FBA<a class="anchor-link" href="#1.-Getting-started-with-GEMs-and-FBA">&#182;</a></h1>
 </div>
 </div>
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
-<h2 id="Authors:">Authors:<a class="anchor-link" href="#Authors:">&#182;</a></h2><ul>
+<h2 id="Authors">Authors<a class="anchor-link" href="#Authors">&#182;</a></h2><ul>
 <li>Arianna Basile, MRC Toxicology Unit, University of Cambridge</li>
 <li>Francisco Zorrilla, MRC Toxicology Unit, University of Cambridge</li>
 </ul>
@@ -14273,15 +14273,15 @@ <h2 id="Authors:">Authors:<a class="anchor-link" href="#Authors:">&#182;</a></h2
 </div>
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
-<h2 id="Learning-Outcomes">Learning Outcomes<a class="anchor-link" href="#Learning-Outcomes">&#182;</a></h2><p>In this tutorial you will use <a href="https://cobrapy.readthedocs.io/en/latest/">cobrapy</a> to learn the following:</p>
+<h2 id="Learning-outcomes">Learning outcomes<a class="anchor-link" href="#Learning-outcomes">&#182;</a></h2><p>In this tutorial you will use <a href="https://cobrapy.readthedocs.io/en/latest/">cobrapy</a> to learn the following:</p>
 <ul>
 <li><strong>1.1</strong>: Import a metabolic reconstruction</li>
 <li><strong>1.2</strong>: Inspect the reactions of your model</li>
 <li><strong>1.3</strong>: Inspect the metabolites in your model</li>
 <li><strong>1.4</strong>: Inspect the genes in your model</li>
 <li><strong>1.4.1</strong>: Perform in-silico gene knockout experiments</li>
 </ul>
-
+<h2 id="Setup">Setup<a class="anchor-link" href="#Setup">&#182;</a></h2>
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
 <div class="jp-Cell-inputWrapper">
@@ -14415,7 +14415,7 @@ <h2 id="1.1-Import-a-reconstruction">1.1 Import a reconstruction<a class="anchor
                 <td>iMM904</td>
             </tr><tr>
                 <td><strong>Memory address</strong></td>
-                <td>0x07ff0fba967c0</td>
+                <td>0x07fbaaa7c5670</td>
             </tr><tr>
                 <td><strong>Number of metabolites</strong></td>
                 <td>1226</td>
@@ -14482,7 +14482,7 @@ <h2 id="1.1-Import-a-reconstruction">1.1 Import a reconstruction<a class="anchor
                 <td><strong>Name</strong></td><td>Exo 1 3 beta glucan glucohydrase</td>
             </tr><tr>
                 <td><strong>Memory address</strong></td>
-                <td>0x07ff10a88fa90</td>
+                <td>0x07fba992dc850</td>
             </tr><tr>
                 <td><strong>Stoichiometry</strong></td>
                 <td>
@@ -14624,7 +14624,7 @@ <h2 id="1.2-Reactions">1.2 Reactions<a class="anchor-link" href="#1.2-Reactions"
                 <td><strong>Name</strong></td><td>Glucose-6-phosphate isomerase</td>
             </tr><tr>
                 <td><strong>Memory address</strong></td>
-                <td>0x07ff10b150fa0</td>
+                <td>0x07fba79f02be0</td>
             </tr><tr>
                 <td><strong>Stoichiometry</strong></td>
                 <td>
@@ -15073,14 +15073,14 @@ <h2 id="1.3-Metabolites">1.3 Metabolites<a class="anchor-link" href="#1.3-Metabo
                 <td><strong>Name</strong></td><td>ATP C10H12N5O13P3</td>
             </tr><tr>
                 <td><strong>Memory address</strong></td>
-                <td>0x07ff10a4e71c0</td>
+                <td>0x07fba79ac2f10</td>
             </tr><tr>
                 <td><strong>Formula</strong></td><td>C10H12N5O13P3</td>
             </tr><tr>
                 <td><strong>Compartment</strong></td><td>c</td>
             </tr><tr>
                 <td><strong>In 149 reaction(s)</strong></td><td>
-                    FMNAT, GLYTRS, DTMPK, ADK1, FACOAL180, ETHAK, RNTR1, FACOAL182, NDPK4, INSK, CYSTRS, FACOAL140, NDPK2, GLNS, AASAD1, PRAGSr, PROTRS, ACCOAC, PRPPS, NDPK9, HEX1, MEVK1, HETZK, TMPK, PRFGS, NDPK8,...</td>
+                    CYSTRS, NADK, GLUCYS, GK1, UMPK, NMNAT, FACOAL181, ATPPRT, FACOAL160, URIK1, ADNK1, ATPtm_H, INSK, PRAIS, PIN3K_SC, DHFS, DHAK, HETZK, GLUK, PMPK, ACCOAC, HISTRS, NDPK1, TMDPPK, PHETRS, PRAGSr,...</td>
             </tr>
         </table>
 </div>
@@ -15308,12 +15308,12 @@ <h2 id="1.4-Genes">1.4 Genes<a class="anchor-link" href="#1.4-Genes">&#182;</a><
                 <td><strong>Name</strong></td><td>PGI1</td>
             </tr><tr>
                 <td><strong>Memory address</strong></td>
-                <td>0x07ff10a7dcf10</td>
+                <td>0x07fba99229c10</td>
             </tr><tr>
                 <td><strong>Functional</strong></td><td>True</td>
             </tr><tr>
                 <td><strong>In 3 reaction(s)</strong></td><td>
-                    PGI, G6PI, G6PI3</td>
+                    G6PI3, G6PI, PGI</td>
             </tr>
         </table>
 </div>

diff --git a/notebooks/1_fba.ipynb b/notebooks/1_fba.ipynb
@@ -4,14 +4,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 1. Getting Started"
+    "# 1. Getting started with GEMs and FBA"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Authors: \n",
+    "## Authors\n",
     "* Arianna Basile, MRC Toxicology Unit, University of Cambridge\n",
     "* Francisco Zorrilla, MRC Toxicology Unit, University of Cambridge"
    ]
@@ -20,15 +20,17 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Learning Outcomes\n",
+    "## Learning outcomes\n",
     "\n",
     "In this tutorial you will use [cobrapy](https://cobrapy.readthedocs.io/en/latest/) to learn the following:\n",
     "\n",
     "* **1.1**: Import a metabolic reconstruction\n",
     "* **1.2**: Inspect the reactions of your model\n",
     "* **1.3**: Inspect the metabolites in your model\n",
     "* **1.4**: Inspect the genes in your model\n",
-    "* **1.4.1**: Perform in-silico gene knockout experiments"
+    "* **1.4.1**: Perform in-silico gene knockout experiments\n",
+    "\n",
+    "## Setup"
    ]
   },
   {
@@ -41,7 +43,7 @@
     "import cobra\n",
     "\n",
     "# Enable autocompleting with tab key\n",
-    "%config Completer.use_jedi = False\n"
+    "%config Completer.use_jedi = False"
    ]
   },
   {
@@ -123,7 +125,7 @@
        "                <td>iMM904</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-       "                <td>0x07ff0fba967c0</td>\n",
+       "                <td>0x07fbaaa7c5670</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Number of metabolites</strong></td>\n",
        "                <td>1226</td>\n",
@@ -143,7 +145,7 @@
        "          </table>"
       ],
       "text/plain": [
-       "<Model iMM904 at 0x7ff0fba967c0>"
+       "<Model iMM904 at 0x7fbaaa7c5670>"
       ]
      },
      "execution_count": 4,
@@ -178,7 +180,7 @@
        "                <td><strong>Name</strong></td><td>Exo 1 3 beta glucan glucohydrase</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-       "                <td>0x07ff10a88fa90</td>\n",
+       "                <td>0x07fba992dc850</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Stoichiometry</strong></td>\n",
        "                <td>\n",
@@ -196,7 +198,7 @@
        "        "
       ],
       "text/plain": [
-       "<Reaction 13BGHe at 0x7ff10a88fa90>"
+       "<Reaction 13BGHe at 0x7fba992dc850>"
       ]
      },
      "execution_count": 5,
@@ -294,7 +296,7 @@
        "                <td><strong>Name</strong></td><td>Glucose-6-phosphate isomerase</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-       "                <td>0x07ff10b150fa0</td>\n",
+       "                <td>0x07fba79f02be0</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Stoichiometry</strong></td>\n",
        "                <td>\n",
@@ -312,7 +314,7 @@
        "        "
       ],
       "text/plain": [
-       "<Reaction PGI at 0x7ff10b150fa0>"
+       "<Reaction PGI at 0x7fba79f02be0>"
       ]
      },
      "execution_count": 7,
@@ -602,19 +604,19 @@
        "                <td><strong>Name</strong></td><td>ATP C10H12N5O13P3</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-       "                <td>0x07ff10a4e71c0</td>\n",
+       "                <td>0x07fba79ac2f10</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Formula</strong></td><td>C10H12N5O13P3</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Compartment</strong></td><td>c</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>In 149 reaction(s)</strong></td><td>\n",
-       "                    FMNAT, GLYTRS, DTMPK, ADK1, FACOAL180, ETHAK, RNTR1, FACOAL182, NDPK4, INSK, CYSTRS, FACOAL140, NDPK2, GLNS, AASAD1, PRAGSr, PROTRS, ACCOAC, PRPPS, NDPK9, HEX1, MEVK1, HETZK, TMPK, PRFGS, NDPK8,...</td>\n",
+       "                    CYSTRS, NADK, GLUCYS, GK1, UMPK, NMNAT, FACOAL181, ATPPRT, FACOAL160, URIK1, ADNK1, ATPtm_H, INSK, PRAIS, PIN3K_SC, DHFS, DHAK, HETZK, GLUK, PMPK, ACCOAC, HISTRS, NDPK1, TMDPPK, PHETRS, PRAGSr,...</td>\n",
        "            </tr>\n",
        "        </table>"
       ],
       "text/plain": [
-       "<Metabolite atp_c at 0x7ff10a4e71c0>"
+       "<Metabolite atp_c at 0x7fba79ac2f10>"
       ]
      },
      "execution_count": 16,
@@ -764,17 +766,17 @@
        "                <td><strong>Name</strong></td><td>PGI1</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-       "                <td>0x07ff10a7dcf10</td>\n",
+       "                <td>0x07fba99229c10</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Functional</strong></td><td>True</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>In 3 reaction(s)</strong></td><td>\n",
-       "                    PGI, G6PI, G6PI3</td>\n",
+       "                    G6PI3, G6PI, PGI</td>\n",
        "            </tr>\n",
        "        </table>"
       ],
       "text/plain": [
-       "<Gene YBR196C at 0x7ff10a7dcf10>"
+       "<Gene YBR196C at 0x7fba99229c10>"
       ]
      },
      "execution_count": 21,

diff --git a/notebooks/1_fba.md b/notebooks/1_fba.md
@@ -1,10 +1,10 @@
-# 1. Getting Started
+# 1. Getting started with GEMs and FBA
 
-## Authors: 
+## Authors
 * Arianna Basile, MRC Toxicology Unit, University of Cambridge
 * Francisco Zorrilla, MRC Toxicology Unit, University of Cambridge
 
-## Learning Outcomes
+## Learning outcomes
 
 In this tutorial you will use [cobrapy](https://cobrapy.readthedocs.io/en/latest/) to learn the following:
 
@@ -14,14 +14,15 @@ In this tutorial you will use [cobrapy](https://cobrapy.readthedocs.io/en/latest
 * **1.4**: Inspect the genes in your model
 * **1.4.1**: Perform in-silico gene knockout experiments
 
+## Setup
+
 
 ```python
 # Import required packages
 import cobra
 
 # Enable autocompleting with tab key
 %config Completer.use_jedi = False
-
 ```
 
 ## 1.1 Import a reconstruction
@@ -70,7 +71,7 @@ model_yeast
         <td>iMM904</td>
     </tr><tr>
         <td><strong>Memory address</strong></td>
-        <td>0x07ff0fba967c0</td>
+        <td>0x07fbaaa7c5670</td>
     </tr><tr>
         <td><strong>Number of metabolites</strong></td>
         <td>1226</td>
@@ -109,7 +110,7 @@ model_yeast.reactions[2]
         <td><strong>Name</strong></td><td>Exo 1 3 beta glucan glucohydrase</td>
     </tr><tr>
         <td><strong>Memory address</strong></td>
-        <td>0x07ff10a88fa90</td>
+        <td>0x07fba992dc850</td>
     </tr><tr>
         <td><strong>Stoichiometry</strong></td>
         <td>
@@ -187,7 +188,7 @@ pgi
         <td><strong>Name</strong></td><td>Glucose-6-phosphate isomerase</td>
     </tr><tr>
         <td><strong>Memory address</strong></td>
-        <td>0x07ff10b150fa0</td>
+        <td>0x07fba79f02be0</td>
     </tr><tr>
         <td><strong>Stoichiometry</strong></td>
         <td>
@@ -367,14 +368,14 @@ atp
         <td><strong>Name</strong></td><td>ATP C10H12N5O13P3</td>
     </tr><tr>
         <td><strong>Memory address</strong></td>
-        <td>0x07ff10a4e71c0</td>
+        <td>0x07fba79ac2f10</td>
     </tr><tr>
         <td><strong>Formula</strong></td><td>C10H12N5O13P3</td>
     </tr><tr>
         <td><strong>Compartment</strong></td><td>c</td>
     </tr><tr>
         <td><strong>In 149 reaction(s)</strong></td><td>
-            FMNAT, GLYTRS, DTMPK, ADK1, FACOAL180, ETHAK, RNTR1, FACOAL182, NDPK4, INSK, CYSTRS, FACOAL140, NDPK2, GLNS, AASAD1, PRAGSr, PROTRS, ACCOAC, PRPPS, NDPK9, HEX1, MEVK1, HETZK, TMPK, PRFGS, NDPK8,...</td>
+            CYSTRS, NADK, GLUCYS, GK1, UMPK, NMNAT, FACOAL181, ATPPRT, FACOAL160, URIK1, ADNK1, ATPtm_H, INSK, PRAIS, PIN3K_SC, DHFS, DHAK, HETZK, GLUK, PMPK, ACCOAC, HISTRS, NDPK1, TMDPPK, PHETRS, PRAGSr,...</td>
     </tr>
 </table>
 
@@ -456,12 +457,12 @@ pgi_gene
         <td><strong>Name</strong></td><td>PGI1</td>
     </tr><tr>
         <td><strong>Memory address</strong></td>
-        <td>0x07ff10a7dcf10</td>
+        <td>0x07fba99229c10</td>
     </tr><tr>
         <td><strong>Functional</strong></td><td>True</td>
     </tr><tr>
         <td><strong>In 3 reaction(s)</strong></td><td>
-            PGI, G6PI, G6PI3</td>
+            G6PI3, G6PI, PGI</td>
     </tr>
 </table>