build model examples

Author: Fxe

examples/build_metabolic_model.ipynb

@@ -57,7 +57,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -66,7 +66,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -79,7 +79,7 @@
        "                <td>ecoli.core</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Memory address</strong></td>\n",
-       "                <td>0x07fe3b14c4f50</td>\n",
+       "                <td>0x07faf31a00190</td>\n",
        "            </tr><tr>\n",
        "                <td><strong>Number of metabolites</strong></td>\n",
        "                <td>190</td>\n",
@@ -99,10 +99,10 @@
        "          </table>"
       ],
       "text/plain": [
-       "<Model ecoli.core at 0x7fe3b14c4f50>"
+       "<Model ecoli.core at 0x7faf31a00190>"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -226,7 +226,7 @@
        "</table>"
       ],
       "text/plain": [
-       "<cobra.summary.model_summary.ModelSummary at 0x7fa682e4f7d0>"
+       "<cobra.summary.model_summary.ModelSummary at 0x7faf4344bd90>"
       ]
      },
      "execution_count": 9,
@@ -238,6 +238,118 @@
     "model.summary()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<h3>Objective</h3><p>1.0 bio1 = 0.1229368143626848</p><h4>Uptake</h4><table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th>Metabolite</th>\n",
+       "      <th>Reaction</th>\n",
+       "      <th>Flux</th>\n",
+       "      <th>C-Number</th>\n",
+       "      <th>C-Flux</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <td>cpd00007_e0</td>\n",
+       "      <td>EX_cpd00007_e0</td>\n",
+       "      <td>1.371</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0.00%</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <td>cpd00009_e0</td>\n",
+       "      <td>EX_cpd00009_e0</td>\n",
+       "      <td>0.5182</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0.00%</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <td>cpd00027_e0</td>\n",
+       "      <td>EX_cpd00027_e0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>6</td>\n",
+       "      <td>100.00%</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table><h4>Secretion</h4><table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th>Metabolite</th>\n",
+       "      <th>Reaction</th>\n",
+       "      <th>Flux</th>\n",
+       "      <th>C-Number</th>\n",
+       "      <th>C-Flux</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <td>cpd00001_e0</td>\n",
+       "      <td>EX_cpd00001_e0</td>\n",
+       "      <td>-2.812</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0.00%</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <td>cpd00011_e0</td>\n",
+       "      <td>EX_cpd00011_e0</td>\n",
+       "      <td>-0.5044</td>\n",
+       "      <td>1</td>\n",
+       "      <td>100.00%</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <td>cpd00067_e0</td>\n",
+       "      <td>EX_cpd00067_e0</td>\n",
+       "      <td>-1.749</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0.00%</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <td>cpd11416_c0</td>\n",
+       "      <td>SK_cpd11416_c0</td>\n",
+       "      <td>-0.1229</td>\n",
+       "      <td>0</td>\n",
+       "      <td>0.00%</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>"
+      ],
+      "text/plain": [
+       "<cobra.summary.model_summary.ModelSummary at 0x7faf31083d10>"
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "model.objective = 'bio1'\n",
+    "model.medium = {\n",
+    "    'EX_cpd00067_e0': 1000,\n",
+    "    'EX_cpd00027_e0': 1,\n",
+    "    'EX_cpd00007_e0': 1000,\n",
+    "    'EX_cpd00001_e0': 1000,\n",
+    "    'EX_cpd00009_e0': 1000,\n",
+    "    \n",
+    "}\n",
+    "model.summary()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": 10,