DP_SA_summarymodel_1.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "import cobra\n",
    "import pandas as pd\n",
    "import escher"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Dolosigranulum pigrum (DP)\n",
    "# Staphylococcus aureus (SA)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Compound</th>\n",
       "      <th>BiGG</th>\n",
       "      <th>ModelSeed</th>\n",
       "      <th>KEGG</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Alanine</td>\n",
       "      <td>ala__L</td>\n",
       "      <td>cpd00035</td>\n",
       "      <td>C00041</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Arginine</td>\n",
       "      <td>arg__L</td>\n",
       "      <td>cpd00051</td>\n",
       "      <td>C00062</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Cysteine</td>\n",
       "      <td>cys__L</td>\n",
       "      <td>cpd00084</td>\n",
       "      <td>C00097</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Glutamic acid</td>\n",
       "      <td>glu__L</td>\n",
       "      <td>cpd00023</td>\n",
       "      <td>C00025</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Glycine</td>\n",
       "      <td>gly</td>\n",
       "      <td>cpd00033</td>\n",
       "      <td>C00037</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Histidine</td>\n",
       "      <td>his__L</td>\n",
       "      <td>cpd00119</td>\n",
       "      <td>C00135</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Leucine</td>\n",
       "      <td>leu__L</td>\n",
       "      <td>cpd00107</td>\n",
       "      <td>C00123</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Lysine</td>\n",
       "      <td>lys__L</td>\n",
       "      <td>cpd00039</td>\n",
       "      <td>C00047</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Ornithine</td>\n",
       "      <td>orn</td>\n",
       "      <td>cpd00064</td>\n",
       "      <td>C00077</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Phenylalanine</td>\n",
       "      <td>phe__L</td>\n",
       "      <td>cpd00066</td>\n",
       "      <td>C00079</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Proline</td>\n",
       "      <td>pro__L</td>\n",
       "      <td>cpd00129</td>\n",
       "      <td>C00148</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Serine</td>\n",
       "      <td>ser__L</td>\n",
       "      <td>cpd00054</td>\n",
       "      <td>C00065</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Threonine</td>\n",
       "      <td>thr__L</td>\n",
       "      <td>cpd00161</td>\n",
       "      <td>C00188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Tryptophane</td>\n",
       "      <td>trp__L</td>\n",
       "      <td>cpd00065</td>\n",
       "      <td>C00078</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Valine</td>\n",
       "      <td>val__L</td>\n",
       "      <td>cpd00156</td>\n",
       "      <td>C00183</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>citric acid</td>\n",
       "      <td>cit</td>\n",
       "      <td>cpd00137</td>\n",
       "      <td>C00158</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Fumaric acid</td>\n",
       "      <td>fum</td>\n",
       "      <td>cpd00106</td>\n",
       "      <td>C00122</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>maleic acid</td>\n",
       "      <td>male</td>\n",
       "      <td>cpd00996</td>\n",
       "      <td>C01384</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>pyruvic acid</td>\n",
       "      <td>pyr</td>\n",
       "      <td>cpd00020</td>\n",
       "      <td>C00022</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>succinic acid</td>\n",
       "      <td>succ</td>\n",
       "      <td>cpd00036</td>\n",
       "      <td>C00042</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>glucose</td>\n",
       "      <td>glc__D</td>\n",
       "      <td>cpd00027</td>\n",
       "      <td>C00031</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>Urea</td>\n",
       "      <td>urea</td>\n",
       "      <td>cpd00073</td>\n",
       "      <td>C00086</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>Sodium</td>\n",
       "      <td>na1</td>\n",
       "      <td>cpd00971</td>\n",
       "      <td>C01330</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>Chloride</td>\n",
       "      <td>cl</td>\n",
       "      <td>cpd00099</td>\n",
       "      <td>C00698</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>Potassium</td>\n",
       "      <td>k</td>\n",
       "      <td>cpd00205</td>\n",
       "      <td>C00238</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>Phosphate</td>\n",
       "      <td>pi</td>\n",
       "      <td>cpd00009</td>\n",
       "      <td>C00009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>Magnesium</td>\n",
       "      <td>mg2</td>\n",
       "      <td>cpd00254</td>\n",
       "      <td>C00305</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>Sulphate</td>\n",
       "      <td>so4</td>\n",
       "      <td>cpd00048</td>\n",
       "      <td>C00059</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>2,2'-Bipyridine</td>\n",
       "      <td>NaN</td>\n",
       "      <td>cpd25442</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>Calcium</td>\n",
       "      <td>ca2</td>\n",
       "      <td>cpd00063</td>\n",
       "      <td>C00076</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>ZnCl2</td>\n",
       "      <td>zn2</td>\n",
       "      <td>cpd00034</td>\n",
       "      <td>C00038</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>MnCl2</td>\n",
       "      <td>mn2</td>\n",
       "      <td>cpd00030</td>\n",
       "      <td>C00034</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>H3BO3</td>\n",
       "      <td>NaN</td>\n",
       "      <td>cpd09225</td>\n",
       "      <td>C12486</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>CoCl2</td>\n",
       "      <td>cobalt2</td>\n",
       "      <td>cpd00149</td>\n",
       "      <td>C00175</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>CuCl2</td>\n",
       "      <td>cu2</td>\n",
       "      <td>cpd00058</td>\n",
       "      <td>C00070</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>NiCl2</td>\n",
       "      <td>ni2</td>\n",
       "      <td>cpd00244</td>\n",
       "      <td>C00291</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>MoNa2O4</td>\n",
       "      <td>mobd</td>\n",
       "      <td>cpd11574</td>\n",
       "      <td>C06232</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>Cyanocobalamine</td>\n",
       "      <td>adocbl</td>\n",
       "      <td>cpd01826</td>\n",
       "      <td>C02823</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>p-Aminobenzoic acid</td>\n",
       "      <td>4abz</td>\n",
       "      <td>cpd00443</td>\n",
       "      <td>C00568</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>Biotin</td>\n",
       "      <td>btn</td>\n",
       "      <td>cpd00104</td>\n",
       "      <td>C00120</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>Nicotinic acid</td>\n",
       "      <td>nac</td>\n",
       "      <td>cpd00218</td>\n",
       "      <td>C00253</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>Ca-D-Pantothenic acid</td>\n",
       "      <td>pnto__R</td>\n",
       "      <td>cpd00644</td>\n",
       "      <td>C00864</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>Pyridoxamine-2HCl</td>\n",
       "      <td>pydam</td>\n",
       "      <td>cpd00419</td>\n",
       "      <td>C00534</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>Thiamine-dichloride</td>\n",
       "      <td>thm</td>\n",
       "      <td>cpd00305</td>\n",
       "      <td>C00378</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>Riboflavin</td>\n",
       "      <td>ribflv</td>\n",
       "      <td>cpd00220</td>\n",
       "      <td>C00255</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>Oxygen</td>\n",
       "      <td>o2</td>\n",
       "      <td>cpd00007</td>\n",
       "      <td>C00007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>Fe3+</td>\n",
       "      <td>fe2</td>\n",
       "      <td>cpd10516</td>\n",
       "      <td>C14819</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>Water</td>\n",
       "      <td>h2o</td>\n",
       "      <td>cpd00001</td>\n",
       "      <td>C00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>Co2</td>\n",
       "      <td>co2</td>\n",
       "      <td>cpd00011</td>\n",
       "      <td>C00011</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                 Compound     BiGG ModelSeed    KEGG\n",
       "0                 Alanine   ala__L  cpd00035  C00041\n",
       "1                Arginine   arg__L  cpd00051  C00062\n",
       "2                Cysteine   cys__L  cpd00084  C00097\n",
       "3           Glutamic acid   glu__L  cpd00023  C00025\n",
       "4                 Glycine      gly  cpd00033  C00037\n",
       "5               Histidine   his__L  cpd00119  C00135\n",
       "6                 Leucine   leu__L  cpd00107  C00123\n",
       "7                  Lysine   lys__L  cpd00039  C00047\n",
       "8               Ornithine      orn  cpd00064  C00077\n",
       "9           Phenylalanine   phe__L  cpd00066  C00079\n",
       "10                Proline   pro__L  cpd00129  C00148\n",
       "11                 Serine   ser__L  cpd00054  C00065\n",
       "12              Threonine   thr__L  cpd00161  C00188\n",
       "13            Tryptophane   trp__L  cpd00065  C00078\n",
       "14                 Valine   val__L  cpd00156  C00183\n",
       "15            citric acid      cit  cpd00137  C00158\n",
       "16           Fumaric acid      fum  cpd00106  C00122\n",
       "17            maleic acid     male  cpd00996  C01384\n",
       "18           pyruvic acid      pyr  cpd00020  C00022\n",
       "19          succinic acid     succ  cpd00036  C00042\n",
       "20                glucose   glc__D  cpd00027  C00031\n",
       "21                   Urea     urea  cpd00073  C00086\n",
       "22                 Sodium      na1  cpd00971  C01330\n",
       "23               Chloride       cl  cpd00099  C00698\n",
       "24              Potassium        k  cpd00205  C00238\n",
       "25              Phosphate       pi  cpd00009  C00009\n",
       "26              Magnesium      mg2  cpd00254  C00305\n",
       "27               Sulphate      so4  cpd00048  C00059\n",
       "28        2,2'-Bipyridine      NaN  cpd25442     NaN\n",
       "29                Calcium      ca2  cpd00063  C00076\n",
       "30                  ZnCl2      zn2  cpd00034  C00038\n",
       "31                  MnCl2      mn2  cpd00030  C00034\n",
       "32                  H3BO3      NaN  cpd09225  C12486\n",
       "33                  CoCl2  cobalt2  cpd00149  C00175\n",
       "34                  CuCl2      cu2  cpd00058  C00070\n",
       "35                  NiCl2      ni2  cpd00244  C00291\n",
       "36                MoNa2O4     mobd  cpd11574  C06232\n",
       "37        Cyanocobalamine   adocbl  cpd01826  C02823\n",
       "38    p-Aminobenzoic acid     4abz  cpd00443  C00568\n",
       "39                 Biotin      btn  cpd00104  C00120\n",
       "40         Nicotinic acid      nac  cpd00218  C00253\n",
       "41  Ca-D-Pantothenic acid  pnto__R  cpd00644  C00864\n",
       "42      Pyridoxamine-2HCl    pydam  cpd00419  C00534\n",
       "43    Thiamine-dichloride      thm  cpd00305  C00378\n",
       "44             Riboflavin   ribflv  cpd00220  C00255\n",
       "45                 Oxygen       o2  cpd00007  C00007\n",
       "46                   Fe3+      fe2  cpd10516  C14819\n",
       "47                  Water      h2o  cpd00001  C00001\n",
       "48                    Co2      co2  cpd00011  C00011"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Import SNM3 compund files\n",
    "snm3 = pd.read_csv(\"SNM3.csv\", sep=\";\")\n",
    "snm3"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2) SNM growth testing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "model_DP = cobra.io.read_sbml_model(\"models/consistent_DP.xml\")\n",
    "model_SA = cobra.io.read_sbml_model(\"models/consistent_iYS854.xml\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We will use as default:\n",
    "* Lower bound -10\n",
    "* Lower bound O2 -20\n",
    "* Lower bound Fe -0.1\n",
    "* Upper bound: 1000"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of exchange reactions: 64\n",
      "Number of exchange reactions: 83\n"
     ]
    }
   ],
   "source": [
    "print(f\"Number of exchange reactions: {len(model_DP.exchanges)}\")\n",
    "print(f\"Number of exchange reactions: {len(model_SA.exchanges)}\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Checking bounds\n",
    "for f in model_DP.exchanges:\n",
    "    if f.id == \"EX_o2_e\":\n",
    "        f.lower_bound=-20\n",
    "    elif f.id == \"EX_fe2_e\":\n",
    "        f.lower_bound=-0.1\n",
    "    else: \n",
    "        f.lower_bound=-10\n",
    "    f.upper_bound=1000"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Checking bounds\n",
    "for f in model_SA.exchanges:\n",
    "    if f.id == \"EX_o2_e\":\n",
    "        f.lower_bound=-20\n",
    "    elif f.id == \"EX_fe2_e\":\n",
    "        f.lower_bound=-0.1\n",
    "    else: \n",
    "        f.lower_bound=-10\n",
    "    f.upper_bound=1000"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.38177836171798285\n"
     ]
    }
   ],
   "source": [
    "# Check for growth with all exchanges turend on\n",
    "sol = model_DP.optimize()\n",
    "print(sol.objective_value)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "5.026388539834129\n"
     ]
    }
   ],
   "source": [
    "# Check for growth with all exchanges turend on\n",
    "sol = model_SA.optimize()\n",
    "print(sol.objective_value)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "From this summary we observe that for maximal growth the bacterium needs most importantly glucose, L-glutamate, phosphate, glycin, L-arginine, oxygen and L-leucin. As checked by the next for loop all the necessary metabolites are available in SNM3, except L-Isoleucine and Meso-2,6-Diaminoheptanedioate.\n",
    "\n",
    "One further have to check if those two metabolites are essential for growth or not."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "So they are not synthesizable. We will now test if the model can grow on SNM3 media, which we define as following:\n",
    "* The SNM3 media contains all metbolites listed in \"snm3.csv\" that **have a BiGG ID** listed and **are exchange reactions of the model**.\n",
    "* The concentration is set to 10, except for o2 it is set to 20. This is equivalent with having all inward exchange reactions that are in the SNM3 media to -10 (o2 to -20) else to 0."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.0\n"
     ]
    }
   ],
   "source": [
    "# Create full snm3 media \n",
    "snm3_media = dict()\n",
    "ex_ids = [e.id for e in model_DP.exchanges]\n",
    "for id in snm3[\"BiGG\"]:\n",
    "    id = \"EX_\" + str(id) + \"_e\"\n",
    "    if id in ex_ids:\n",
    "        snm3_media[id] = 10\n",
    "        if id == \"EX_o2_e\":\n",
    "            snm3_media[id] = 20\n",
    "        if \"EX_fe\" in id:\n",
    "            snm3_media[id] = 0.1\n",
    "# Tets for growth...\n",
    "with model_DP:\n",
    "    model_DP.medium = snm3_media\n",
    "    print(model_DP.slim_optimize())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.28236539253224846\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<h3>Objective</h3><p>1.0 Growth = 0.28236539253224846</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>26dap__M_e</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>0.02734</td>\n",
       "      <td>7</td>\n",
       "      <td>0.27%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4abz_e</td>\n",
       "      <td>EX_4abz_e</td>\n",
       "      <td>0.0001829</td>\n",
       "      <td>7</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>ala__L_e</td>\n",
       "      <td>EX_ala__L_e</td>\n",
       "      <td>0.6182</td>\n",
       "      <td>3</td>\n",
       "      <td>2.63%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>arg__L_e</td>\n",
       "      <td>EX_arg__L_e</td>\n",
       "      <td>0.4395</td>\n",
       "      <td>6</td>\n",
       "      <td>3.74%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>ca2_e</td>\n",
       "      <td>EX_ca2_e</td>\n",
       "      <td>0.01468</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cl_e</td>\n",
       "      <td>EX_cl_e</td>\n",
       "      <td>0.01659</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cobalt2_e</td>\n",
       "      <td>EX_cobalt2_e</td>\n",
       "      <td>0.009982</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cu2_e</td>\n",
       "      <td>EX_cu2_e</td>\n",
       "      <td>0.009257</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cys__L_e</td>\n",
       "      <td>EX_cys__L_e</td>\n",
       "      <td>0.02654</td>\n",
       "      <td>3</td>\n",
       "      <td>0.11%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>fe2_e</td>\n",
       "      <td>EX_fe2_e</td>\n",
       "      <td>0.02107</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>glc__D_e</td>\n",
       "      <td>EX_glc__D_e</td>\n",
       "      <td>10</td>\n",
       "      <td>6</td>\n",
       "      <td>85.12%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>glu__L_e</td>\n",
       "      <td>EX_glu__L_e</td>\n",
       "      <td>0.1714</td>\n",
       "      <td>5</td>\n",
       "      <td>1.22%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>gly_e</td>\n",
       "      <td>EX_gly_e</td>\n",
       "      <td>0.2819</td>\n",
       "      <td>2</td>\n",
       "      <td>0.80%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>his__L_e</td>\n",
       "      <td>EX_his__L_e</td>\n",
       "      <td>0.02591</td>\n",
       "      <td>6</td>\n",
       "      <td>0.22%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>ile__L_e</td>\n",
       "      <td>EX_ile__L_e</td>\n",
       "      <td>0.07944</td>\n",
       "      <td>6</td>\n",
       "      <td>0.68%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>k_e</td>\n",
       "      <td>EX_k_e</td>\n",
       "      <td>0.01505</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>leu__L_e</td>\n",
       "      <td>EX_leu__L_e</td>\n",
       "      <td>0.1232</td>\n",
       "      <td>6</td>\n",
       "      <td>1.05%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>lys__L_e</td>\n",
       "      <td>EX_lys__L_e</td>\n",
       "      <td>0.09384</td>\n",
       "      <td>6</td>\n",
       "      <td>0.80%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>met__L_e</td>\n",
       "      <td>EX_met__L_e</td>\n",
       "      <td>0.04209</td>\n",
       "      <td>5</td>\n",
       "      <td>0.30%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>mg2_e</td>\n",
       "      <td>EX_mg2_e</td>\n",
       "      <td>0.0242</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>mn2_e</td>\n",
       "      <td>EX_mn2_e</td>\n",
       "      <td>0.01071</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>na1_e</td>\n",
       "      <td>EX_na1_e</td>\n",
       "      <td>0.02559</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>nac_e</td>\n",
       "      <td>EX_nac_e</td>\n",
       "      <td>0.003363</td>\n",
       "      <td>6</td>\n",
       "      <td>0.03%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>ni2_e</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>0.01002</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>o2_e</td>\n",
       "      <td>EX_o2_e</td>\n",
       "      <td>2.25</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>phe__L_e</td>\n",
       "      <td>EX_phe__L_e</td>\n",
       "      <td>0.08837</td>\n",
       "      <td>9</td>\n",
       "      <td>1.13%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>pi_e</td>\n",
       "      <td>EX_pi_e</td>\n",
       "      <td>0.2414</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>pro__L_e</td>\n",
       "      <td>EX_pro__L_e</td>\n",
       "      <td>0.06045</td>\n",
       "      <td>5</td>\n",
       "      <td>0.43%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>ribflv_e</td>\n",
       "      <td>EX_ribflv_e</td>\n",
       "      <td>0.000122</td>\n",
       "      <td>17</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>so4_e</td>\n",
       "      <td>EX_so4_e</td>\n",
       "      <td>0.006124</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>thm_e</td>\n",
       "      <td>EX_thm_e</td>\n",
       "      <td>6.098E-05</td>\n",
       "      <td>12</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>thr__L_e</td>\n",
       "      <td>EX_thr__L_e</td>\n",
       "      <td>0.06937</td>\n",
       "      <td>4</td>\n",
       "      <td>0.39%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>trp__L_e</td>\n",
       "      <td>EX_trp__L_e</td>\n",
       "      <td>0.01554</td>\n",
       "      <td>11</td>\n",
       "      <td>0.24%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>val__L_e</td>\n",
       "      <td>EX_val__L_e</td>\n",
       "      <td>0.1172</td>\n",
       "      <td>5</td>\n",
       "      <td>0.83%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>zn2_e</td>\n",
       "      <td>EX_zn2_e</td>\n",
       "      <td>0.008994</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>mql8_c</td>\n",
       "      <td>Sink_mql8</td>\n",
       "      <td>2.734E-05</td>\n",
       "      <td>51</td>\n",
       "      <td>0.00%</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>acald_e</td>\n",
       "      <td>EX_acald_e</td>\n",
       "      <td>-18.49</td>\n",
       "      <td>2</td>\n",
       "      <td>62.84%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>co2_e</td>\n",
       "      <td>EX_co2_e</td>\n",
       "      <td>-4.047</td>\n",
       "      <td>1</td>\n",
       "      <td>6.88%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>for_e</td>\n",
       "      <td>EX_for_e</td>\n",
       "      <td>-15.3</td>\n",
       "      <td>1</td>\n",
       "      <td>26.01%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>fum_e</td>\n",
       "      <td>EX_fum_e</td>\n",
       "      <td>-0.1791</td>\n",
       "      <td>4</td>\n",
       "      <td>1.22%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>glyclt_e</td>\n",
       "      <td>EX_glyclt_e</td>\n",
       "      <td>-0.0001829</td>\n",
       "      <td>2</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>h2o_e</td>\n",
       "      <td>EX_h2o_e</td>\n",
       "      <td>-7.687</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>orn_e</td>\n",
       "      <td>EX_orn_e</td>\n",
       "      <td>-0.3586</td>\n",
       "      <td>5</td>\n",
       "      <td>3.05%</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>"
      ],
      "text/plain": [
       "<cobra.summary.model_summary.ModelSummary at 0x7fa37d9fa400>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# This model need these metabolites for growth, hence we will include them in the medium!\n",
    "snm3_media[\"EX_ile__L_e\"] = 10\n",
    "snm3_media[\"EX_met__L_e\"] = 10\n",
    "snm3_media[\"EX_26dap__M_e\"] = 10\n",
    "\n",
    "with model_DP:\n",
    "    model_DP.medium = snm3_media\n",
    "    print(model_DP.slim_optimize())\n",
    "    summary = model_DP.summary()\n",
    "    \n",
    "summary"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra.flux_analysis import flux_variability_analysis\n",
    "fva_DP = cobra.flux_analysis.flux_variability_analysis(model_DP)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Sticking them together\n",
    "df_fluxes = fva.copy()\n",
    "df_fluxes[\"flux\"] = sol.fluxes\n",
    "df_fluxes.to_excel(\"fluxes_DP.xlsx\")\n",
    "df_fluxes.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Exchange fluxes fva, for all non-zero exchanges\n",
    "fva_ex_DP = model_DP.summary(fva=1.0)\n",
    "fva_ex_DP = fva_ex_DP.to_frame()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Get necessary values for plotting\n",
    "x = []\n",
    "y_fluxes = []\n",
    "y_min_flux = []\n",
    "y_max_flux = []\n",
    "for _, data in fva_ex.iterrows():\n",
    "    id = str(data.metabolite[:-2])\n",
    "    f = data.factor*data.flux \n",
    "    f_min = data.factor*data.minimum \n",
    "    f_max = data.factor*data.maximum\n",
    "\n",
    "    if id in snm3[\"BiGG\"].tolist() and not (f_min == 0 and f_max == 0):\n",
    "        x.append(id + \"_e\")\n",
    "        y_fluxes.append(f)\n",
    "        y_min_flux.append(f_min)\n",
    "        y_max_flux.append(f_max)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2.5586946126134027\n"
     ]
    }
   ],
   "source": [
    "# Create full snm3 media \n",
    "snm3_media = dict()\n",
    "ex_ids = [e.id for e in model_SA.exchanges]\n",
    "for id in snm3[\"BiGG\"]:\n",
    "    id = \"EX_\" + str(id) + \"_e\"\n",
    "    if id in ex_ids:\n",
    "        snm3_media[id] = 10\n",
    "        if id == \"EX_o2_e\":\n",
    "            snm3_media[id] = 20\n",
    "        if \"EX_fe\" in id:\n",
    "            snm3_media[id] = 0.1\n",
    "        if \"EX_orn\" in id:\n",
    "            snm3_media[id] = 0.0   \n",
    "            \n",
    "# Test for growth...\n",
    "with model_SA:\n",
    "    model_SA.medium = snm3_media\n",
    "    print(model_SA.slim_optimize())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2.5586946126134027\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<h3>Objective</h3><p>1.0 BIOMASS_iYS_wild_type = 2.5586946126134027</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>arg__L_e</td>\n",
       "      <td>EX_arg__L_e</td>\n",
       "      <td>4.354</td>\n",
       "      <td>6</td>\n",
       "      <td>12.06%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cl_e</td>\n",
       "      <td>EX_cl_e</td>\n",
       "      <td>0.01267</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cys__L_e</td>\n",
       "      <td>EX_cys__L_e</td>\n",
       "      <td>0.4614</td>\n",
       "      <td>3</td>\n",
       "      <td>0.64%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>fe2_e</td>\n",
       "      <td>EX_fe2_e</td>\n",
       "      <td>0.03776</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>glc__D_e</td>\n",
       "      <td>EX_glc__D_e</td>\n",
       "      <td>10</td>\n",
       "      <td>6</td>\n",
       "      <td>27.70%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>glu__L_e</td>\n",
       "      <td>EX_glu__L_e</td>\n",
       "      <td>10</td>\n",
       "      <td>5</td>\n",
       "      <td>23.09%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>his__L_e</td>\n",
       "      <td>EX_his__L_e</td>\n",
       "      <td>0.1542</td>\n",
       "      <td>6</td>\n",
       "      <td>0.43%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>k_e</td>\n",
       "      <td>EX_k_e</td>\n",
       "      <td>0.4751</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>leu__L_e</td>\n",
       "      <td>EX_leu__L_e</td>\n",
       "      <td>0.8035</td>\n",
       "      <td>6</td>\n",
       "      <td>2.23%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>lys__L_e</td>\n",
       "      <td>EX_lys__L_e</td>\n",
       "      <td>0.9223</td>\n",
       "      <td>6</td>\n",
       "      <td>2.56%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>mg2_e</td>\n",
       "      <td>EX_mg2_e</td>\n",
       "      <td>0.02112</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>mn2_e</td>\n",
       "      <td>EX_mn2_e</td>\n",
       "      <td>0.001684</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>mobd_e</td>\n",
       "      <td>EX_mobd_e</td>\n",
       "      <td>1.791E-05</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>na1_e</td>\n",
       "      <td>EX_na1_e</td>\n",
       "      <td>5.091</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>nac_e</td>\n",
       "      <td>EX_nac_e</td>\n",
       "      <td>0.0002162</td>\n",
       "      <td>6</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>o2_e</td>\n",
       "      <td>EX_o2_e</td>\n",
       "      <td>20</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>phe__L_e</td>\n",
       "      <td>EX_phe__L_e</td>\n",
       "      <td>0.2924</td>\n",
       "      <td>9</td>\n",
       "      <td>1.22%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>pyr_e</td>\n",
       "      <td>EX_pyr_e</td>\n",
       "      <td>10</td>\n",
       "      <td>3</td>\n",
       "      <td>13.85%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>ribflv_e</td>\n",
       "      <td>EX_ribflv_e</td>\n",
       "      <td>0.0007638</td>\n",
       "      <td>17</td>\n",
       "      <td>0.01%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>ser__L_e</td>\n",
       "      <td>EX_ser__L_e</td>\n",
       "      <td>10</td>\n",
       "      <td>3</td>\n",
       "      <td>13.85%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>so4_e</td>\n",
       "      <td>EX_so4_e</td>\n",
       "      <td>0.01056</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>thm_e</td>\n",
       "      <td>EX_thm_e</td>\n",
       "      <td>0.001141</td>\n",
       "      <td>12</td>\n",
       "      <td>0.01%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>trp__L_e</td>\n",
       "      <td>EX_trp__L_e</td>\n",
       "      <td>0.03925</td>\n",
       "      <td>11</td>\n",
       "      <td>0.20%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>val__L_e</td>\n",
       "      <td>EX_val__L_e</td>\n",
       "      <td>0.9404</td>\n",
       "      <td>5</td>\n",
       "      <td>2.17%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>zn2_e</td>\n",
       "      <td>EX_zn2_e</td>\n",
       "      <td>0.000829</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2fe1s_c</td>\n",
       "      <td>SK_2fe1s_c</td>\n",
       "      <td>0.0006985</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>apoACP_c</td>\n",
       "      <td>SK_apoACP_c</td>\n",
       "      <td>0.1969</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</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>5drib_c</td>\n",
       "      <td>DM_5drib_c</td>\n",
       "      <td>-0.002303</td>\n",
       "      <td>5</td>\n",
       "      <td>0.01%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>amob_c</td>\n",
       "      <td>DM_amob_c</td>\n",
       "      <td>-5.117E-06</td>\n",
       "      <td>15</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>co2_e</td>\n",
       "      <td>EX_co2_e</td>\n",
       "      <td>-27.98</td>\n",
       "      <td>1</td>\n",
       "      <td>21.99%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>etoh_e</td>\n",
       "      <td>EX_etoh_e</td>\n",
       "      <td>-1.473</td>\n",
       "      <td>2</td>\n",
       "      <td>2.32%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>glyclt_e</td>\n",
       "      <td>EX_glyclt_e</td>\n",
       "      <td>-0.001141</td>\n",
       "      <td>2</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>h2o_e</td>\n",
       "      <td>EX_h2o_e</td>\n",
       "      <td>-27.88</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>lac__L_e</td>\n",
       "      <td>EX_lac__L_e</td>\n",
       "      <td>-30.87</td>\n",
       "      <td>3</td>\n",
       "      <td>72.79%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>nh4_e</td>\n",
       "      <td>EX_nh4_e</td>\n",
       "      <td>-13.2</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>urea_e</td>\n",
       "      <td>EX_urea_e</td>\n",
       "      <td>-3.498</td>\n",
       "      <td>1</td>\n",
       "      <td>2.75%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>ahcys_c</td>\n",
       "      <td>SK_ahcys_c</td>\n",
       "      <td>-0.01264</td>\n",
       "      <td>14</td>\n",
       "      <td>0.14%</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>"
      ],
      "text/plain": [
       "<cobra.summary.model_summary.ModelSummary at 0x7fa37d92f9a0>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "with model_SA:\n",
    "    model_SA.medium = snm3_media\n",
    "    print(model_SA.slim_optimize())\n",
    "    summary = model_SA.summary()\n",
    "    \n",
    "summary"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>minimum</th>\n",
       "      <th>maximum</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>10M3HDHL</th>\n",
       "      <td>0.015238</td>\n",
       "      <td>0.015238</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10M3OACPO</th>\n",
       "      <td>0.290758</td>\n",
       "      <td>0.290758</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10M3OUO</th>\n",
       "      <td>0.015238</td>\n",
       "      <td>0.015238</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10MDOD</th>\n",
       "      <td>0.290758</td>\n",
       "      <td>0.290758</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10MTDAO</th>\n",
       "      <td>0.290758</td>\n",
       "      <td>0.290758</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GLYCLTt</th>\n",
       "      <td>-0.002242</td>\n",
       "      <td>-0.002242</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>r2535</th>\n",
       "      <td>-178.841332</td>\n",
       "      <td>10.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UAG2EMA</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>172.348617</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GLUt3</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>1180.388228</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASPte</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>1186.112436</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>928 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              minimum      maximum\n",
       "10M3HDHL     0.015238     0.015238\n",
       "10M3OACPO    0.290758     0.290758\n",
       "10M3OUO      0.015238     0.015238\n",
       "10MDOD       0.290758     0.290758\n",
       "10MTDAO      0.290758     0.290758\n",
       "...               ...          ...\n",
       "GLYCLTt     -0.002242    -0.002242\n",
       "r2535     -178.841332    10.000000\n",
       "UAG2EMA      0.000000   172.348617\n",
       "GLUt3        0.000000  1180.388228\n",
       "ASPte        0.000000  1186.112436\n",
       "\n",
       "[928 rows x 2 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from cobra.flux_analysis import flux_variability_analysis\n",
    "flux_variability_analysis(model_SA, model_SA.reactions)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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