{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import logging"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "logging.basicConfig(level=\"INFO\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra.io import load_model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra.flux_analysis import flux_variability_analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:cobra.core.model:The current solver interface glpk doesn't support setting the optimality tolerance.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Scaling...\n",
      " A: min|aij| =  1.000e+00  max|aij| =  1.000e+00  ratio =  1.000e+00\n",
      "Problem data seem to be well scaled\n"
     ]
    }
   ],
   "source": [
    "model = load_model(\"iJO1366\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 7.15 s, sys: 119 ms, total: 7.27 s\n",
      "Wall time: 7.55 s\n"
     ]
    },
    {
     "data": {
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       "    <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>DM_4crsol_c</th>\n",
       "      <td>0.000208</td>\n",
       "      <td>0.000219</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DM_5drib_c</th>\n",
       "      <td>0.000210</td>\n",
       "      <td>0.112258</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DM_aacald_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DM_amob_c</th>\n",
       "      <td>0.000002</td>\n",
       "      <td>0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DM_mththf_c</th>\n",
       "      <td>0.000418</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "      <th>ZN2abcpp</th>\n",
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       "    <tr>\n",
       "      <th>ZN2t3pp</th>\n",
       "      <td>0.000000</td>\n",
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       "    <tr>\n",
       "      <th>ZN2tpp</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>47.370318</td>\n",
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       "    <tr>\n",
       "      <th>ZNabcpp</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>9.474064</td>\n",
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       "    <tr>\n",
       "      <th>Zn2tex</th>\n",
       "      <td>0.000318</td>\n",
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      ],
      "text/plain": [
       "              minimum    maximum\n",
       "DM_4crsol_c  0.000208   0.000219\n",
       "DM_5drib_c   0.000210   0.112258\n",
       "DM_aacald_c  0.000000   0.000000\n",
       "DM_amob_c    0.000002   0.000002\n",
       "DM_mththf_c  0.000418   0.515309\n",
       "...               ...        ...\n",
       "ZN2abcpp     0.000000  11.842500\n",
       "ZN2t3pp      0.000000  47.370000\n",
       "ZN2tpp       0.000000  47.370318\n",
       "ZNabcpp      0.000000   9.474064\n",
       "Zn2tex       0.000318   0.000335\n",
       "\n",
       "[2583 rows x 2 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%time flux_variability_analysis(model, fraction_of_optimum=0.95, processes=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 106 ms, sys: 75.7 ms, total: 182 ms\n",
      "Wall time: 4.74 s\n"
     ]
    },
    {
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       "      <th>maximum</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>DM_4crsol_c</th>\n",
       "      <td>0.000208</td>\n",
       "      <td>0.000219</td>\n",
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       "    <tr>\n",
       "      <th>DM_5drib_c</th>\n",
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       "      <td>0.112258</td>\n",
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       "    <tr>\n",
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       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
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       "      <th>DM_amob_c</th>\n",
       "      <td>0.000002</td>\n",
       "      <td>0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DM_mththf_c</th>\n",
       "      <td>0.000418</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <th>ZN2t3pp</th>\n",
       "      <td>0.000000</td>\n",
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       "</table>\n",
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      "text/plain": [
       "              minimum    maximum\n",
       "DM_4crsol_c  0.000208   0.000219\n",
       "DM_5drib_c   0.000210   0.112258\n",
       "DM_aacald_c  0.000000   0.000000\n",
       "DM_amob_c    0.000002   0.000002\n",
       "DM_mththf_c  0.000418   0.515309\n",
       "...               ...        ...\n",
       "ZN2abcpp     0.000000  11.842500\n",
       "ZN2t3pp      0.000000  47.370000\n",
       "ZN2tpp       0.000000  47.370318\n",
       "ZNabcpp      0.000000   9.474064\n",
       "Zn2tex       0.000318   0.000335\n",
       "\n",
       "[2583 rows x 2 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%time flux_variability_analysis(model, fraction_of_optimum=0.95, processes=4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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