Master_Code.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import mfapy\n",
    "%matplotlib inline\n",
    "import numpy as np\n",
    "import scipy.integrate\n",
    "from matplotlib import pyplot as plt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Enter the name of the metabolic model .txt file: Elim2_model.txt\n",
      "Enter the name of the .csv file containing the parameters: Elim2_status.csv\n",
      "Enter the name of the MDV .txt file: Elim2_mdv.txt\n"
     ]
    }
   ],
   "source": [
    "# User input code goes here:\n",
    "\n",
    "simulation_model = input(\"Enter the name of the metabolic model .txt file: \")\n",
    "\n",
    "simulation_csv = input(\"Enter the name of the .csv file containing the parameters: \")\n",
    "\n",
    "MDV_data = input(\"Enter the name of the MDV .txt file: \")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Caution: Formate was not used in the metabolid network\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Sets up model variables using simulation model.txt file\n",
    "reactions, reversible, metabolites, target_fragments = mfapy.mfapyio.load_metabolic_model(simulation_model, format=\"text\")\n",
    "model = mfapy.metabolicmodel.MetabolicModel(reactions, reversible, metabolites, target_fragments)\n",
    "\n",
    "#loads states and values from .csv file\n",
    "flux = model.load_states(simulation_csv, format = 'csv')\n",
    "model.set_constraints_from_state_dict(flux)\n",
    "model.update()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Generation of CarbonSource instance\n",
    "cs1 = model.generate_carbon_source_template()\n",
    "cs1.set_each_isotopomer('SubsCO2',{'#0': 0.01, '#1': 0.99}, correction = 'yes')\n",
    "cs1.set_each_isotopomer('Subsmeoh',{'#0': 1.0, '#1': 0.0}, correction = 'yes')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Load MDV data\n",
    "mdv1 = model.load_mdv_data(MDV_data) #string variable from user input\n",
    "\n",
    "#include more if there are more data files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Flux estimation Step 1: Setting experimments\n",
    "model.set_experiment('ex1', mdv1, cs1)\n",
    "#include more for more data sets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "# Flux estimation step 2: Generation of intical flux vectors\n",
    "initialstate, flux_initial = model.generate_initial_states(50, 4, method =\"normal\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "# Flux estimation step 3: Fitting model\n",
    "\n",
    "#GN_CRS2_LM    \n",
    "initialstate, RSS, flux_opt_GN_CRS2_LM = model.fitting_flux(method = \"GN_CRS2_LM\", flux = flux_initial)\n",
    "\n",
    "#SLSQP\n",
    "initialstate, RSS, flux_opt_SLSQP = model.fitting_flux(method = \"SLSQP\", flux = flux_initial)\n",
    "\n",
    "#LN_SBPLX\n",
    "initialstate, RSS, flux_opt_LN_SBPLX = model.fitting_flux(method = \"LN_SBPLX\", flux = flux_initial)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Id             Reaction                 External i GN_CRS2\n",
      "RSS                                               800435.91\n",
      "Thres                                                38.89\n",
      "p_value                                               0.00\n",
      "Id             Reaction                 External i GN_CRS2 Type     Value Stdev    lb    ub Atom_mapping             \n",
      "r1             SubsGlc-->G6P            (kegg:R028     0.0 fixed      0.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r2             G6P-->F6P                (kegg:R007   110.9 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r3             F6P-->G6P                (kegg:R007   186.7 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r4             F6P-->FBP                (kegg:R007   725.0 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r5             FBP-->F6P                (kegg:R010   781.6 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r6             FBP-->DHAP+GAP           (kegg:R010   563.2 free       1.0   1.0   0.01000.0 ABCDEF-->CBA+DEF         \n",
      "r7             DHAP+GAP-->FBP           (kegg:R010   619.8 free       1.0   1.0   0.01000.0 CBA+DEF-->ABCDEF         \n",
      "r8             DHAP-->GAP               (kegg:R010   660.8 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r9             GAP-->DHAP               (kegg:R010   717.9 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r10            GAP-->PGA                (kegg:R010   263.5 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r11            PGA-->GAP                (kegg:R015   327.8 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r12            PGA-->PEP                (kegg:R015   611.7 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r13            PEP-->PGA                (kegg:R002   682.9 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r14            PEP-->Pyr                (kegg:R011   675.5 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r15            Pyr-->PEP                (kegg:R003   891.0 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r16            Pyr-->AcCOA+CO2in        (kegg:R007    54.4 free       1.0   1.0   0.01000.0 ABC-->BC+A               \n",
      "r17            AcCOA+Oxa-->IsoCit       (kegg:R007    21.2 free       1.0   1.0   0.01000.0 AB+CDEF-->FEDBAC         \n",
      "r18            IsoCit-->aKG+CO2in       (kegg:R011    16.5 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDE+F         \n",
      "r19            aKG-->Suc+CO2in          (kegg:R021    11.5 free       1.0   1.0   0.01000.0 ABCDE-->BCDE+A           \n",
      "r20            Suc-->Fum                (kegg:R021   951.9 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r21            Fum-->Suc                (kegg:R010   935.6 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r22            Fum-->Mal                (kegg:R010   954.3 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r23            Mal-->Fum                (kegg:R003   938.1 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r24            Mal-->Oxa                (kegg:R003    65.3 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r25            Oxa-->Mal                (kegg:R003   176.7 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r26            IsoCit+AcCOA-->Mal+Suc   (kegg:R002     4.8 free       1.0   1.0   0.01000.0 ABCDEF+GH-->ABHG+FCDE    \n",
      "r27            G6P-->m6PG               (kegg:R008    74.9 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r28            m6PG-->Ru5P+CO2in        (kegg:R015    34.4 free       1.0   1.0   0.01000.0 ABCDEF-->BCDEF+A         \n",
      "r29            Ru5P-->R5P               (kegg:R010   158.2 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r30            R5P-->Ru5P               (kegg:R010   143.5 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r31            Ru5P-->Xu5P              (kegg:R015   117.1 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r32            Xu5P-->Ru5P              (kegg:R015    97.5 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r33            R5P+Xu5P-->S7P+GAP       (kegg:R016   686.6 free       1.0   1.0   0.01000.0 ABCDE+FGHIJ-->FGABCDE+HIJ\n",
      "r34            GAP+S7P-->Xu5P+R5P       (kegg:R016   676.0 free       1.0   1.0   0.01000.0 HIJ+FGABCDE-->FGHIJ+ABCDE\n",
      "r35            GAP+S7P-->F6P+E4P        (kegg:R085   664.4 free       1.0   1.0   0.01000.0 ABC+DEFGHIJ-->DEFABC+GHIJ\n",
      "r36            E4P+F6P-->S7P+GAP        (kegg:R085   653.8 free       1.0   1.0   0.01000.0 GHIJ+DEFABC-->DEFGHIJ+ABC\n",
      "r37            E4P+Xu5P-->F6P+GAP       (kegg:R010   121.2 free       1.0   1.0   0.01000.0 ABCD+EFGHI-->EFABCD+GHI  \n",
      "r38            GAP+F6P-->Xu5P+E4P       (kegg:R010   112.2 free       1.0   1.0   0.01000.0 GHI+EFABCD-->EFGHI+ABCD  \n",
      "r39            m6PG-->Pyr+GAP           (kegg:R007    40.5 free       1.0   1.0   0.01000.0 ABCDEF-->ABC+DEF         \n",
      "r40            PEP+CO2in-->Oxa          (kegg:Lace   487.0 free       1.0   1.0   0.01000.0 ABC+D-->ABCD             \n",
      "r41            Oxa-->PEP+CO2in          (kegg:Subs   346.1 free       1.0   1.0   0.01000.0 ABCD-->ABC+D             \n",
      "r42            Mal-->Pyr+CO2in          (kegg:R002   132.4 free       1.0   1.0   0.01000.0 ABCD-->ABC+D             \n",
      "r49            AcCOA-->Acetate          (kegg:Aspe     4.3 free       1.0   1.0   0.01000.0 AB-->AB                  \n",
      "r50            Acetate-->Acetateex      (kegg:R004     4.3 fitting   36.8   2.8   0.01000.0 nd                       \n",
      "r56            SubsCO2-->CO2in          (kegg:Subs   105.3 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r57            CO2in-->CO2ex            (kegg:Glu)     3.8 free       1.0   1.0   0.01000.0 nd                       \n",
      "r58            Pyr-->Ala                (kegg:Arg)    10.0 pseudo     1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r59            Oxa-->Asp                (kegg:R003    10.0 pseudo     1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r60            Oxa-->Thr                (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r61            aKG-->Glu                (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r62            E4P+PEP+PEP-->Phe        (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCD+EFG+HIJ-->EFGIJABCD \n",
      "r63            E4P+PEP+PEP-->Tyr        (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCD+EFG+HIJ-->EFGIJABCD \n",
      "r64            Oxa+Pyr-->Ile            (kegg:R015    10.0 pseudo     1.0   1.0   0.01000.0 ABCD+EFG-->ABFGCD        \n",
      "r65            AcCOA+Pyr+Pyr-->Leu      (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 AB+CDE+FGH-->ABDEGH      \n",
      "r66            Pyr+Pyr-->Val            (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABC+DEF-->ABECF          \n",
      "r67            PGA-->Ser                (kegg:Biom     4.3 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r68            Ser-->Gly+MEETHF         (kegg:Glu2   773.8 free       1.0   1.0   0.01000.0 ABC-->AB+C               \n",
      "r69            Gly+MEETHF-->Ser         (kegg:Biom   771.1 free       1.0   1.0   0.01000.0 AB+C-->ABC               \n",
      "r72            G6P-->Biomass            (kegg:Biom     1.0 fixed      1.0   1.0   0.01000.0 nd                       \n",
      "r73            F6P-->Biomass            (kegg:Biom     0.3 fixed      0.3   1.0   0.01000.0 nd                       \n",
      "r74            DHAP-->Biomass           (kegg:Biom     0.6 fixed      0.6   1.0   0.01000.0 nd                       \n",
      "r75            PGA-->Biomass            (kegg:CO2e     2.6 fixed      2.6   1.0   0.01000.0 nd                       \n",
      "r76            Ser-->Biomass            (kegg:Subs     1.6 fixed      1.6   1.0   0.01000.0 nd                       \n",
      "r77            Gly-->Biomass            (keggPGAex     2.7 fixed      2.7   1.0   0.01000.0 nd                       \n",
      "r78            MEETHF-->Biomass         (kegg:FAex     3.1 fixed      3.1   1.0   0.01000.0 nd                       \n",
      "r79            PEP-->Biomass            (kegg:MAL_     3.3 fixed      3.3   1.0   0.01000.0 nd                       \n",
      "r80            Pyr-->Biomass            (kegg:MAL_    13.1 fixed     13.1   1.0   0.01000.0 nd                       \n",
      "r81            AcCOA-->Biomass          (kegg:OXA_    13.6 fixed     13.6   1.0   0.01000.0 nd                       \n",
      "r82            aKG-->Biomass            (kegg:OXA_     5.0 fixed      5.0   1.0   0.01000.0 nd                       \n",
      "r83            Oxa-->Biomass            (kegg:ATP)     8.3 fixed      8.3   1.0   0.01000.0 nd                       \n",
      "r84            R5P-->Biomass            (kegg:NADH     4.2 fixed      4.2   1.0   0.01000.0 nd                       \n",
      "r85            E4P-->Biomass            (kegg:NADP     1.7 fixed      1.7   1.0   0.01000.0 nd                       \n",
      "r86            Ala-->Alaex              (kegg:Arg)    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r87            Asp-->Aspex              (kegg:R003    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r88            Thr-->Threx              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r89            Glu-->Gluex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r90            Phe-->Pheex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r91            Tyr-->Tyrex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r92            Ile-->Ileex              (kegg:R015    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r93            Leu-->Leuex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r94            Val-->Valex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r104           Subsmeoh-->meoh          (kegg:MTI/   100.0 fixed    100.0   1.0   0.01000.0 A-->A                    \n",
      "r105           meoh-->METHF             (kegg:TBD)   100.0 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r106           METHF-->MEETHF           (kegg:TBD)   661.5 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r107           MEETHF-->METHF           (kegg:TBD)   661.1 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r108           CO2in+METHF-->AcCOA      (kegg:TBD)    99.6 free       1.0   1.0   0.01000.0 A+B-->AB                 \n",
      "r109           AcCOA+CO2in-->Pyr        (kegg:R007   110.1 free       1.0   1.0   0.01000.0 BC+A-->ABC               \n",
      "PGI            r2<=>r3                  (kegg:R007   -75.8 free       1.0   1.0-300.0 300.0                          \n",
      "FBA            r4<=>r5                  (kegg:R010   -56.6 free       1.0   1.0-300.0 300.0                          \n",
      "TPI            r8<=>r9                  (kegg:R010   -57.2 free       1.0   1.0-300.0 300.0                          \n",
      "GAPDH          r10<=>r11                (kegg:R010   -64.3 free       1.0   1.0-300.0 300.0                          \n",
      "PEPH           r12<=>r13                (kegg:R015   -71.2 free       1.0   1.0-300.0 300.0                          \n",
      "SDH            r20<=>r21                (kegg:R021    16.2 free       1.0   1.0-300.0 300.0                          \n",
      "MDH            r24<=>r25                (kegg:R003  -111.4 free       1.0   1.0-300.0 300.0                          \n",
      "RPI            r29<=>r30                (kegg:R010    14.8 free       1.0   1.0-300.0 300.0                          \n",
      "RBE            r31<=>r32                (kegg:R015    19.6 free       1.0   1.0-300.0 300.0                          \n",
      "TKT1           r33<=>r34                (kegg:R016    10.6 free       1.0   1.0-300.0 300.0                          \n",
      "TAL            r35<=>r36                (kegg:R085    10.6 free       1.0   1.0-300.0 300.0                          \n",
      "TKT2           r37<=>r38                (kegg:R010     9.0 free       1.0   1.0-300.0 300.0                          \n",
      "FH             r22<=>r23                (kegg:R010    16.2 free       1.0   1.0-300.0 300.0                          \n",
      "THF            r106<=>r107              (kegg:TBD)     0.4 free       1.0   1.0-300.0 300.0                          \n",
      "PFOR           r16<=>r109               (kegg:R007   -55.7 free       1.0   1.0-300.0 300.0                          \n",
      "Experiment     Fragment_N               Time       GN_CRS2     Use  Ratio Stdev\n",
      "ex1            AlaMes_0                 0.00        0.0735       1 0.1711  0.00\n",
      "ex1            AlaMes_1                 0.00        0.3570       1 0.3666  0.00\n",
      "ex1            AlaMes_2                 0.00        0.4786       1 0.3955  0.00\n",
      "ex1            AlaMes_3                 0.00        0.0908       1 0.0668  0.00\n",
      "ex1            AspMes_0                 0.00        0.0190       1 0.0491  0.00\n",
      "ex1            AspMes_1                 0.00        0.1467       1 0.2283  0.00\n",
      "ex1            AspMes_2                 0.00        0.3874       1 0.3903  0.00\n",
      "ex1            AspMes_3                 0.00        0.3772       1 0.2899  0.00\n",
      "ex1            AspMes_4                 0.00        0.0697       1 0.0424  0.00\n",
      "ex1            GluMes_0                 0.00        0.0146       1 0.0281  0.00\n",
      "ex1            GluMes_1                 0.00        0.1218       1 0.1522  0.01\n",
      "ex1            GluMes_2                 0.00        0.3511       1 0.4344  0.00\n",
      "ex1            GluMes_3                 0.00        0.3894       1 0.3083  0.00\n",
      "ex1            GluMes_4                 0.00        0.1150       1 0.0704  0.00\n",
      "ex1            GluMes_5                 0.00        0.0080       1 0.0067  0.00\n",
      "ex1            GlyMes_0                 0.00        0.1485       1 0.2079  0.02\n",
      "ex1            GlyMes_1                 0.00        0.4952       1 0.4306  0.03\n",
      "ex1            GlyMes_2                 0.00        0.3563       1 0.3616  0.01\n",
      "ex1            IleMes_0                 0.00        0.0045       1 0.0414  0.00\n",
      "ex1            IleMes_1                 0.00        0.0463       1 0.2209  0.00\n",
      "ex1            IleMes_2                 0.00        0.1838       1 0.3536  0.00\n",
      "ex1            IleMes_3                 0.00        0.3474       1 0.2747  0.00\n",
      "ex1            IleMes_4                 0.00        0.3059       1 0.0932  0.00\n",
      "ex1            IleMes_5                 0.00        0.1012       1 0.0150  0.00\n",
      "ex1            IleMes_6                 0.00        0.0109       1 0.0013  0.00\n",
      "ex1            PheMes_0                 0.00        0.0006       1 0.0068  0.01\n",
      "ex1            PheMes_1                 0.00        0.0075       1 0.0479  0.00\n",
      "ex1            PheMes_2                 0.00        0.0425       1 0.1279  0.00\n",
      "ex1            PheMes_3                 0.00        0.1333       1 0.2236  0.00\n",
      "ex1            PheMes_4                 0.00        0.2506       1 0.2757  0.00\n",
      "ex1            PheMes_5                 0.00        0.2864       1 0.2054  0.00\n",
      "ex1            PheMes_6                 0.00        0.1931       1 0.0891  0.00\n",
      "ex1            PheMes_7                 0.00        0.0717       1 0.0205  0.00\n",
      "ex1            PheMes_8                 0.00        0.0134       1 0.0028  0.00\n",
      "ex1            PheMes_9                 0.00        0.0010       1 0.0002  0.00\n",
      "ex1            SerMes_0                 0.00        0.1440       1 0.1944  0.01\n",
      "ex1            SerMes_1                 0.00        0.4847       1 0.3909  0.01\n",
      "ex1            SerMes_2                 0.00        0.3608       1 0.3555  0.00\n",
      "ex1            SerMes_3                 0.00        0.0105       1 0.0592  0.00\n",
      "ex1            ThrMes_0                 0.00        0.0190       1 0.0517  0.00\n",
      "ex1            ThrMes_1                 0.00        0.1467       1 0.2460  0.00\n",
      "ex1            ThrMes_2                 0.00        0.3874       1 0.3859  0.00\n",
      "ex1            ThrMes_3                 0.00        0.3772       1 0.2817  0.00\n",
      "ex1            ThrMes_4                 0.00        0.0697       1 0.0346  0.00\n",
      "ex1            TyrMes_0                 0.00        0.0006       1 0.0202  0.00\n",
      "ex1            TyrMes_1                 0.00        0.0075       1 0.0456  0.00\n",
      "ex1            TyrMes_2                 0.00        0.0425       1 0.1255  0.00\n",
      "ex1            TyrMes_3                 0.00        0.1333       1 0.2152  0.00\n",
      "ex1            TyrMes_4                 0.00        0.2506       1 0.2615  0.00\n",
      "ex1            TyrMes_5                 0.00        0.2864       1 0.2087  0.00\n",
      "ex1            TyrMes_6                 0.00        0.1931       1 0.0936  0.00\n",
      "ex1            TyrMes_7                 0.00        0.0717       1 0.0255  0.00\n",
      "ex1            TyrMes_8                 0.00        0.0134       1 0.0039  0.00\n",
      "ex1            TyrMes_9                 0.00        0.0010       1 0.0004  0.00\n",
      "ex1            ValMes_0                 0.00        0.0174       1 0.1302  0.00\n",
      "ex1            ValMes_1                 0.00        0.1293       1 0.2622  0.00\n",
      "ex1            ValMes_2                 0.00        0.3416       1 0.3395  0.00\n",
      "ex1            ValMes_3                 0.00        0.3677       1 0.2167  0.00\n",
      "ex1            ValMes_4                 0.00        0.1299       1 0.0473  0.00\n",
      "ex1            ValMes_5                 0.00        0.0142       1 0.0041  0.00\n",
      "\n"
     ]
    }
   ],
   "source": [
    "#Print results of each method onto the console\n",
    "model.show_results([(\"GN_CRS2_LM\", flux_opt_GN_CRS2_LM[0])])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Id             Reaction                 External i   SLSQP\n",
      "RSS                                               462854.64\n",
      "Thres                                                38.89\n",
      "p_value                                               0.00\n",
      "Id             Reaction                 External i   SLSQP Type     Value Stdev    lb    ub Atom_mapping             \n",
      "r1             SubsGlc-->G6P            (kegg:R028     0.0 fixed      0.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r2             G6P-->F6P                (kegg:R007   259.6 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r3             F6P-->G6P                (kegg:R007   272.1 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r4             F6P-->FBP                (kegg:R007   791.7 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r5             FBP-->F6P                (kegg:R010   800.3 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r6             FBP-->DHAP+GAP           (kegg:R010   567.2 free       1.0   1.0   0.01000.0 ABCDEF-->CBA+DEF         \n",
      "r7             DHAP+GAP-->FBP           (kegg:R010   575.7 free       1.0   1.0   0.01000.0 CBA+DEF-->ABCDEF         \n",
      "r8             DHAP-->GAP               (kegg:R010   695.4 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r9             GAP-->DHAP               (kegg:R010   704.5 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r10            GAP-->PGA                (kegg:R010   381.0 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r11            PGA-->GAP                (kegg:R015   397.2 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r12            PGA-->PEP                (kegg:R015   617.7 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r13            PEP-->PGA                (kegg:R002   640.9 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r14            PEP-->Pyr                (kegg:R011   668.9 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r15            Pyr-->PEP                (kegg:R003   833.1 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r16            Pyr-->AcCOA+CO2in        (kegg:R007   100.3 free       1.0   1.0   0.01000.0 ABC-->BC+A               \n",
      "r17            AcCOA+Oxa-->IsoCit       (kegg:R007    33.2 free       1.0   1.0   0.01000.0 AB+CDEF-->FEDBAC         \n",
      "r18            IsoCit-->aKG+CO2in       (kegg:R011     5.0 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDE+F         \n",
      "r19            aKG-->Suc+CO2in          (kegg:R021     0.0 free       1.0   1.0   0.01000.0 ABCDE-->BCDE+A           \n",
      "r20            Suc-->Fum                (kegg:R021   925.1 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r21            Fum-->Suc                (kegg:R010   896.9 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r22            Fum-->Mal                (kegg:R010   904.4 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r23            Mal-->Fum                (kegg:R003   876.2 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r24            Mal-->Oxa                (kegg:R003    66.9 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r25            Oxa-->Mal                (kegg:R003   163.1 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r26            IsoCit+AcCOA-->Mal+Suc   (kegg:R002    28.1 free       1.0   1.0   0.01000.0 ABCDEF+GH-->ABHG+FCDE    \n",
      "r27            G6P-->m6PG               (kegg:R008    11.5 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r28            m6PG-->Ru5P+CO2in        (kegg:R015    11.4 free       1.0   1.0   0.01000.0 ABCDEF-->BCDEF+A         \n",
      "r29            Ru5P-->R5P               (kegg:R010   140.5 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r30            R5P-->Ru5P               (kegg:R010   133.4 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r31            Ru5P-->Xu5P              (kegg:R015    88.8 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r32            Xu5P-->Ru5P              (kegg:R015    84.5 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r33            R5P+Xu5P-->S7P+GAP       (kegg:R016   711.0 free       1.0   1.0   0.01000.0 ABCDE+FGHIJ-->FGABCDE+HIJ\n",
      "r34            GAP+S7P-->Xu5P+R5P       (kegg:R016   708.0 free       1.0   1.0   0.01000.0 HIJ+FGABCDE-->FGHIJ+ABCDE\n",
      "r35            GAP+S7P-->F6P+E4P        (kegg:R085   692.4 free       1.0   1.0   0.01000.0 ABC+DEFGHIJ-->DEFABC+GHIJ\n",
      "r36            E4P+F6P-->S7P+GAP        (kegg:R085   689.4 free       1.0   1.0   0.01000.0 GHIJ+DEFABC-->DEFGHIJ+ABC\n",
      "r37            E4P+Xu5P-->F6P+GAP       (kegg:R010   130.4 free       1.0   1.0   0.01000.0 ABCD+EFGHI-->EFABCD+GHI  \n",
      "r38            GAP+F6P-->Xu5P+E4P       (kegg:R010   129.1 free       1.0   1.0   0.01000.0 GHI+EFABCD-->EFGHI+ABCD  \n",
      "r39            m6PG-->Pyr+GAP           (kegg:R007     0.1 free       1.0   1.0   0.01000.0 ABCDEF-->ABC+DEF         \n",
      "r40            PEP+CO2in-->Oxa          (kegg:Lace   529.0 free       1.0   1.0   0.01000.0 ABC+D-->ABCD             \n",
      "r41            Oxa-->PEP+CO2in          (kegg:Subs   391.4 free       1.0   1.0   0.01000.0 ABCD-->ABC+D             \n",
      "r42            Mal-->Pyr+CO2in          (kegg:R002   152.5 free       1.0   1.0   0.01000.0 ABCD-->ABC+D             \n",
      "r49            AcCOA-->Acetate          (kegg:Aspe     0.0 free       1.0   1.0   0.01000.0 AB-->AB                  \n",
      "r50            Acetate-->Acetateex      (kegg:R004     0.0 fitting   36.8   2.8   0.01000.0 nd                       \n",
      "r56            SubsCO2-->CO2in          (kegg:Subs    96.2 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r57            CO2in-->CO2ex            (kegg:Glu)     3.3 free       1.0   1.0   0.01000.0 nd                       \n",
      "r58            Pyr-->Ala                (kegg:Arg)    10.0 pseudo     1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r59            Oxa-->Asp                (kegg:R003    10.0 pseudo     1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r60            Oxa-->Thr                (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r61            aKG-->Glu                (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r62            E4P+PEP+PEP-->Phe        (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCD+EFG+HIJ-->EFGIJABCD \n",
      "r63            E4P+PEP+PEP-->Tyr        (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCD+EFG+HIJ-->EFGIJABCD \n",
      "r64            Oxa+Pyr-->Ile            (kegg:R015    10.0 pseudo     1.0   1.0   0.01000.0 ABCD+EFG-->ABFGCD        \n",
      "r65            AcCOA+Pyr+Pyr-->Leu      (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 AB+CDE+FGH-->ABDEGH      \n",
      "r66            Pyr+Pyr-->Val            (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABC+DEF-->ABECF          \n",
      "r67            PGA-->Ser                (kegg:Biom     4.3 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r68            Ser-->Gly+MEETHF         (kegg:Glu2   753.1 free       1.0   1.0   0.01000.0 ABC-->AB+C               \n",
      "r69            Gly+MEETHF-->Ser         (kegg:Biom   750.4 free       1.0   1.0   0.01000.0 AB+C-->ABC               \n",
      "r72            G6P-->Biomass            (kegg:Biom     1.0 fixed      1.0   1.0   0.01000.0 nd                       \n",
      "r73            F6P-->Biomass            (kegg:Biom     0.3 fixed      0.3   1.0   0.01000.0 nd                       \n",
      "r74            DHAP-->Biomass           (kegg:Biom     0.6 fixed      0.6   1.0   0.01000.0 nd                       \n",
      "r75            PGA-->Biomass            (kegg:CO2e     2.6 fixed      2.6   1.0   0.01000.0 nd                       \n",
      "r76            Ser-->Biomass            (kegg:Subs     1.6 fixed      1.6   1.0   0.01000.0 nd                       \n",
      "r77            Gly-->Biomass            (keggPGAex     2.7 fixed      2.7   1.0   0.01000.0 nd                       \n",
      "r78            MEETHF-->Biomass         (kegg:FAex     3.1 fixed      3.1   1.0   0.01000.0 nd                       \n",
      "r79            PEP-->Biomass            (kegg:MAL_     3.3 fixed      3.3   1.0   0.01000.0 nd                       \n",
      "r80            Pyr-->Biomass            (kegg:MAL_    13.1 fixed     13.1   1.0   0.01000.0 nd                       \n",
      "r81            AcCOA-->Biomass          (kegg:OXA_    13.6 fixed     13.6   1.0   0.01000.0 nd                       \n",
      "r82            aKG-->Biomass            (kegg:OXA_     5.0 fixed      5.0   1.0   0.01000.0 nd                       \n",
      "r83            Oxa-->Biomass            (kegg:ATP)     8.3 fixed      8.3   1.0   0.01000.0 nd                       \n",
      "r84            R5P-->Biomass            (kegg:NADH     4.2 fixed      4.2   1.0   0.01000.0 nd                       \n",
      "r85            E4P-->Biomass            (kegg:NADP     1.7 fixed      1.7   1.0   0.01000.0 nd                       \n",
      "r86            Ala-->Alaex              (kegg:Arg)    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r87            Asp-->Aspex              (kegg:R003    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r88            Thr-->Threx              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r89            Glu-->Gluex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r90            Phe-->Pheex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r91            Tyr-->Tyrex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r92            Ile-->Ileex              (kegg:R015    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r93            Leu-->Leuex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r94            Val-->Valex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r104           Subsmeoh-->meoh          (kegg:MTI/   100.0 fixed    100.0   1.0   0.01000.0 A-->A                    \n",
      "r105           meoh-->METHF             (kegg:TBD)   100.0 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r106           METHF-->MEETHF           (kegg:TBD)   688.5 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r107           MEETHF-->METHF           (kegg:TBD)   688.1 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r108           CO2in+METHF-->AcCOA      (kegg:TBD)    99.6 free       1.0   1.0   0.01000.0 A+B-->AB                 \n",
      "r109           AcCOA+CO2in-->Pyr        (kegg:R007   124.9 free       1.0   1.0   0.01000.0 BC+A-->ABC               \n",
      "PGI            r2<=>r3                  (kegg:R007   -12.5 free       1.0   1.0-300.0 300.0                          \n",
      "FBA            r4<=>r5                  (kegg:R010    -8.6 free       1.0   1.0-300.0 300.0                          \n",
      "TPI            r8<=>r9                  (kegg:R010    -9.2 free       1.0   1.0-300.0 300.0                          \n",
      "GAPDH          r10<=>r11                (kegg:R010   -16.3 free       1.0   1.0-300.0 300.0                          \n",
      "PEPH           r12<=>r13                (kegg:R015   -23.2 free       1.0   1.0-300.0 300.0                          \n",
      "SDH            r20<=>r21                (kegg:R021    28.2 free       1.0   1.0-300.0 300.0                          \n",
      "MDH            r24<=>r25                (kegg:R003   -96.2 free       1.0   1.0-300.0 300.0                          \n",
      "RPI            r29<=>r30                (kegg:R010     7.1 free       1.0   1.0-300.0 300.0                          \n",
      "RBE            r31<=>r32                (kegg:R015     4.3 free       1.0   1.0-300.0 300.0                          \n",
      "TKT1           r33<=>r34                (kegg:R016     3.0 free       1.0   1.0-300.0 300.0                          \n",
      "TAL            r35<=>r36                (kegg:R085     3.0 free       1.0   1.0-300.0 300.0                          \n",
      "TKT2           r37<=>r38                (kegg:R010     1.3 free       1.0   1.0-300.0 300.0                          \n",
      "FH             r22<=>r23                (kegg:R010    28.2 free       1.0   1.0-300.0 300.0                          \n",
      "THF            r106<=>r107              (kegg:TBD)     0.4 free       1.0   1.0-300.0 300.0                          \n",
      "PFOR           r16<=>r109               (kegg:R007   -24.6 free       1.0   1.0-300.0 300.0                          \n",
      "Experiment     Fragment_N               Time         SLSQP     Use  Ratio Stdev\n",
      "ex1            AlaMes_0                 0.00        0.0893       1 0.1711  0.00\n",
      "ex1            AlaMes_1                 0.00        0.3949       1 0.3666  0.00\n",
      "ex1            AlaMes_2                 0.00        0.4531       1 0.3955  0.00\n",
      "ex1            AlaMes_3                 0.00        0.0628       1 0.0668  0.00\n",
      "ex1            AspMes_0                 0.00        0.0212       1 0.0491  0.00\n",
      "ex1            AspMes_1                 0.00        0.1629       1 0.2283  0.00\n",
      "ex1            AspMes_2                 0.00        0.4084       1 0.3903  0.00\n",
      "ex1            AspMes_3                 0.00        0.3569       1 0.2899  0.00\n",
      "ex1            AspMes_4                 0.00        0.0506       1 0.0424  0.00\n",
      "ex1            GluMes_0                 0.00        0.0201       1 0.0281  0.00\n",
      "ex1            GluMes_1                 0.00        0.1534       1 0.1522  0.01\n",
      "ex1            GluMes_2                 0.00        0.3872       1 0.4344  0.00\n",
      "ex1            GluMes_3                 0.00        0.3563       1 0.3083  0.00\n",
      "ex1            GluMes_4                 0.00        0.0786       1 0.0704  0.00\n",
      "ex1            GluMes_5                 0.00        0.0044       1 0.0067  0.00\n",
      "ex1            GlyMes_0                 0.00        0.1594       1 0.2079  0.02\n",
      "ex1            GlyMes_1                 0.00        0.5094       1 0.4306  0.03\n",
      "ex1            GlyMes_2                 0.00        0.3312       1 0.3616  0.01\n",
      "ex1            IleMes_0                 0.00        0.0068       1 0.0414  0.00\n",
      "ex1            IleMes_1                 0.00        0.0648       1 0.2209  0.00\n",
      "ex1            IleMes_2                 0.00        0.2285       1 0.3536  0.00\n",
      "ex1            IleMes_3                 0.00        0.3686       1 0.2747  0.00\n",
      "ex1            IleMes_4                 0.00        0.2632       1 0.0932  0.00\n",
      "ex1            IleMes_5                 0.00        0.0633       1 0.0150  0.00\n",
      "ex1            IleMes_6                 0.00        0.0048       1 0.0013  0.00\n",
      "ex1            PheMes_0                 0.00        0.0012       1 0.0068  0.01\n",
      "ex1            PheMes_1                 0.00        0.0141       1 0.0479  0.00\n",
      "ex1            PheMes_2                 0.00        0.0678       1 0.1279  0.00\n",
      "ex1            PheMes_3                 0.00        0.1793       1 0.2236  0.00\n",
      "ex1            PheMes_4                 0.00        0.2812       1 0.2757  0.00\n",
      "ex1            PheMes_5                 0.00        0.2646       1 0.2054  0.00\n",
      "ex1            PheMes_6                 0.00        0.1439       1 0.0891  0.00\n",
      "ex1            PheMes_7                 0.00        0.0417       1 0.0205  0.00\n",
      "ex1            PheMes_8                 0.00        0.0059       1 0.0028  0.00\n",
      "ex1            PheMes_9                 0.00        0.0003       1 0.0002  0.00\n",
      "ex1            SerMes_0                 0.00        0.1551       1 0.1944  0.01\n",
      "ex1            SerMes_1                 0.00        0.5000       1 0.3909  0.01\n",
      "ex1            SerMes_2                 0.00        0.3362       1 0.3555  0.00\n",
      "ex1            SerMes_3                 0.00        0.0086       1 0.0592  0.00\n",
      "ex1            ThrMes_0                 0.00        0.0212       1 0.0517  0.00\n",
      "ex1            ThrMes_1                 0.00        0.1629       1 0.2460  0.00\n",
      "ex1            ThrMes_2                 0.00        0.4084       1 0.3859  0.00\n",
      "ex1            ThrMes_3                 0.00        0.3569       1 0.2817  0.00\n",
      "ex1            ThrMes_4                 0.00        0.0506       1 0.0346  0.00\n",
      "ex1            TyrMes_0                 0.00        0.0012       1 0.0202  0.00\n",
      "ex1            TyrMes_1                 0.00        0.0141       1 0.0456  0.00\n",
      "ex1            TyrMes_2                 0.00        0.0678       1 0.1255  0.00\n",
      "ex1            TyrMes_3                 0.00        0.1793       1 0.2152  0.00\n",
      "ex1            TyrMes_4                 0.00        0.2812       1 0.2615  0.00\n",
      "ex1            TyrMes_5                 0.00        0.2646       1 0.2087  0.00\n",
      "ex1            TyrMes_6                 0.00        0.1439       1 0.0936  0.00\n",
      "ex1            TyrMes_7                 0.00        0.0417       1 0.0255  0.00\n",
      "ex1            TyrMes_8                 0.00        0.0059       1 0.0039  0.00\n",
      "ex1            TyrMes_9                 0.00        0.0003       1 0.0004  0.00\n",
      "ex1            ValMes_0                 0.00        0.0287       1 0.1302  0.00\n",
      "ex1            ValMes_1                 0.00        0.1792       1 0.2622  0.00\n",
      "ex1            ValMes_2                 0.00        0.3847       1 0.3395  0.00\n",
      "ex1            ValMes_3                 0.00        0.3220       1 0.2167  0.00\n",
      "ex1            ValMes_4                 0.00        0.0795       1 0.0473  0.00\n",
      "ex1            ValMes_5                 0.00        0.0059       1 0.0041  0.00\n",
      "\n"
     ]
    }
   ],
   "source": [
    "model.show_results([(\"SLSQP\", flux_opt_SLSQP[0])])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Id             Reaction                 External i LN_SBPL\n",
      "RSS                                               56894.39\n",
      "Thres                                                38.89\n",
      "p_value                                               0.00\n",
      "Id             Reaction                 External i LN_SBPL Type     Value Stdev    lb    ub Atom_mapping             \n",
      "r1             SubsGlc-->G6P            (kegg:R028     0.0 fixed      0.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r2             G6P-->F6P                (kegg:R007   544.0 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r3             F6P-->G6P                (kegg:R007   551.0 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r4             F6P-->FBP                (kegg:R007   991.5 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r5             FBP-->F6P                (kegg:R010  1000.0 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r6             FBP-->DHAP+GAP           (kegg:R010   991.5 free       1.0   1.0   0.01000.0 ABCDEF-->CBA+DEF         \n",
      "r7             DHAP+GAP-->FBP           (kegg:R010  1000.0 free       1.0   1.0   0.01000.0 CBA+DEF-->ABCDEF         \n",
      "r8             DHAP-->GAP               (kegg:R010   127.0 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r9             GAP-->DHAP               (kegg:R010   136.1 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r10            GAP-->PGA                (kegg:R010    54.6 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r11            PGA-->GAP                (kegg:R015    70.7 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r12            PGA-->PEP                (kegg:R015    17.6 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r13            PEP-->PGA                (kegg:R002    40.7 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r14            PEP-->Pyr                (kegg:R011   369.6 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r15            Pyr-->PEP                (kegg:R003   404.1 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r16            Pyr-->AcCOA+CO2in        (kegg:R007    33.6 free       1.0   1.0   0.01000.0 ABC-->BC+A               \n",
      "r17            AcCOA+Oxa-->IsoCit       (kegg:R007    35.4 free       1.0   1.0   0.01000.0 AB+CDEF-->FEDBAC         \n",
      "r18            IsoCit-->aKG+CO2in       (kegg:R011     8.5 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDE+F         \n",
      "r19            aKG-->Suc+CO2in          (kegg:R021     3.5 free       1.0   1.0   0.01000.0 ABCDE-->BCDE+A           \n",
      "r20            Suc-->Fum                (kegg:R021   910.3 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r21            Fum-->Suc                (kegg:R010   879.9 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r22            Fum-->Mal                (kegg:R010   728.4 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r23            Mal-->Fum                (kegg:R003   698.0 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r24            Mal-->Oxa                (kegg:R003   995.1 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r25            Oxa-->Mal                (kegg:R003   959.5 free       1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r26            IsoCit+AcCOA-->Mal+Suc   (kegg:R002    27.0 free       1.0   1.0   0.01000.0 ABCDEF+GH-->ABHG+FCDE    \n",
      "r27            G6P-->m6PG               (kegg:R008     6.0 free       1.0   1.0   0.01000.0 ABCDEF-->ABCDEF          \n",
      "r28            m6PG-->Ru5P+CO2in        (kegg:R015     3.2 free       1.0   1.0   0.01000.0 ABCDEF-->BCDEF+A         \n",
      "r29            Ru5P-->R5P               (kegg:R010    22.4 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r30            R5P-->Ru5P               (kegg:R010    18.0 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r31            Ru5P-->Xu5P              (kegg:R015    15.1 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r32            Xu5P-->Ru5P              (kegg:R015    16.2 free       1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r33            R5P+Xu5P-->S7P+GAP       (kegg:R016   999.3 free       1.0   1.0   0.01000.0 ABCDE+FGHIJ-->FGABCDE+HIJ\n",
      "r34            GAP+S7P-->Xu5P+R5P       (kegg:R016   999.0 free       1.0   1.0   0.01000.0 HIJ+FGABCDE-->FGHIJ+ABCDE\n",
      "r35            GAP+S7P-->F6P+E4P        (kegg:R085   999.6 free       1.0   1.0   0.01000.0 ABC+DEFGHIJ-->DEFABC+GHIJ\n",
      "r36            E4P+F6P-->S7P+GAP        (kegg:R085   999.4 free       1.0   1.0   0.01000.0 GHIJ+DEFABC-->DEFGHIJ+ABC\n",
      "r37            E4P+Xu5P-->F6P+GAP       (kegg:R010   998.6 free       1.0   1.0   0.01000.0 ABCD+EFGHI-->EFABCD+GHI  \n",
      "r38            GAP+F6P-->Xu5P+E4P       (kegg:R010  1000.0 free       1.0   1.0   0.01000.0 GHI+EFABCD-->EFGHI+ABCD  \n",
      "r39            m6PG-->Pyr+GAP           (kegg:R007     2.8 free       1.0   1.0   0.01000.0 ABCDEF-->ABC+DEF         \n",
      "r40            PEP+CO2in-->Oxa          (kegg:Lace     8.1 free       1.0   1.0   0.01000.0 ABC+D-->ABCD             \n",
      "r41            Oxa-->PEP+CO2in          (kegg:Subs     0.0 free       1.0   1.0   0.01000.0 ABCD-->ABC+D             \n",
      "r42            Mal-->Pyr+CO2in          (kegg:R002    21.8 free       1.0   1.0   0.01000.0 ABCD-->ABC+D             \n",
      "r49            AcCOA-->Acetate          (kegg:Aspe     0.5 free       1.0   1.0   0.01000.0 AB-->AB                  \n",
      "r50            Acetate-->Acetateex      (kegg:R004     0.5 fitting   36.8   2.8   0.01000.0 nd                       \n",
      "r56            SubsCO2-->CO2in          (kegg:Subs    93.8 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r57            CO2in-->CO2ex            (kegg:Glu)     0.0 free       1.0   1.0   0.01000.0 nd                       \n",
      "r58            Pyr-->Ala                (kegg:Arg)    10.0 pseudo     1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r59            Oxa-->Asp                (kegg:R003    10.0 pseudo     1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r60            Oxa-->Thr                (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCD-->ABCD              \n",
      "r61            aKG-->Glu                (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCDE-->ABCDE            \n",
      "r62            E4P+PEP+PEP-->Phe        (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCD+EFG+HIJ-->EFGIJABCD \n",
      "r63            E4P+PEP+PEP-->Tyr        (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABCD+EFG+HIJ-->EFGIJABCD \n",
      "r64            Oxa+Pyr-->Ile            (kegg:R015    10.0 pseudo     1.0   1.0   0.01000.0 ABCD+EFG-->ABFGCD        \n",
      "r65            AcCOA+Pyr+Pyr-->Leu      (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 AB+CDE+FGH-->ABDEGH      \n",
      "r66            Pyr+Pyr-->Val            (kegg:Biom    10.0 pseudo     1.0   1.0   0.01000.0 ABC+DEF-->ABECF          \n",
      "r67            PGA-->Ser                (kegg:Biom     4.3 free       1.0   1.0   0.01000.0 ABC-->ABC                \n",
      "r68            Ser-->Gly+MEETHF         (kegg:Glu2   858.1 free       1.0   1.0   0.01000.0 ABC-->AB+C               \n",
      "r69            Gly+MEETHF-->Ser         (kegg:Biom   855.4 free       1.0   1.0   0.01000.0 AB+C-->ABC               \n",
      "r72            G6P-->Biomass            (kegg:Biom     1.0 fixed      1.0   1.0   0.01000.0 nd                       \n",
      "r73            F6P-->Biomass            (kegg:Biom     0.3 fixed      0.3   1.0   0.01000.0 nd                       \n",
      "r74            DHAP-->Biomass           (kegg:Biom     0.6 fixed      0.6   1.0   0.01000.0 nd                       \n",
      "r75            PGA-->Biomass            (kegg:CO2e     2.6 fixed      2.6   1.0   0.01000.0 nd                       \n",
      "r76            Ser-->Biomass            (kegg:Subs     1.6 fixed      1.6   1.0   0.01000.0 nd                       \n",
      "r77            Gly-->Biomass            (keggPGAex     2.7 fixed      2.7   1.0   0.01000.0 nd                       \n",
      "r78            MEETHF-->Biomass         (kegg:FAex     3.1 fixed      3.1   1.0   0.01000.0 nd                       \n",
      "r79            PEP-->Biomass            (kegg:MAL_     3.3 fixed      3.3   1.0   0.01000.0 nd                       \n",
      "r80            Pyr-->Biomass            (kegg:MAL_    13.1 fixed     13.1   1.0   0.01000.0 nd                       \n",
      "r81            AcCOA-->Biomass          (kegg:OXA_    13.6 fixed     13.6   1.0   0.01000.0 nd                       \n",
      "r82            aKG-->Biomass            (kegg:OXA_     5.0 fixed      5.0   1.0   0.01000.0 nd                       \n",
      "r83            Oxa-->Biomass            (kegg:ATP)     8.3 fixed      8.3   1.0   0.01000.0 nd                       \n",
      "r84            R5P-->Biomass            (kegg:NADH     4.2 fixed      4.2   1.0   0.01000.0 nd                       \n",
      "r85            E4P-->Biomass            (kegg:NADP     1.7 fixed      1.7   1.0   0.01000.0 nd                       \n",
      "r86            Ala-->Alaex              (kegg:Arg)    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r87            Asp-->Aspex              (kegg:R003    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r88            Thr-->Threx              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r89            Glu-->Gluex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r90            Phe-->Pheex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r91            Tyr-->Tyrex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r92            Ile-->Ileex              (kegg:R015    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r93            Leu-->Leuex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r94            Val-->Valex              (kegg:Biom    10.0 fixed     10.0   1.0   0.01000.0 nd                       \n",
      "r104           Subsmeoh-->meoh          (kegg:MTI/   100.0 fixed    100.0   1.0   0.01000.0 A-->A                    \n",
      "r105           meoh-->METHF             (kegg:TBD)   100.0 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r106           METHF-->MEETHF           (kegg:TBD)     0.4 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r107           MEETHF-->METHF           (kegg:TBD)     0.0 free       1.0   1.0   0.01000.0 A-->A                    \n",
      "r108           CO2in+METHF-->AcCOA      (kegg:TBD)    99.6 free       1.0   1.0   0.01000.0 A+B-->AB                 \n",
      "r109           AcCOA+CO2in-->Pyr        (kegg:R007    56.7 free       1.0   1.0   0.01000.0 BC+A-->ABC               \n",
      "PGI            r2<=>r3                  (kegg:R007    -7.0 free       1.0   1.0-300.0 300.0                          \n",
      "FBA            r4<=>r5                  (kegg:R010    -8.5 free       1.0   1.0-300.0 300.0                          \n",
      "TPI            r8<=>r9                  (kegg:R010    -9.1 free       1.0   1.0-300.0 300.0                          \n",
      "GAPDH          r10<=>r11                (kegg:R010   -16.2 free       1.0   1.0-300.0 300.0                          \n",
      "PEPH           r12<=>r13                (kegg:R015   -23.1 free       1.0   1.0-300.0 300.0                          \n",
      "SDH            r20<=>r21                (kegg:R021    30.4 free       1.0   1.0-300.0 300.0                          \n",
      "MDH            r24<=>r25                (kegg:R003    35.6 free       1.0   1.0-300.0 300.0                          \n",
      "RPI            r29<=>r30                (kegg:R010     4.4 free       1.0   1.0-300.0 300.0                          \n",
      "RBE            r31<=>r32                (kegg:R015    -1.2 free       1.0   1.0-300.0 300.0                          \n",
      "TKT1           r33<=>r34                (kegg:R016     0.2 free       1.0   1.0-300.0 300.0                          \n",
      "TAL            r35<=>r36                (kegg:R085     0.2 free       1.0   1.0-300.0 300.0                          \n",
      "TKT2           r37<=>r38                (kegg:R010    -1.4 free       1.0   1.0-300.0 300.0                          \n",
      "FH             r22<=>r23                (kegg:R010    30.4 free       1.0   1.0-300.0 300.0                          \n",
      "THF            r106<=>r107              (kegg:TBD)     0.4 free       1.0   1.0-300.0 300.0                          \n",
      "PFOR           r16<=>r109               (kegg:R007   -23.1 free       1.0   1.0-300.0 300.0                          \n",
      "Experiment     Fragment_N               Time       LN_SBPL     Use  Ratio Stdev\n",
      "ex1            AlaMes_0                 0.00        0.0550       1 0.1711  0.00\n",
      "ex1            AlaMes_1                 0.00        0.3464       1 0.3666  0.00\n",
      "ex1            AlaMes_2                 0.00        0.5774       1 0.3955  0.00\n",
      "ex1            AlaMes_3                 0.00        0.0212       1 0.0668  0.00\n",
      "ex1            AspMes_0                 0.00        0.0263       1 0.0491  0.00\n",
      "ex1            AspMes_1                 0.00        0.2494       1 0.2283  0.00\n",
      "ex1            AspMes_2                 0.00        0.5893       1 0.3903  0.00\n",
      "ex1            AspMes_3                 0.00        0.1314       1 0.2899  0.00\n",
      "ex1            AspMes_4                 0.00        0.0037       1 0.0424  0.00\n",
      "ex1            GluMes_0                 0.00        0.0216       1 0.0281  0.00\n",
      "ex1            GluMes_1                 0.00        0.2242       1 0.1522  0.01\n",
      "ex1            GluMes_2                 0.00        0.6020       1 0.4344  0.00\n",
      "ex1            GluMes_3                 0.00        0.1449       1 0.3083  0.00\n",
      "ex1            GluMes_4                 0.00        0.0072       1 0.0704  0.00\n",
      "ex1            GluMes_5                 0.00        0.0001       1 0.0067  0.00\n",
      "ex1            GlyMes_0                 0.00        0.0898       1 0.2079  0.02\n",
      "ex1            GlyMes_1                 0.00        0.4135       1 0.4306  0.03\n",
      "ex1            GlyMes_2                 0.00        0.4967       1 0.3616  0.01\n",
      "ex1            IleMes_0                 0.00        0.0084       1 0.0414  0.00\n",
      "ex1            IleMes_1                 0.00        0.0962       1 0.2209  0.00\n",
      "ex1            IleMes_2                 0.00        0.3492       1 0.3536  0.00\n",
      "ex1            IleMes_3                 0.00        0.4311       1 0.2747  0.00\n",
      "ex1            IleMes_4                 0.00        0.1077       1 0.0932  0.00\n",
      "ex1            IleMes_5                 0.00        0.0072       1 0.0150  0.00\n",
      "ex1            IleMes_6                 0.00        0.0001       1 0.0013  0.00\n",
      "ex1            PheMes_0                 0.00        0.0005       1 0.0068  0.01\n",
      "ex1            PheMes_1                 0.00        0.0070       1 0.0479  0.00\n",
      "ex1            PheMes_2                 0.00        0.0437       1 0.1279  0.00\n",
      "ex1            PheMes_3                 0.00        0.1472       1 0.2236  0.00\n",
      "ex1            PheMes_4                 0.00        0.2853       1 0.2757  0.00\n",
      "ex1            PheMes_5                 0.00        0.3114       1 0.2054  0.00\n",
      "ex1            PheMes_6                 0.00        0.1697       1 0.0891  0.00\n",
      "ex1            PheMes_7                 0.00        0.0329       1 0.0205  0.00\n",
      "ex1            PheMes_8                 0.00        0.0022       1 0.0028  0.00\n",
      "ex1            PheMes_9                 0.00        0.0000       1 0.0002  0.00\n",
      "ex1            SerMes_0                 0.00        0.0777       1 0.1944  0.01\n",
      "ex1            SerMes_1                 0.00        0.3699       1 0.3909  0.01\n",
      "ex1            SerMes_2                 0.00        0.4857       1 0.3555  0.00\n",
      "ex1            SerMes_3                 0.00        0.0666       1 0.0592  0.00\n",
      "ex1            ThrMes_0                 0.00        0.0263       1 0.0517  0.00\n",
      "ex1            ThrMes_1                 0.00        0.2494       1 0.2460  0.00\n",
      "ex1            ThrMes_2                 0.00        0.5893       1 0.3859  0.00\n",
      "ex1            ThrMes_3                 0.00        0.1314       1 0.2817  0.00\n",
      "ex1            ThrMes_4                 0.00        0.0037       1 0.0346  0.00\n",
      "ex1            TyrMes_0                 0.00        0.0005       1 0.0202  0.00\n",
      "ex1            TyrMes_1                 0.00        0.0070       1 0.0456  0.00\n",
      "ex1            TyrMes_2                 0.00        0.0437       1 0.1255  0.00\n",
      "ex1            TyrMes_3                 0.00        0.1472       1 0.2152  0.00\n",
      "ex1            TyrMes_4                 0.00        0.2853       1 0.2615  0.00\n",
      "ex1            TyrMes_5                 0.00        0.3114       1 0.2087  0.00\n",
      "ex1            TyrMes_6                 0.00        0.1697       1 0.0936  0.00\n",
      "ex1            TyrMes_7                 0.00        0.0329       1 0.0255  0.00\n",
      "ex1            TyrMes_8                 0.00        0.0022       1 0.0039  0.00\n",
      "ex1            TyrMes_9                 0.00        0.0000       1 0.0004  0.00\n",
      "ex1            ValMes_0                 0.00        0.0175       1 0.1302  0.00\n",
      "ex1            ValMes_1                 0.00        0.1456       1 0.2622  0.00\n",
      "ex1            ValMes_2                 0.00        0.4091       1 0.3395  0.00\n",
      "ex1            ValMes_3                 0.00        0.3920       1 0.2167  0.00\n",
      "ex1            ValMes_4                 0.00        0.0350       1 0.0473  0.00\n",
      "ex1            ValMes_5                 0.00        0.0008       1 0.0041  0.00\n",
      "\n"
     ]
    }
   ],
   "source": [
    "model.show_results([(\"LN_SBPLX\", flux_opt_LN_SBPLX[0])])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Output fitted metabolic flux into CSV file\n",
    "    \n",
    "model.show_results([(\"GN_CRS2_LM\", flux_opt_GN_CRS2_LM[0])], filename = \"Elim2_output_GN_CRS2_LM.csv\",  checkrss = \"on\", format = \"csv\")\n",
    "\n",
    "model.show_results([(\"SLSQP\", flux_opt_SLSQP[0])], filename = \"Elim2_output_SLSQP.csv\",  checkrss = \"on\", format = \"csv\")\n",
    "\n",
    "model.show_results([(\"LN_SBPLX\", flux_opt_LN_SBPLX[0])], filename = \"Elim2_output_LN_SBPLX.csv\",  checkrss = \"on\", format = \"csv\")"
   ]
  }
 ],
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