Generate SORGHUM tissue specific models.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Modelling metabolism in SORGHUM"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Generating SORGHUM core model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from cobra import io\n",
    "from cobra.core import Metabolite, Reaction\n",
    "from cobra import flux_analysis\n",
    "from Functions import *\n",
    "from IPython import display\n",
    "import logging\n",
    "logging.basicConfig()\n",
    "logger = logging.getLogger('logger')\n",
    "\n",
    "#import sbml file\n",
    "fname = \"C:\\\\Users\\\\FFAR\\\\Downloads\\\\plantcoremetabolism-model\\\\PlantCoreMetabolism_v1_3_2.xml\"\n",
    "model = io.read_sbml_model(fname)\n",
    "model.solver='glpk'\n",
    "display.clear_output()\n",
    "\n",
    "from sweetlovegroup import transform\n",
    "model = transform.fixModelCompatibilityIssueCobra015(model,fname)\n",
    "\n",
    "\n",
    "#change Biomass_tx to Protein_biomass\n",
    "rxn = model.reactions.get_by_id(\"Biomass_tx\")\n",
    "rxn.id = \"Protein_biomass_tx\"\n",
    "for met in [\"K_b\",\"Ca_b\",\"Mg_b\"]:\n",
    "    met  = model.metabolites.get_by_id(met)\n",
    "    coeff = rxn.metabolites.get(met)\n",
    "    rxn.add_metabolites({met:-1*coeff})\n",
    "met = Metabolite(\"Protein_b\",name=\"Protein_biomass\")\n",
    "formula_dict = rxn.check_mass_balance()\n",
    "met.formula = \"\".join([atom+str(formula_dict[atom]*-1) for atom in formula_dict.keys() if atom != \"charge\"])\n",
    "met.charge = formula_dict[\"charge\"]*-1\n",
    "met.compartment = \"b\"\n",
    "rxn.add_metabolites({met:1})\n",
    "\n",
    "\n",
    "for rxn in model.reactions:\n",
    "    if rxn.lower_bound == -1000:\n",
    "        rxn.lower_bound = -3000\n",
    "    if rxn.upper_bound == 1000:\n",
    "        rxn.upper_bound = 3000\n",
    "\n",
    "\n",
    "model.metabolites.get_by_id(\"aL_1_PHOSPHATIDYL_GLYCEROL_P_m\").remove_from_model()\n",
    "model.metabolites.get_by_id(\"aL_1_PHOSPHATIDYL_GLYCEROL_P_p\").remove_from_model()\n",
    "\n",
    "model.reactions.get_by_id(\"PGPPHOSPHA_RXN_m\").add_metabolites({model.metabolites.get_by_id(\"L_1_PHOSPHATIDYL_GLYCEROL_P_m\"):-0.03,\n",
    "                                                               model.metabolites.get_by_id(\"PROTON_m\"):-0.03})\n",
    "model.reactions.get_by_id(\"PHOSPHAGLYPSYN_RXN_m\").add_metabolites({model.metabolites.get_by_id(\"L_1_PHOSPHATIDYL_GLYCEROL_P_m\"):0.03,\n",
    "                                                                   model.metabolites.get_by_id(\"PROTON_m\"):0.03})\n",
    "model.reactions.get_by_id(\"PGPPHOSPHA_RXN_p\").add_metabolites({model.metabolites.get_by_id(\"L_1_PHOSPHATIDYL_GLYCEROL_P_p\"):-0.03,\n",
    "                                                               model.metabolites.get_by_id(\"PROTON_p\"):-0.03})\n",
    "model.reactions.get_by_id(\"PHOSPHAGLYPSYN_RXN_p\").add_metabolites({model.metabolites.get_by_id(\"L_1_PHOSPHATIDYL_GLYCEROL_P_p\"):0.03,\n",
    "                                                                   model.metabolites.get_by_id(\"PROTON_p\"):0.03})\n",
    "model.reactions.get_by_id(\"LPG_biosynthesis_c\").add_metabolites({model.metabolites.get_by_id(\"L_1_PHOSPHATIDYL_GLYCEROL_P_p\"):-0.03})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Model does not contain SBML fbc package information.\n",
      "WARNING:cobra.io.sbml:SBML package 'layout' not supported by cobrapy, information is not parsed\n",
      "WARNING:cobra.io.sbml:SBML package 'render' not supported by cobrapy, information is not parsed\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UREA_m \"UREA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UREA_m \"UREA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_VAL_c \"VAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_VAL_c \"VAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sVAL_b \"sVAL[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sVAL_b \"sVAL[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYCEROL_3P_c \"GLYCEROL-3P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYCEROL_3P_c \"GLYCEROL-3P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_VAL_m \"VAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_VAL_m \"VAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDCDP_p \"dCDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDCDP_p \"dCDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_N_5_PHOSPHORIBOSYL_ANTHRANILATE_p \"N-5-PHOSPHORIBOSYL-ANTHRANILATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_N_5_PHOSPHORIBOSYL_ANTHRANILATE_p \"N-5-PHOSPHORIBOSYL-ANTHRANILATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UREA_c \"UREA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UREA_c \"UREA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETOACETATE_c \"ACETOACETATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETOACETATE_c \"ACETOACETATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CARBOXYPHENYLAMINO_DEOXYRIBULOSE_P_p \"CARBOXYPHENYLAMINO-DEOXYRIBULOSE-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CARBOXYPHENYLAMINO_DEOXYRIBULOSE_P_p \"CARBOXYPHENYLAMINO-DEOXYRIBULOSE-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sSUCROSE_b \"sSUCROSE[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sSUCROSE_b \"sSUCROSE[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLN_p \"GLN\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLN_p \"GLN\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDELTA3_ISOPENTENYL_PP_p \"DELTA3-ISOPENTENYL-PP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDELTA3_ISOPENTENYL_PP_p \"DELTA3-ISOPENTENYL-PP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_oxo_hexanoyl_ACPs_p \"3_oxo_hexanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_oxo_hexanoyl_ACPs_p \"3_oxo_hexanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_XYLULOSE_5_PHOSPHATE_p \"XYLULOSE-5-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_XYLULOSE_5_PHOSPHATE_p \"XYLULOSE-5-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLN_v \"GLN\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLN_v \"GLN\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLN_m \"GLN\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLN_m \"GLN\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FORMATE_p \"FORMATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FORMATE_p \"FORMATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FORMATE_m \"FORMATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FORMATE_m \"FORMATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pGLN_b \"pGLN[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pGLN_b \"pGLN[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_XYLULOSE_5_PHOSPHATE_c \"XYLULOSE-5-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_XYLULOSE_5_PHOSPHATE_c \"XYLULOSE-5-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FORMATE_c \"FORMATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FORMATE_c \"FORMATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADPH_c \"NADPH\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADPH_c \"NADPH\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DADP_p \"DADP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DADP_p \"DADP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pVAL_b \"pVAL[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pVAL_b \"pVAL[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_INDOLE_3_GLYCEROL_P_p \"INDOLE-3-GLYCEROL-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_INDOLE_3_GLYCEROL_P_p \"INDOLE-3-GLYCEROL-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_1083_m \"CPD-1083\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_1083_m \"CPD-1083\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLN_c \"GLN\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLN_c \"GLN\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDELTA3_ISOPENTENYL_PP_c \"DELTA3-ISOPENTENYL-PP[c]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDELTA3_ISOPENTENYL_PP_c \"DELTA3-ISOPENTENYL-PP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DEHYDROQUINATE_p \"DEHYDROQUINATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DEHYDROQUINATE_p \"DEHYDROQUINATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pPHE_b \"pPHE[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pPHE_b \"pPHE[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SHIKIMATE_5P_p \"SHIKIMATE-5P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SHIKIMATE_5P_p \"SHIKIMATE-5P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ASPARTATE_x \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ASPARTATE_x \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PLASTOQUINOL_1_p \"PLASTOQUINOL_1[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PLASTOQUINOL_1_p \"PLASTOQUINOL_1[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_Oxo_octanoyl_ACPs_p \"3_Oxo_octanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_Oxo_octanoyl_ACPs_p \"3_Oxo_octanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ISOBUTYRYL_COA_x \"ISOBUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ISOBUTYRYL_COA_x \"ISOBUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ALA_tRNAs_c \"ALA_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ALA_tRNAs_c \"ALA_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MET_tRNAs_c \"MET_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MET_tRNAs_c \"MET_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHE_p \"PHE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHE_p \"PHE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADPH_x \"NADPH\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADPH_x \"NADPH\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bCPD_11281_m \"CPD-11281\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bCPD_11281_m \"CPD-11281\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_VAL_v \"VAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_VAL_v \"VAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADPH_p \"NADPH\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADPH_p \"NADPH\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UDP_GLUCOSE_c \"UDP_GLUCOSE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UDP_GLUCOSE_c \"UDP_GLUCOSE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_VAL_p \"VAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_VAL_p \"VAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHE_v \"PHE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHE_v \"PHE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_650_x \"CPD-650\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_650_x \"CPD-650\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HYDROXY_METHYL_BUTENYL_DIP_p \"HYDROXY-METHYL-BUTENYL-DIP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HYDROXY_METHYL_BUTENYL_DIP_p \"HYDROXY-METHYL-BUTENYL-DIP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADPH_m \"NADPH\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADPH_m \"NADPH\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYCEROL_3P_p \"GLYCEROL-3P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYCEROL_3P_p \"GLYCEROL-3P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYCEROL_3P_m \"GLYCEROL-3P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYCEROL_3P_m \"GLYCEROL-3P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MYO_INOSITOL_c \"MYO-INOSITOL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MYO_INOSITOL_c \"MYO-INOSITOL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROPIONYL_COA_x \"PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROPIONYL_COA_x \"PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_TYR_p \"TYR\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TYR_p \"TYR\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sCIT_b \"sCIT[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sCIT_b \"sCIT[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_STARCH_p \"STARCH[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_STARCH_p \"STARCH[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_CITRULLINE_p \"L-CITRULLINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_CITRULLINE_p \"L-CITRULLINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ISOBUTYRYL_COA_m \"ISOBUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ISOBUTYRYL_COA_m \"ISOBUTYRYL-COA\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROPIONYL_COA_c \"PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROPIONYL_COA_c \"PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_CITRULLINE_m \"L-CITRULLINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_CITRULLINE_m \"L-CITRULLINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_TYR_v \"TYR\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TYR_v \"TYR\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ISOBUTYRYL_COA_c \"ISOBUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ISOBUTYRYL_COA_c \"ISOBUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHE_c \"PHE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHE_c \"PHE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sPHE_b \"sPHE[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sPHE_b \"sPHE[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_GLT_tRNAs_c \"Charged_GLT_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_GLT_tRNAs_c \"Charged_GLT_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROPIONYL_COA_m \"PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROPIONYL_COA_m \"PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_pi_t \"X_pi[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_pi_t \"X_pi[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLC_6_P_p \"GLC-6-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLC_6_P_p \"GLC-6-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_P_SERINE_p \"3-P-SERINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_P_SERINE_p \"3-P-SERINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_CITRULLINE_c \"L-CITRULLINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_CITRULLINE_c \"L-CITRULLINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CHORISMATE_p \"CHORISMATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CHORISMATE_p \"CHORISMATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_1_PHOSPHATIDYL_ETHANOLAMINE_r \"L-1-PHOSPHATIDYL-ETHANOLAMINE[r]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_1_PHOSPHATIDYL_ETHANOLAMINE_r \"L-1-PHOSPHATIDYL-ETHANOLAMINE[r]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LYS_tRNAs_c \"LYS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LYS_tRNAs_c \"LYS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_TYR_c \"TYR\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TYR_c \"TYR\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sTYR_b \"sTYR[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sTYR_b \"sTYR[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pTYR_b \"pTYR[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pTYR_b \"pTYR[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUC_COA_m \"SUC-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUC_COA_m \"SUC-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DPG_p \"DPG\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DPG_p \"DPG\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_N_ALPHA_ACETYLORNITHINE_p \"N-ALPHA-ACETYLORNITHINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_N_ALPHA_ACETYLORNITHINE_p \"N-ALPHA-ACETYLORNITHINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aADP_c \"aADP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aADP_c \"aADP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aADP_m \"aADP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aADP_m \"aADP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aADP_p \"aADP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aADP_p \"aADP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_METHYL_3_HYDROXY_BUTYRYL_COA_c \"2-METHYL-3-HYDROXY-BUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_METHYL_3_HYDROXY_BUTYRYL_COA_c \"2-METHYL-3-HYDROXY-BUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DPG_c \"DPG\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DPG_c \"DPG\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_METHYL_3_HYDROXY_BUTYRYL_COA_m \"2-METHYL-3-HYDROXY-BUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_METHYL_3_HYDROXY_BUTYRYL_COA_m \"2-METHYL-3-HYDROXY-BUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLC_6_P_c \"GLC-6-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLC_6_P_c \"GLC-6-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_METHYL_3_HYDROXY_BUTYRYL_COA_x \"2-METHYL-3-HYDROXY-BUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_METHYL_3_HYDROXY_BUTYRYL_COA_x \"2-METHYL-3-HYDROXY-BUTYRYL-COA\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUCROSE_6P_c \"SUCROSE-6P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUCROSE_6P_c \"SUCROSE-6P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORIBOSYL_CARBOXY_AMINOIMIDAZOLE_p \"PHOSPHORIBOSYL-CARBOXY-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORIBOSYL_CARBOXY_AMINOIMIDAZOLE_p \"PHOSPHORIBOSYL-CARBOXY-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_GLN_tRNAs_c \"Charged_GLN_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_GLN_tRNAs_c \"Charged_GLN_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SO3_m \"SO3\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SO3_m \"SO3\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_1777_c \"CPD-1777\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_1777_c \"CPD-1777\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AMP_c \"AMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AMP_c \"AMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHATIDYL_CHOLINE_r \"PHOSPHATIDYL-CHOLINE[r]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHATIDYL_CHOLINE_r \"PHOSPHATIDYL-CHOLINE[r]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PALMITATE_p \"PALMITATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PALMITATE_p \"PALMITATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SO3_p \"SO3\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SO3_p \"SO3\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FRUCTOSE_16_DIPHOSPHATE_p \"FRUCTOSE-16-DIPHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FRUCTOSE_16_DIPHOSPHATE_p \"FRUCTOSE-16-DIPHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_METHYL_ACETO_ACETYL_COA_c \"2-METHYL-ACETO-ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_METHYL_ACETO_ACETYL_COA_c \"2-METHYL-ACETO-ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sFUM_b \"sFUM[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sFUM_b \"sFUM[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PALMITATE_x \"PALMITATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PALMITATE_x \"PALMITATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_METHYL_ACETO_ACETYL_COA_m \"2-METHYL-ACETO-ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_METHYL_ACETO_ACETYL_COA_m \"2-METHYL-ACETO-ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PALMITATE_c \"PALMITATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PALMITATE_c \"PALMITATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sGABA_b \"sGABA[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sGABA_b \"sGABA[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_METHYL_ACETO_ACETYL_COA_x \"2-METHYL-ACETO-ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_METHYL_ACETO_ACETYL_COA_x \"2-METHYL-ACETO-ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Trans_D2_decenoyl_ACPs_p \"Trans_D2_decenoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Trans_D2_decenoyl_ACPs_p \"Trans_D2_decenoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_CO2_t \"X_CO2[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_CO2_t \"X_CO2[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FRUCTOSE_16_DIPHOSPHATE_c \"FRUCTOSE-16-DIPHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FRUCTOSE_16_DIPHOSPHATE_c \"FRUCTOSE-16-DIPHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_7014_p \"CPD-7014\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_7014_p \"CPD-7014\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MALONATE_S_ALD_m \"MALONATE-S-ALD\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MALONATE_S_ALD_m \"MALONATE-S-ALD\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPRPP_p \"aPRPP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPRPP_p \"aPRPP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCDP_m \"CDP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCDP_m \"CDP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCDP_p \"CDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCDP_p \"CDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CONIFERYL_ALCOHOL_c \"CONIFERYL-ALCOHOL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CONIFERYL_ALCOHOL_c \"CONIFERYL-ALCOHOL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AMP_m \"AMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AMP_m \"AMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDADP_p \"dADP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDADP_p \"dADP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AMP_p \"AMP\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AMP_p \"AMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AMP_x \"AMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AMP_x \"AMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_PHE_tRNAs_c \"Charged_PHE_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_PHE_tRNAs_c \"Charged_PHE_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ALPHA_ALANINE_c \"L-ALPHA-ALANINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ALPHA_ALANINE_c \"L-ALPHA-ALANINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_R_3_Hydroxypalmitoyl_ACPs_p \"R_3_Hydroxypalmitoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_R_3_Hydroxypalmitoyl_ACPs_p \"R_3_Hydroxypalmitoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THF_p \"THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THF_p \"THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HOMO_CYS_c \"HOMO-CYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HOMO_CYS_c \"HOMO-CYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_14927_c \"CPD-14927[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_14927_c \"CPD-14927[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Tetradec_2_enoyl_ACPs_p \"Tetradec_2_enoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Tetradec_2_enoyl_ACPs_p \"Tetradec_2_enoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_14927_x \"CPD-14927[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_14927_x \"CPD-14927[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THF_m \"THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THF_m \"THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ALPHA_ALANINE_v \"L-ALPHA-ALANINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ALPHA_ALANINE_v \"L-ALPHA-ALANINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ALPHA_ALANINE_x \"L-ALPHA-ALANINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ALPHA_ALANINE_x \"L-ALPHA-ALANINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CARBAMYUL_L_ASPARTATE_p \"CARBAMYUL-L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CARBAMYUL_L_ASPARTATE_p \"CARBAMYUL-L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THF_c \"THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THF_c \"THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_14927_p \"CPD-14927[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_14927_p \"CPD-14927[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ALPHA_ALANINE_m \"L-ALPHA-ALANINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ALPHA_ALANINE_m \"L-ALPHA-ALANINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_Mg_t \"X_Mg[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_Mg_t \"X_Mg[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Cytochromes_C_Oxidized_mi \"Cytochromes_C_Oxidized[mi]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Cytochromes_C_Oxidized_mi \"Cytochromes_C_Oxidized[mi]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Cytochromes_C_Oxidized_mc \"Cytochromes_C_Oxidized[mc]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Cytochromes_C_Oxidized_mc \"Cytochromes_C_Oxidized[mc]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Cellulose_b \"Cellulose[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Cellulose_b \"Cellulose[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_10_METHENYL_THF_c \"5-10-METHENYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_10_METHENYL_THF_c \"5-10-METHENYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLC_v \"GLC\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLC_v \"GLC\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_DELTA1_PYRROLINE_5_CARBOXYLATE_c \"L-DELTA1-PYRROLINE-5-CARBOXYLATE_c\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_DELTA1_PYRROLINE_5_CARBOXYLATE_c \"L-DELTA1-PYRROLINE-5-CARBOXYLATE_c\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_METHACRYL_COA_m \"METHACRYL-COA[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_METHACRYL_COA_m \"METHACRYL-COA[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HOMO_CYS_p \"HOMO-CYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HOMO_CYS_p \"HOMO-CYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLT_tRNAs_c \"GLT_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLT_tRNAs_c \"GLT_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_O_PHOSPHO_L_HOMOSERINE_p \"O-PHOSPHO-L-HOMOSERINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_O_PHOSPHO_L_HOMOSERINE_p \"O-PHOSPHO-L-HOMOSERINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETYL_GLU_p \"ACETYL-GLU\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETYL_GLU_p \"ACETYL-GLU\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aSO3_m \"aSO3[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aSO3_m \"aSO3[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_11281_m \"CPD-11281\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_11281_m \"CPD-11281\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_APS_p \"APS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_APS_p \"APS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_DELTA1_PYRROLINE_5_CARBOXYLATE_m \"L-DELTA-PYRROLINE_5-CARBOXYLATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_DELTA1_PYRROLINE_5_CARBOXYLATE_m \"L-DELTA-PYRROLINE_5-CARBOXYLATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_7016_p \"CPD-7016\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_7016_p \"CPD-7016\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPi_x \"aPi[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPi_x \"aPi[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLN_tRNAs_c \"GLN_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLN_tRNAs_c \"GLN_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aSO3_p \"aSO3[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aSO3_p \"aSO3[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_SO4_t \"X_SO4[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_SO4_t \"X_SO4[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CHLOROPHYLL_B_p \"CHLOROPHYLL-B\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CHLOROPHYLL_B_p \"CHLOROPHYLL-B\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_GLC_t \"X_GLC[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_GLC_t \"X_GLC[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ANTHRANILATE_p \"ANTHRANILATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ANTHRANILATE_p \"ANTHRANILATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ADP_c \"ADP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ADP_c \"ADP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HISTIDINAL_p \"HISTIDINAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HISTIDINAL_p \"HISTIDINAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SER_p \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SER_p \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ADP_D_GLUCOSE_p \"ADP-D-GLUCOSE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ADP_D_GLUCOSE_p \"ADP-D-GLUCOSE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SER_m \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SER_m \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aGERANYLGERANYL_PP_p \"GERANYLGERANYL-PP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aGERANYLGERANYL_PP_p \"GERANYLGERANYL-PP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_5441_c \"CPD-5441\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_5441_c \"CPD-5441\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_DEHYDRO_SHIKIMATE_p \"3-DEHYDRO-SHIKIMATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_DEHYDRO_SHIKIMATE_p \"3-DEHYDRO-SHIKIMATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SER_c \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SER_c \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NITRATE_e \"NITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NITRATE_e \"NITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FeIII_c \"FeIII[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FeIII_c \"FeIII[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NITRATE_c \"NITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NITRATE_c \"NITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Oxidized_Plastocyanins_p \"Oxidized_Plastocyanins[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Oxidized_Plastocyanins_p \"Oxidized_Plastocyanins[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SER_x \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SER_x \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUCROSE_e \"SUCROSE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUCROSE_e \"SUCROSE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FRUCTAN_v \"FRUCTAN[v]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FRUCTAN_v \"FRUCTAN[v]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SER_v \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SER_v \"SER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GAP_c \"GAP\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GAP_c \"GAP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUCROSE_c \"SUCROSE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUCROSE_c \"SUCROSE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NITRATE_v \"NITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NITRATE_v \"NITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORIBOSYL_FORMAMIDO_CARBOXAMIDE_p \"PHOSPHORIBOSYL-FORMAMIDO-CARBOXAMIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORIBOSYL_FORMAMIDO_CARBOXAMIDE_p \"PHOSPHORIBOSYL-FORMAMIDO-CARBOXAMIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GAP_p \"GAP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GAP_p \"GAP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUCROSE_v \"SUCROSE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUCROSE_v \"SUCROSE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ADP_m \"ADP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ADP_m \"ADP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ADP_p \"ADP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ADP_p \"ADP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NAD_c \"NAD\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NAD_c \"NAD\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NAD_m \"NAD\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NAD_m \"NAD\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_ENOLPYRUVYL_SHIKIMATE_5P_p \"3-ENOLPYRUVYL-SHIKIMATE-5P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_ENOLPYRUVYL_SHIKIMATE_5P_p \"3-ENOLPYRUVYL-SHIKIMATE-5P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NAD_p \"NAD\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NAD_p \"NAD\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPi_c \"aPi[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPi_c \"aPi[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NAD_x \"NAD\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NAD_x \"NAD\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bDGTP_p \"dGTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bDGTP_p \"dGTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXIDIZED_GLUTATHIONE_m \"OXIDIZED-GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXIDIZED_GLUTATHIONE_m \"OXIDIZED-GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXIDIZED_GLUTATHIONE_p \"OXIDIZED-GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXIDIZED_GLUTATHIONE_p \"OXIDIZED-GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_P_HYDROXY_PHENYLPYRUVATE_p \"P-HYDROXY-PHENYLPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_P_HYDROXY_PHENYLPYRUVATE_p \"P-HYDROXY-PHENYLPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_4_FUMARYL_ACETOACETATE_c \"4-FUMARYL-ACETOACETATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4_FUMARYL_ACETOACETATE_c \"4-FUMARYL-ACETOACETATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_INDOLE_p \"INDOLE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_INDOLE_p \"INDOLE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CMP_m \"CMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CMP_m \"CMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_K_b \"K[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_K_b \"K[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CMP_p \"CMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CMP_p \"CMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CHLOROPHYLLIDE_A_p \"CHLOROPHYLLIDE-A\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CHLOROPHYLLIDE_A_p \"CHLOROPHYLLIDE-A\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCPD_11281_m \"CPD-11281\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCPD_11281_m \"CPD-11281\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_P_HYDROXY_PHENYLPYRUVATE_c \"P-HYDROXY-PHENYLPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_P_HYDROXY_PHENYLPYRUVATE_c \"P-HYDROXY-PHENYLPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACYL_SN_GLYCEROL_3P_p \"ACYL-SN-GLYCEROL-3P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACYL_SN_GLYCEROL_3P_p \"ACYL-SN-GLYCEROL-3P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CDP_ETHANOLAMINE_m \"CDP-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CDP_ETHANOLAMINE_m \"CDP-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pCYS_b \"pCYS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pCYS_b \"pCYS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_WATER_e \"WATER\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_WATER_e \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Myristoyl_ACPs_p \"Myristoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Myristoyl_ACPs_p \"Myristoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_WATER_c \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_WATER_c \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_TYR_tRNAs_c \"Charged_TYR_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_TYR_tRNAs_c \"Charged_TYR_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_GLUTAMATE_GAMMA_SEMIALDEHYDE_c \"L-GLUTAMATE-GAMMA-SEMIALDEHYDE_c\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_GLUTAMATE_GAMMA_SEMIALDEHYDE_c \"L-GLUTAMATE-GAMMA-SEMIALDEHYDE_c\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_PHOSPHORIBOSYL_N_FORMYLGLYCINEAMIDINE_p \"5-PHOSPHORIBOSYL-N-FORMYLGLYCINEAMIDINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_PHOSPHORIBOSYL_N_FORMYLGLYCINEAMIDINE_p \"5-PHOSPHORIBOSYL-N-FORMYLGLYCINEAMIDINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_a5_PHOSPHORIBOSYL_5_AMINOIMIDAZOLE_p \"5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_a5_PHOSPHORIBOSYL_5_AMINOIMIDAZOLE_p \"5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_WATER_x \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_WATER_x \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Plastocyanin_Reduced_p \"Plastocyanin_Reduced[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Plastocyanin_Reduced_p \"Plastocyanin_Reduced[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_WATER_v \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_WATER_v \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_4211_p \"CPD-4211\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_4211_p \"CPD-4211\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_GLUTAMATE_GAMMA_SEMIALDEHYDE_m \"L_GLUTAMATE_GAMMA_SEMIALDEHYDE[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_GLUTAMATE_GAMMA_SEMIALDEHYDE_m \"L_GLUTAMATE_GAMMA_SEMIALDEHYDE[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_WATER_p \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_WATER_p \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_Octenoyl_ACPs_p \"2_Octenoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_Octenoyl_ACPs_p \"2_Octenoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_WATER_m \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_WATER_m \"WATER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHYTYL_PYROPHOSPHATE_p \"PHYTYL-PYROPHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHYTYL_PYROPHOSPHATE_p \"PHYTYL-PYROPHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aL_GLUTAMATE_5_P_c \"aL-GLUTAMATE-5-P_c\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aL_GLUTAMATE_5_P_c \"aL-GLUTAMATE-5-P_c\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MGII_e \"MGII[e]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MGII_e \"MGII[e]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LL_DIAMINOPIMELATE_p \"LL-DIAMINOPIMELATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LL_DIAMINOPIMELATE_p \"LL-DIAMINOPIMELATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MGII_c \"MGII[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MGII_c \"MGII[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_GLUTAMATE_5_P_c \"L-GLUTAMATE-5-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_GLUTAMATE_5_P_c \"L-GLUTAMATE-5-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_PHOSPHO_RIBOSYL_GLYCINEAMIDE_p \"5-PHOSPHO-RIBOSYL-GLYCINEAMIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_PHOSPHO_RIBOSYL_GLYCINEAMIDE_p \"5-PHOSPHO-RIBOSYL-GLYCINEAMIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Oxidized_ferredoxins_p \"Oxidized_ferredoxins[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Oxidized_ferredoxins_p \"Oxidized_ferredoxins[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PYRUVATE_c \"PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PYRUVATE_c \"PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLUTACONYL_COA_x \"GLUTACONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLUTACONYL_COA_x \"GLUTACONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DIOH_ISOVALERATE_p \"DIOH_ISOVALERATE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DIOH_ISOVALERATE_p \"DIOH_ISOVALERATE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETALD_m \"ACETALD\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETALD_m \"ACETALD\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ETOH_c \"ETOH\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ETOH_c \"ETOH\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DATP_p \"DATP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DATP_p \"DATP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLUTACONYL_COA_c \"GLUTACONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLUTACONYL_COA_c \"GLUTACONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sMAL_b \"sMAL[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sMAL_b \"sMAL[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MGII_v \"MGII[v]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MGII_v \"MGII[v]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLUTACONYL_COA_m \"GLUTACONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLUTACONYL_COA_m \"GLUTACONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_METHYL_CROTONYL_COA_m \"3-METHYL-CROTONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_METHYL_CROTONYL_COA_m \"3-METHYL-CROTONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bOXIDIZED_GLUTATHIONE_m \"OXIDIZED-GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bOXIDIZED_GLUTATHIONE_m \"OXIDIZED-GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_NITRATE_t \"X_NITRATE[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_NITRATE_t \"X_NITRATE[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROTON_v \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROTON_v \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HCO3_m \"HCO3\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HCO3_m \"HCO3\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bOXIDIZED_GLUTATHIONE_p \"OXIDIZED-GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bOXIDIZED_GLUTATHIONE_p \"OXIDIZED-GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_HYDROXY_PROPIONATE_m \"3-HYDROXY-PROPIONATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_HYDROXY_PROPIONATE_m \"3-HYDROXY-PROPIONATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROTON_p \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROTON_p \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROTON_l \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROTON_l \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HCO3_c \"HCO3\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HCO3_c \"HCO3\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROTON_m \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROTON_m \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PYRUVATE_x \"PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PYRUVATE_x \"PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROTON_i \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROTON_i \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PYRUVATE_m \"PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PYRUVATE_m \"PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_HYDROXY_PROPIONATE_x \"3-HYDROXY-PROPIONATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_HYDROXY_PROPIONATE_x \"3-HYDROXY-PROPIONATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PYRUVATE_p \"PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PYRUVATE_p \"PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DELTA1_PIPERIDEINE_2_6_DICARBOXYLATE_p \"DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DELTA1_PIPERIDEINE_2_6_DICARBOXYLATE_p \"DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLC_p \"GLC\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLC_p \"GLC\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLC_c \"GLC\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLC_c \"GLC\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLC_e \"GLC\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLC_e \"GLC\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_PG_p \"2-PG\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_PG_p \"2-PG\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROTON_x \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROTON_x \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLT_m \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLT_m \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLT_p \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLT_p \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_TRP_c \"TRP\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TRP_c \"TRP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sTRP_b \"sTRP[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sTRP_b \"sTRP[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLT_c \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLT_c \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_318_p \"CPD-318\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_318_p \"CPD-318\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROTON_c \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROTON_c \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PROTON_e \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROTON_e \"PROTON\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_TRP_p \"TRP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TRP_p \"TRP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_TRP_v \"TRP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TRP_v \"TRP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pTRP_b \"pTRP[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pTRP_b \"pTRP[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DUTP_p \"DUTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DUTP_p \"DUTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLT_v \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLT_v \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HCO3_p \"HCO3\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HCO3_p \"HCO3\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLT_x \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLT_x \"GLT\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CO_A_c \"CO-A\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CO_A_c \"CO-A\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACET_c \"ACET\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACET_c \"ACET\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LEU_tRNAs_c \"LEU_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LEU_tRNAs_c \"LEU_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CO_A_m \"CO-A\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CO_A_m \"CO-A\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_CYS_tRNAs_c \"Charged_CYS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_CYS_tRNAs_c \"Charged_CYS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACET_p \"ACET\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACET_p \"ACET\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CO_A_p \"CO-A\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CO_A_p \"CO-A\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACET_m \"ACET\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACET_m \"ACET\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Reduced_ferredoxins_p \"Reduced_ferredoxins[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Reduced_ferredoxins_p \"Reduced_ferredoxins[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACET_x \"ACET\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACET_x \"ACET\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CO_A_x \"CO-A\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CO_A_x \"CO-A\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MANNITOL_1P_c \"MANNITOL_1P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MANNITOL_1P_c \"MANNITOL_1P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UTP_p \"UTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UTP_p \"UTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DGTP_p \"DGTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DGTP_p \"DGTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CDP_p \"CDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CDP_p \"CDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_PG_c \"2-PG\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_PG_c \"2-PG\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CDP_m \"CDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CDP_m \"CDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_CARBOXY_3_HYDROXY_ISOCAPROATE_p \"3-CARBOXY-3-HYDROXY-ISOCAPROATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_CARBOXY_3_HYDROXY_ISOCAPROATE_p \"3-CARBOXY-3-HYDROXY-ISOCAPROATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_METHYL_BUTYRYL_COA_m \"2-METHYL-BUTYRYL-COA\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_METHYL_BUTYRYL_COA_m \"2-METHYL-BUTYRYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_3_DIHYDRODIPICOLINATE_p \"2-3-DIHYDRODIPICOLINATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_3_DIHYDRODIPICOLINATE_p \"2-3-DIHYDRODIPICOLINATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UTP_c \"UTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UTP_c \"UTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MALONYL_ACP_p \"MALONYL_ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MALONYL_ACP_p \"MALONYL_ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_ASN_tRNAs_c \"Charged_ASN_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_ASN_tRNAs_c \"Charged_ASN_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUCC_S_ALD_m \"SUCC-S-ALD\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUCC_S_ALD_m \"SUCC-S-ALD\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPHYTYL_PYROPHOSPHATE_p \"aPHYTYL-PYROPHOSPHATE_p\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPHYTYL_PYROPHOSPHATE_p \"aPHYTYL-PYROPHOSPHATE_p\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_HYDROXY_PROPIONATE_c \"3-HYDROXY-PROPIONATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_HYDROXY_PROPIONATE_c \"3-HYDROXY-PROPIONATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD1F_130_p \"CPD1F-130\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD1F_130_p \"CPD1F-130\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MAL_p \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MAL_p \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HIS_v \"HIS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HIS_v \"HIS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MAL_m \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MAL_m \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_Ca_t \"X_Ca[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_Ca_t \"X_Ca[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ILE_v \"ILE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ILE_v \"ILE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HIS_p \"HIS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HIS_p \"HIS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_H_t \"X_H[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_H_t \"X_H[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ILE_p \"ILE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ILE_p \"ILE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_RIBULOSE_5P_c \"RIBULOSE-5P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_RIBULOSE_5P_c \"RIBULOSE-5P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MAL_x \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MAL_x \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MAL_v \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MAL_v \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETOACETYL_COA_x \"ACETOACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETOACETYL_COA_x \"ACETOACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PREPHENATE_p \"PREPHENATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PREPHENATE_p \"PREPHENATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_CYSTATHIONINE_p \"L-CYSTATHIONINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_CYSTATHIONINE_p \"L-CYSTATHIONINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_RIBULOSE_5P_p \"RIBULOSE-5P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_RIBULOSE_5P_p \"RIBULOSE-5P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HIS_c \"HIS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HIS_c \"HIS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sHIS_b \"sHIS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sHIS_b \"sHIS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FRU_v \"FRU[v]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FRU_v \"FRU[v]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HIS_m \"HIS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HIS_m \"HIS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GDP_MANNOSE_c \"GDP-MANNOSE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GDP_MANNOSE_c \"GDP-MANNOSE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MAL_c \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MAL_c \"MAL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HOMO_SER_p \"HOMO-SER\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HOMO_SER_p \"HOMO-SER\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_510_c \"CPD-510\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_510_c \"CPD-510\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_HIS_tRNAs_c \"Charged_HIS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_HIS_tRNAs_c \"Charged_HIS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORIBOSYL_AMP_p \"PHOSPHORIBOSYL-AMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORIBOSYL_AMP_p \"PHOSPHORIBOSYL-AMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ASP_tRNAs_c \"ASP_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ASP_tRNAs_c \"ASP_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD1F_114_p \"CPD1F-114\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD1F_114_p \"CPD1F-114\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_LEU_tRNAs_c \"Charged_LEU_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_LEU_tRNAs_c \"Charged_LEU_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Red_Thioredoxin_p \"Reduced thioredoxin[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Red_Thioredoxin_p \"Reduced thioredoxin[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aHS_c \"bHS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aHS_c \"bHS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ERYTHROSE_4P_p \"ERYTHROSE-4P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ERYTHROSE_4P_p \"ERYTHROSE-4P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_67_p \"CPD-67\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_67_p \"CPD-67\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_469_p \"CPD-469\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_469_p \"CPD-469\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bCYS_m \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bCYS_m \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_ALA_tRNAs_c \"Charged_ALA_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_ALA_tRNAs_c \"Charged_ALA_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FRU_c \"FRU[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FRU_c \"FRU[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FRUCTOSE_6P_p \"FRUCTOSE-6P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FRUCTOSE_6P_p \"FRUCTOSE-6P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_S_ADENOSYLMETHIONINE_c \"S-ADENOSYLMETHIONINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_S_ADENOSYLMETHIONINE_c \"S-ADENOSYLMETHIONINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_METHYLENE_THF_m \"METHYLENE-THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_METHYLENE_THF_m \"METHYLENE-THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_METHYLENE_THF_p \"METHYLENE-THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_METHYLENE_THF_p \"METHYLENE-THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aHOMOGENTISATE_c \"HOMOGENTISATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aHOMOGENTISATE_c \"HOMOGENTISATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FRUCTOSE_6P_c \"FRUCTOSE-6P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FRUCTOSE_6P_c \"FRUCTOSE-6P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_METHYLENE_THF_c \"METHYLENE-THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_METHYLENE_THF_c \"METHYLENE-THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_DEHYDRO_ASCORBATE_p \"L-DEHYDRO-ASCORBATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_DEHYDRO_ASCORBATE_p \"L-DEHYDRO-ASCORBATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MET_p \"MET\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MET_p \"MET\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_P_RIBOSYL_N_FORMYLGLYCINEAMIDE_p \"5-P-RIBOSYL-N-FORMYLGLYCINEAMIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_P_RIBOSYL_N_FORMYLGLYCINEAMIDE_p \"5-P-RIBOSYL-N-FORMYLGLYCINEAMIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UBIQUINOL_mc \"UBIQUINOL[mc]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UBIQUINOL_mc \"UBIQUINOL[mc]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2K_ADIPATE_c \"2K-ADIPATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2K_ADIPATE_c \"2K-ADIPATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Octanoyl_ACPs_p \"Octanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Octanoyl_ACPs_p \"Octanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UBIQUINOL_mi \"UBIQUINOL[mi]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UBIQUINOL_mi \"UBIQUINOL[mi]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ASPARTATE_c \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ASPARTATE_c \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ASPARTATE_m \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ASPARTATE_m \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MET_c \"MET\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MET_c \"MET\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sMET_b \"sMET[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sMET_b \"sMET[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ASPARTATE_p \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ASPARTATE_p \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ASPARTATE_v \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ASPARTATE_v \"L-ASPARTATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_oxo_decanoyl_ACPs_p \"3_oxo_decanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_oxo_decanoyl_ACPs_p \"3_oxo_decanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ADENOSYL_HOMO_CYS_c \"ADENOSYL-HOMO-CYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ADENOSYL_HOMO_CYS_c \"ADENOSYL-HOMO-CYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MANNOSE_6P_c \"MANNOSE-6P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MANNOSE_6P_c \"MANNOSE-6P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ATP_p \"ATP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ATP_p \"ATP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ATP_m \"ATP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ATP_m \"ATP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bHISTIDINAL_p \"bHISTIDINAL[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bHISTIDINAL_p \"bHISTIDINAL[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ADENYLOSUCC_p \"ADENYLOSUCC\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ADENYLOSUCC_p \"ADENYLOSUCC\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ATP_c \"ATP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ATP_c \"ATP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2K_ADIPATE_m \"2K-ADIPATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2K_ADIPATE_m \"2K-ADIPATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_DEHYDRO_ASCORBATE_m \"L-DEHYDRO-ASCORBATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_DEHYDRO_ASCORBATE_m \"L-DEHYDRO-ASCORBATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ARGININO_SUCCINATE_p \"L-ARGININO-SUCCINATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ARGININO_SUCCINATE_p \"L-ARGININO-SUCCINATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pMET_b \"pMET[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pMET_b \"pMET[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ATP_x \"ATP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ATP_x \"ATP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CYS_v \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CYS_v \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pILE_b \"pILE[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pILE_b \"pILE[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Palmitoyl_ACPs_p \"Palmitoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Palmitoyl_ACPs_p \"Palmitoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ETHANOL_AMINE_c \"ETHANOL-AMINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ETHANOL_AMINE_c \"ETHANOL-AMINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_RIBOSE_5P_p \"RIBOSE_5P[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_RIBOSE_5P_p \"RIBOSE_5P[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UDP_GLUCURONATE_c \"UDP-GLUCURONATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UDP_GLUCURONATE_c \"UDP-GLUCURONATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CYS_p \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CYS_p \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CARBON_DIOXIDE_x \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CARBON_DIOXIDE_x \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CYS_m \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CYS_m \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ILE_c \"ILE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ILE_c \"ILE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sILE_b \"sILE[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sILE_b \"sILE[b]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CARBON_DIOXIDE_p \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CARBON_DIOXIDE_p \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_a5_PHOSPHO_RIBOSYL_GLYCINEAMIDE_p \"5-PHOSPHO-RIBOSYL-GLYCINEAMIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_a5_PHOSPHO_RIBOSYL_GLYCINEAMIDE_p \"5-PHOSPHO-RIBOSYL-GLYCINEAMIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CARBON_DIOXIDE_m \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CARBON_DIOXIDE_m \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pHIS_b \"pHIS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pHIS_b \"pHIS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_KETOBUTYRATE_m \"3-KETOBUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_KETOBUTYRATE_m \"3-KETOBUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MET_v \"MET\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MET_v \"MET\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CYS_c \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CYS_c \"CYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sCYS_b \"sCYS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sCYS_b \"sCYS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ILE_m \"ILE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ILE_m \"ILE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CARBON_DIOXIDE_e \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CARBON_DIOXIDE_e \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CARBON_DIOXIDE_c \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CARBON_DIOXIDE_c \"CARBON-DIOXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FUM_p \"FUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FUM_p \"FUM\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FUM_m \"FUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FUM_m \"FUM\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_KETOGLUTARATE_c \"2-KETOGLUTARATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_KETOGLUTARATE_c \"2-KETOGLUTARATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_Hexadecenoyl_ACPs_p \"2_Hexadecenoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_Hexadecenoyl_ACPs_p \"2_Hexadecenoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DUMP_c \"DUMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DUMP_c \"DUMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FUM_c \"FUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FUM_c \"FUM\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Protein_polymerisation_cost_c \"Protein_polymerisation_cost[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_OXOBUTANOATE_p \"2-OXOBUTANOATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_OXOBUTANOATE_p \"2-OXOBUTANOATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DUMP_p \"DUMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DUMP_p \"DUMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_KETOGLUTARATE_m \"2-KETOGLUTARATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_KETOGLUTARATE_m \"2-KETOGLUTARATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DUMP_m \"DUMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DUMP_m \"DUMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Butanoyl_ACPs_p \"Butanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Butanoyl_ACPs_p \"Butanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCIT_v \"aCIT[v]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCIT_v \"aCIT[v]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UMP_p \"UMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UMP_p \"UMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_THR_tRNAs_c \"Charged_THR_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_THR_tRNAs_c \"Charged_THR_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_KETOGLUTARATE_p \"2-KETOGLUTARATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_KETOGLUTARATE_p \"2-KETOGLUTARATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_IMIDAZOLE_ACETOL_P_p \"IMIDAZOLE-ACETOL-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_IMIDAZOLE_ACETOL_P_p \"IMIDAZOLE-ACETOL-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_KETOGLUTARATE_x \"2-KETOGLUTARATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_KETOGLUTARATE_x \"2-KETOGLUTARATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bDGDP_p \"dGDP[p]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bDGDP_p \"dGDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2K_4CH3_PENTANOATE_m \"2K-4CH3-PENTANOATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2K_4CH3_PENTANOATE_m \"2K-4CH3-PENTANOATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2K_4CH3_PENTANOATE_p \"2K-4CH3-PENTANOATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2K_4CH3_PENTANOATE_p \"2K-4CH3-PENTANOATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FUM_v \"FUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FUM_v \"FUM\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Pi_x \"Pi[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Pi_x \"Pi[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GMP_p \"GMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GMP_p \"GMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sSUC_b \"sSUC[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sSUC_b \"sSUC[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aGMP_c \"aGMP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aGMP_c \"aGMP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_NH4_t \"X_NH4[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_NH4_t \"X_NH4[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Cytochromes_C_Reduced_mi \"Cytochromes_C_Reduced[mi]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Cytochromes_C_Reduced_mi \"Cytochromes_C_Reduced[mi]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_12173_m \"CPD-12173[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_12173_m \"CPD-12173[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FattyAcid_b \"FattyAcid[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FattyAcid_b \"FattyAcid[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DIHYDROFOLATE_m \"DIHYDROFOLATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DIHYDROFOLATE_m \"DIHYDROFOLATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Beta_3_hydroxybutyryl_ACPs_p \"Beta_3_hydroxybutyryl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Beta_3_hydroxybutyryl_ACPs_p \"Beta_3_hydroxybutyryl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDGTP_p \"dGTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDGTP_p \"dGTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_VAL_tRNAs_c \"VAL_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_VAL_tRNAs_c \"VAL_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDUTP_p \"dUTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDUTP_p \"dUTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CIS_ACONITATE_c \"CIS-ACONITATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CIS_ACONITATE_c \"CIS-ACONITATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GMP_c \"GMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GMP_c \"GMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CIS_ACONITATE_m \"CIS-ACONITATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CIS_ACONITATE_m \"CIS-ACONITATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MALTOSE_p \"MALTOSE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MALTOSE_p \"MALTOSE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Cytochromes_C_Reduced_mc \"Cytochromes_C_Reduced[mc]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Cytochromes_C_Reduced_mc \"Cytochromes_C_Reduced[mc]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_ASP_tRNAs_c \"Charged_ASP_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_ASP_tRNAs_c \"Charged_ASP_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CELLULOSE_c \"CELLULOSE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CELLULOSE_c \"CELLULOSE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_4_MALEYL_ACETOACETATE_c \"4-MALEYL-ACETOACETATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4_MALEYL_ACETOACETATE_c \"4-MALEYL-ACETOACETATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYOX_x \"GLYOX\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYOX_x \"GLYOX\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_oxo_dodecanoyl_ACPs_p \"3_oxo_dodecanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_oxo_dodecanoyl_ACPs_p \"3_oxo_dodecanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bHIS_v \"bHIS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bHIS_v \"bHIS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CTP_m \"CTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CTP_m \"CTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MALTOSE_c \"MALTOSE[c]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MALTOSE_c \"MALTOSE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UDP_D_XYLOSE_c \"UDP-D-XYLOSE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UDP_D_XYLOSE_c \"UDP-D-XYLOSE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CTP_p \"CTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CTP_p \"CTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DGDP_p \"DGDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DGDP_p \"DGDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CAII_v \"CAII[v]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CAII_v \"CAII[v]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_1_KETO_2_METHYLVALERATE_p \"1-KETO-2-METHYLVALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_1_KETO_2_METHYLVALERATE_p \"1-KETO-2-METHYLVALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DCTP_p \"DCTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DCTP_p \"DCTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CAII_c \"CAII[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CAII_c \"CAII[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GDP_c \"GDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GDP_c \"GDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CAII_e \"CAII[e]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CAII_e \"CAII[e]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aP_HYDROXY_PHENYLPYRUVATE_c \"P-HYDROXY-PHENYLPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aP_HYDROXY_PHENYLPYRUVATE_c \"P-HYDROXY-PHENYLPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Pi_c \"Pi[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Pi_c \"Pi[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GDP_m \"GDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GDP_m \"GDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_HISTIDINOL_P_p \"L-HISTIDINOL-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_HISTIDINOL_P_p \"L-HISTIDINOL-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_TYR_tRNAs_c \"TYR_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TYR_tRNAs_c \"TYR_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_468_c \"CPD-468\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_468_c \"CPD-468\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDTTP_c \"dTTP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDTTP_c \"dTTP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Pi_e \"Pi[e]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Pi_e \"Pi[e]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_H2O_t \"X_H2O[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_H2O_t \"X_H2O[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GDP_p \"GDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GDP_p \"GDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aP_HYDROXY_PHENYLPYRUVATE_p \"P-HYDROXY-PHENYLPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aP_HYDROXY_PHENYLPYRUVATE_p \"P-HYDROXY-PHENYLPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Pi_p \"Pi[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Pi_p \"Pi[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Glycerol_b \"Glycerol[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Glycerol_b \"Glycerol[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Pi_m \"Pi[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Pi_m \"Pi[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DUDP_p \"DUDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DUDP_p \"DUDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CROTONYL_COA_x \"CROTONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CROTONYL_COA_x \"CROTONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HISTIDINOL_p \"HISTIDINOL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HISTIDINOL_p \"HISTIDINOL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_XANTHOSINE_5_PHOSPHATE_c \"XANTHOSINE-5-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_XANTHOSINE_5_PHOSPHATE_c \"XANTHOSINE-5-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UDP_p \"UDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UDP_p \"UDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PLASTOQUINONE_p \"PLASTOQUINONE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PLASTOQUINONE_p \"PLASTOQUINONE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aIMP_c \"aIMP[c]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aIMP_c \"aIMP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_ILE_tRNAs_c \"Charged_ILE_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_ILE_tRNAs_c \"Charged_ILE_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DTTP_c \"dTTP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DTTP_c \"dTTP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_1_L_MYO_INOSITOL_1_P_c \"1-L-MYO-INOSITOL-1-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_1_L_MYO_INOSITOL_1_P_c \"1-L-MYO-INOSITOL-1-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THREO_DS_ISO_CITRATE_x \"THREO-DS-ISO-CITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THREO_DS_ISO_CITRATE_x \"THREO-DS-ISO-CITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_PHOSPHATIDATE_p \"L-PHOSPHATIDATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_PHOSPHATIDATE_p \"L-PHOSPHATIDATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_PHOSPHATIDATE_m \"L-PHOSPHATIDATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_PHOSPHATIDATE_m \"L-PHOSPHATIDATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHYTOL_p \"PHYTOL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHYTOL_p \"PHYTOL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Reduced_Ferroproteins_m \"Reduced_Ferroproteins[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Reduced_Ferroproteins_m \"Reduced_Ferroproteins[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UBIQUINONE_mi \"UBIQUINONE[mi]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UBIQUINONE_mi \"UBIQUINONE[mi]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UDP_c \"UDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UDP_c \"UDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CARBAMOYL_P_p \"CARBAMOYL-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CARBAMOYL_P_p \"CARBAMOYL-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UBIQUINONE_mc \"UBIQUINONE[mc]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UBIQUINONE_mc \"UBIQUINONE[mc]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SULFATE_e \"SULFATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SULFATE_e \"SULFATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_7100_p \"CPD-7100\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_7100_p \"CPD-7100\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SULFATE_c \"SULFATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SULFATE_c \"SULFATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADP_x \"NADP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADP_x \"NADP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SULFATE_p \"SULFATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SULFATE_p \"SULFATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SULFATE_m \"SULFATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SULFATE_m \"SULFATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADP_p \"NADP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADP_p \"NADP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NITRITE_p \"NITRITE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NITRITE_p \"NITRITE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ARG_p \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ARG_p \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ARG_m \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ARG_m \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADP_m \"NADP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADP_m \"NADP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLC_1_P_c \"GLC-1-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLC_1_P_c \"GLC-1-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Ca_b \"Ca[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Ca_b \"Ca[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NITRITE_c \"NITRITE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NITRITE_c \"NITRITE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADP_c \"NADP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADP_c \"NADP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ARG_v \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ARG_v \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_ACETO_LACTATE_p \"2-ACETO-LACTATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_ACETO_LACTATE_p \"2-ACETO-LACTATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GDP_D_GLUCOSE_c \"GDP-D-GLUCOSE\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GDP_D_GLUCOSE_c \"GDP-D-GLUCOSE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXYGEN_MOLECULE_e \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXYGEN_MOLECULE_e \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXYGEN_MOLECULE_c \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXYGEN_MOLECULE_c \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ARG_c \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ARG_c \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sARG_b \"sARG[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sARG_b \"sARG[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sGLN_b \"sGLN[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sGLN_b \"sGLN[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ARG_tRNAs_c \"ARG_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ARG_tRNAs_c \"ARG_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aGTP_c \"aGTP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aGTP_c \"aGTP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pARG_b \"pARG[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pARG_b \"pARG[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HOMOGENTISATE_c \"HOMOGENTISATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HOMOGENTISATE_c \"HOMOGENTISATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLC_1_P_p \"GLC-1-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLC_1_P_p \"GLC-1-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aGTP_m \"aGTP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aGTP_m \"aGTP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACP_p \"ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACP_p \"ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_PRO_tRNAs_c \"Charged_PRO_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_PRO_tRNAs_c \"Charged_PRO_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DTMP_m \"dTMP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DTMP_m \"dTMP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aGTP_p \"aGTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aGTP_p \"aGTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PRO_tRNAs_c \"Charged_PRO_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PRO_tRNAs_c \"Charged_PRO_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_HYDROXY_PROPIONYL_COA_x \"3-HYDROXY-PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_HYDROXY_PROPIONYL_COA_x \"3-HYDROXY-PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DI_H_OROTATE_p \"DI-H-OROTATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DI_H_OROTATE_p \"DI-H-OROTATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_HYDROXY_PROPIONYL_COA_m \"3-HYDROXY-PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_HYDROXY_PROPIONYL_COA_m \"3-HYDROXY-PROPIONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DTMP_c \"dTMP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DTMP_c \"dTMP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CIT_m \"CIT\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CIT_m \"CIT\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETALD_c \"ACETALD\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETALD_c \"ACETALD\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CIT_c \"CIT\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CIT_c \"CIT\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORIBOSYL_ATP_p \"PHOSPHORIBOSYL-ATP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORIBOSYL_ATP_p \"PHOSPHORIBOSYL-ATP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Dodecanoyl_ACPs_p \"Dodecanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Dodecanoyl_ACPs_p \"Dodecanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPHOSPHORYL_ETHANOLAMINE_c \"PHOSPHORYL-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPHOSPHORYL_ETHANOLAMINE_c \"PHOSPHORYL-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HYDROGEN_PEROXIDE_p \"HYDROGEN-PEROXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HYDROGEN_PEROXIDE_p \"HYDROGEN-PEROXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CIT_x \"CIT\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CIT_x \"CIT\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_IMP_c \"IMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_IMP_c \"IMP\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CIT_v \"CIT\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CIT_v \"CIT\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HYDROGEN_PEROXIDE_x \"HYDROGEN-PEROXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HYDROGEN_PEROXIDE_x \"HYDROGEN-PEROXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HYDROGEN_PEROXIDE_c \"HYDROGEN-PEROXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HYDROGEN_PEROXIDE_c \"HYDROGEN-PEROXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_VAL_tRNAs_c \"Charged_VAL_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_VAL_tRNAs_c \"Charged_VAL_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HIS_tRNAs_c \"HIS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HIS_tRNAs_c \"HIS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MESO_DIAMINOPIMELATE_p \"MESO-DIAMINOPIMELATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MESO_DIAMINOPIMELATE_p \"MESO-DIAMINOPIMELATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_Hydroxy_octanoyl_ACPs_p \"3_Hydroxy_octanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_Hydroxy_octanoyl_ACPs_p \"3_Hydroxy_octanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPHOSPHORYL_ETHANOLAMINE_m \"PHOSPHORYL-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPHOSPHORYL_ETHANOLAMINE_m \"PHOSPHORYL-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HYDROGEN_PEROXIDE_m \"HYDROGEN-PEROXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HYDROGEN_PEROXIDE_m \"HYDROGEN-PEROXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aMAL_v \"aMAL[v]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aMAL_v \"aMAL[v]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_IMP_p \"IMP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_IMP_p \"IMP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_D_THREO_HYDROXY_3_CARBOXY_ISOCAPROATE_p \"2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_D_THREO_HYDROXY_3_CARBOXY_ISOCAPROATE_p \"2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MALONYL_COA_p \"MALONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MALONYL_COA_p \"MALONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_D_SEDOHEPTULOSE_7_P_p \"D-SEDOHEPTULOSE-7-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_D_SEDOHEPTULOSE_7_P_p \"D-SEDOHEPTULOSE-7-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aUDP_p \"aUDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aUDP_p \"aUDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETYL_COA_p \"ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETYL_COA_p \"ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXYGEN_MOLECULE_x \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXYGEN_MOLECULE_x \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETYL_COA_m \"ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETYL_COA_m \"ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Hexanoyl_ACPs_p \"Hexanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Hexanoyl_ACPs_p \"Hexanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aUDP_c \"aUDP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aUDP_c \"aUDP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYCERATE_c \"GLYCERATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYCERATE_c \"GLYCERATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXYGEN_MOLECULE_p \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXYGEN_MOLECULE_p \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Ox_Thioredoxin_p \"Oxidized thioredoxin[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Ox_Thioredoxin_p \"Oxidized thioredoxin[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORYL_CHOLINE_c \"PHOSPHORYL-CHOLINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORYL_CHOLINE_c \"PHOSPHORYL-CHOLINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETYL_COA_c \"ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETYL_COA_c \"ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXYGEN_MOLECULE_m \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXYGEN_MOLECULE_m \"OXYGEN-MOLECULE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYCERATE_p \"GLYCERATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYCERATE_p \"GLYCERATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_7015_p \"CPD-7015\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_7015_p \"CPD-7015\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_R_3_hydroxyhexanoyl_ACPs_p \"R_3_hydroxyhexanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_R_3_hydroxyhexanoyl_ACPs_p \"R_3_hydroxyhexanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bGMP_p \"GMP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bGMP_p \"GMP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORIBOSYL_FORMIMINO_AICAR_P_p \"PHOSPHORIBOSYL-FORMIMINO-AICAR-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORIBOSYL_FORMIMINO_AICAR_P_p \"PHOSPHORIBOSYL-FORMIMINO-AICAR-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_TRANS_3_METHYL_GLUTACONYL_COA_m \"TRANS-3-METHYL-GLUTACONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TRANS_3_METHYL_GLUTACONYL_COA_m \"TRANS-3-METHYL-GLUTACONYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ASN_tRNAs_c \"ASN_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ASN_tRNAs_c \"ASN_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLY_tRNAs_c \"GLY_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLY_tRNAs_c \"GLY_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYCERATE_x \"GLYCERATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYCERATE_x \"GLYCERATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Starch_b \"Starch[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Starch_b \"Starch[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bGMP_c \"aGMP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bGMP_c \"aGMP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CYS_tRNAs_c \"Charged_CYS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CYS_tRNAs_c \"Charged_CYS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORYL_CHOLINE_m \"PHOSPHORYL-CHOLINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORYL_CHOLINE_m \"PHOSPHORYL-CHOLINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETYL_COA_x \"ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETYL_COA_x \"ACETYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Crotonyl_ACPs_p \"Crotonyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Crotonyl_ACPs_p \"Crotonyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pASN_b \"pASN[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pASN_b \"pASN[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDUDP_p \"dUDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDUDP_p \"dUDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DIACYLGLYCEROL_r \"DIACYLGLYCEROL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DIACYLGLYCEROL_r \"DIACYLGLYCEROL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_BETA_ASPARTYL_P_p \"L-BETA-ASPARTYL-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_BETA_ASPARTYL_P_p \"L-BETA-ASPARTYL-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCPD_5441_c \"CPD-5441[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCPD_5441_c \"CPD-5441[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DIACYLGLYCEROL_p \"DIACYLGLYCEROL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DIACYLGLYCEROL_p \"DIACYLGLYCEROL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ADENOSINE_c \"ADENOSINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ADENOSINE_c \"ADENOSINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Beta_hydroxydecanoyl_ACPs_p \"Beta_hydroxydecanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Beta_hydroxydecanoyl_ACPs_p \"Beta_hydroxydecanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_KETO_3_METHYL_VALERATE_m \"2-KETO-3-METHYL-VALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_KETO_3_METHYL_VALERATE_m \"2-KETO-3-METHYL-VALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_LYS_tRNAs_c \"Charged_LYS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_LYS_tRNAs_c \"Charged_LYS_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETYLSERINE_p \"ACETYLSERINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETYLSERINE_p \"ACETYLSERINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_KETO_3_METHYL_VALERATE_p \"2-KETO-3-METHYL-VALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_KETO_3_METHYL_VALERATE_p \"2-KETO-3-METHYL-VALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_2961_c \"CPD-2961\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_2961_c \"CPD-2961\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SER_tRNAs_c \"SER_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SER_tRNAs_c \"SER_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_2961_p \"CPD-2961\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_2961_p \"CPD-2961\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pSER_b \"pSER[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pSER_b \"pSER[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HS_c \"HS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HS_c \"HS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_MET_tRNAs_c \"Charged_MET_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_MET_tRNAs_c \"Charged_MET_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Xylan_b \"Xylan[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Xylan_b \"Xylan[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_G3P_c \"G3P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_G3P_c \"G3P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_Biomass_t \"X_Biomass[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_Biomass_t \"X_Biomass[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_HS_p \"HS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_HS_p \"HS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_4_AMINO_BUTYRATE_m \"4-AMINO-BUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4_AMINO_BUTYRATE_m \"4-AMINO-BUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_659_p \"CPD-659\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_659_p \"CPD-659\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Heteroglycans_c \"Heteroglycans\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Heteroglycans_c \"Heteroglycans\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_4_AMINO_BUTYRATE_v \"4-AMINO-BUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4_AMINO_BUTYRATE_v \"4-AMINO-BUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD1F_131_p \"CPD1F-131\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD1F_131_p \"CPD1F-131\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THR_p \"THR\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THR_p \"THR\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sASP_b \"sASP[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sASP_b \"sASP[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_KI_v \"KI[v]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_KI_v \"KI[v]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MANNOSE_1P_c \"MANNOSE-1P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MANNOSE_1P_c \"MANNOSE-1P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THR_c \"THR\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THR_c \"THR\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sTHR_b \"sTHR[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sTHR_b \"sTHR[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPPI_x \"aPPI[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPPI_x \"aPPI[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACRYLYL_COA_x \"ACRYLYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACRYLYL_COA_x \"ACRYLYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SHIKIMATE_p \"SHIKIMATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SHIKIMATE_p \"SHIKIMATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ASCORBATE_p \"ASCORBATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ASCORBATE_p \"ASCORBATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_D_RIBULOSE_15_P2_p \"D-RIBULOSE-15-P2\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_D_RIBULOSE_15_P2_p \"D-RIBULOSE-15-P2\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACRYLYL_COA_m \"ACRYLYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACRYLYL_COA_m \"ACRYLYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ASCORBATE_m \"ASCORBATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ASCORBATE_m \"ASCORBATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Photon_e \"Photon[e]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCPD_406_c \"CPD-406[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCPD_406_c \"CPD-406[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDCTP_p \"dCTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDCTP_p \"dCTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Photon_p \"Photon[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDGDP_p \"dGDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDGDP_p \"dGDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PPI_p \"PPI\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PPI_p \"PPI\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPPI_c \"aPPI[c]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPPI_c \"aPPI[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACRYLYL_COA_c \"ACRYLYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACRYLYL_COA_c \"ACRYLYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETYLSERINE_c \"ACETYLSERINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETYLSERINE_c \"ACETYLSERINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CHLOROPHYLL_A_p \"CHLOROPHYLL-A\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CHLOROPHYLL_A_p \"CHLOROPHYLL-A\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Palmitate_b \"Palmitate[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Palmitate_b \"Palmitate[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PPI_m \"PPI\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PPI_m \"PPI\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MANNITOL_c \"MANNITOL\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MANNITOL_c \"MANNITOL\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AICAR_p \"AICAR\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AICAR_p \"AICAR\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PRPP_p \"PRPP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PRPP_p \"PRPP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PPI_x \"PPI\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PPI_x \"PPI\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THR_v \"THR\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THR_v \"THR\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_P_RIBOSYL_4_SUCCCARB_AMINOIMIDAZOLE_p \"P-RIBOSYL-4-SUCCCARB-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_P_RIBOSYL_4_SUCCCARB_AMINOIMIDAZOLE_p \"P-RIBOSYL-4-SUCCCARB-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDTDP_c \"dTDP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDTDP_c \"dTDP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pTHR_b \"pTHR[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pTHR_b \"pTHR[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PPI_c \"PPI\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PPI_c \"PPI\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_PHOSPHORIBOSYL_5_AMINOIMIDAZOLE_p \"5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_PHOSPHORIBOSYL_5_AMINOIMIDAZOLE_p \"5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DIHYDROXY_ACETONE_PHOSPHATE_c \"DIHYDROXY-ACETONE-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DIHYDROXY_ACETONE_PHOSPHATE_c \"DIHYDROXY-ACETONE-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pALA_b \"pALA[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pALA_b \"pALA[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OROTIDINE_5_PHOSPHATE_p \"OROTIDINE-5-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OROTIDINE_5_PHOSPHATE_p \"OROTIDINE-5-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_R_3_hydroxydodecanoyl_ACPs_p \"R_3_hydroxydodecanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_R_3_hydroxydodecanoyl_ACPs_p \"R_3_hydroxydodecanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DIHYDROXY_ACETONE_PHOSPHATE_p \"DIHYDROXY-ACETONE-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DIHYDROXY_ACETONE_PHOSPHATE_p \"DIHYDROXY-ACETONE-PHOSPHATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bARG_p \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bARG_p \"ARG\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DCDP_p \"DCDP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DCDP_p \"DCDP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GTP_p \"GTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GTP_p \"GTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_oxo_palmitoyl_ACPs_p \"3_oxo_palmitoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_oxo_palmitoyl_ACPs_p \"3_oxo_palmitoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_KI_e \"KI[e]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_KI_e \"KI[e]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_KI_c \"KI[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_KI_c \"KI[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_XYLAN_c \"XYLAN[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_XYLAN_c \"XYLAN[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THR_tRNAs_c \"THR_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THR_tRNAs_c \"THR_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DTDP_c \"dTDP[c]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DTDP_c \"dTDP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_K_t \"X_K[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_K_t \"X_K[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aATP_x \"aATP[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aATP_x \"aATP[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_4_AMINO_BUTYRATE_c \"4-AMINO-BUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4_AMINO_BUTYRATE_c \"4-AMINO-BUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GTP_m \"GTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GTP_m \"GTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ISOVALERYL_COA_m \"ISOVALERYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ISOVALERYL_COA_m \"ISOVALERYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sSER_b \"sSER[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sSER_b \"sSER[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GTP_c \"GTP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GTP_c \"GTP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_G3P_p \"G3P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_G3P_p \"G3P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pGLU_b \"pGLU[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pGLU_b \"pGLU[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_406_c \"CPD-406\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_406_c \"CPD-406\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLUTATHIONE_p \"GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLUTATHIONE_p \"GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_oxo_myristoyl_ACPs_p \"3_oxo_myristoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_oxo_myristoyl_ACPs_p \"3_oxo_myristoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aATP_p \"aATP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aATP_p \"aATP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bPPI_m \"PPI[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bPPI_m \"PPI[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Protein_processing_cost_c \"Protein_processing_cost[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLUTATHIONE_m \"GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLUTATHIONE_m \"GLUTATHIONE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aATP_m \"aATP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aATP_m \"aATP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_bPPI_p \"bPPI[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_bPPI_p \"bPPI[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aATP_c \"aATP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aATP_c \"aATP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_GLY_tRNAs_c \"Charged_GLY_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_GLY_tRNAs_c \"Charged_GLY_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_Sucrose_t \"X_Sucrose[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_Sucrose_t \"X_Sucrose[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aHYDROXY_METHYL_BUTENYL_DIP_p \"HYDROXY-METHYL-BUTENYL-DIP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aHYDROXY_METHYL_BUTENYL_DIP_p \"HYDROXY-METHYL-BUTENYL-DIP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_Phloem_contribution_t \"X_Phloem_contribution[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_O2_t \"X_O2[t]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_X_O2_t \"X_O2[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Mg_b \"Mg[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Mg_b \"Mg[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aGDP_m \"aGDP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aGDP_m \"aGDP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aGDP_p \"aGDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aGDP_p \"aGDP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OROTATE_p \"OROTATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OROTATE_p \"OROTATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aGDP_c \"aGDP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aGDP_c \"aGDP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THREO_DS_ISO_CITRATE_c \"THREO-DS-ISO-CITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THREO_DS_ISO_CITRATE_c \"THREO-DS-ISO-CITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCTP_m \"CTP[m]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCTP_m \"CTP[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_D_SEDOHEPTULOSE_1_7_P2_p \"D-SEDOHEPTULOSE-1-7-P2\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_D_SEDOHEPTULOSE_1_7_P2_p \"D-SEDOHEPTULOSE-1-7-P2\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_R_3_hydroxymyristoyl_ACPs_p \"R_3_hydroxymyristoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_R_3_hydroxymyristoyl_ACPs_p \"R_3_hydroxymyristoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SACCHAROPINE_c \"SACCHAROPINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SACCHAROPINE_c \"SACCHAROPINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADH_x \"NADH\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADH_x \"NADH\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_X_Photon_t \"X_Photon[t]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_THREO_DS_ISO_CITRATE_m \"THREO-DS-ISO-CITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_THREO_DS_ISO_CITRATE_m \"THREO-DS-ISO-CITRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_a5_P_BETA_D_RIBOSYL_AMINE_p \"5-P-BETA-D-RIBOSYL-AMINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_a5_P_BETA_D_RIBOSYL_AMINE_p \"5-P-BETA-D-RIBOSYL-AMINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADH_p \"NADH\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADH_p \"NADH\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aUTP_c \"aUTP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aUTP_c \"aUTP[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PRO_m \"PRO\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PRO_m \"PRO\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pPRO_b \"pPRO[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pPRO_b \"pPRO[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCTP_p \"CTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCTP_p \"CTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GERANYLGERANYL_PP_p \"GERANYLGERANYL-PP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GERANYLGERANYL_PP_p \"GERANYLGERANYL-PP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pLYS_b \"pLYS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pLYS_b \"pLYS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Oxidized_Ferroproteins_m \"Oxidized_Ferroproteins[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Oxidized_Ferroproteins_m \"Oxidized_Ferroproteins[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LEU_v \"LEU\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LEU_v \"LEU\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_P_HYDROXYPYRUVATE_p \"3-P-HYDROXYPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_P_HYDROXYPYRUVATE_p \"3-P-HYDROXYPYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADH_m \"NADH\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADH_m \"NADH\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_a5_PHOSPHORIBOSYL_N_FORMYLGLYCINEAMIDINE_p \"5-PHOSPHORIBOSYL-N-FORMYLGLYCINEAMIDINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_a5_PHOSPHORIBOSYL_N_FORMYLGLYCINEAMIDINE_p \"5-PHOSPHORIBOSYL-N-FORMYLGLYCINEAMIDINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_NADH_c \"NADH\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_NADH_c \"NADH\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aUTP_p \"UTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aUTP_p \"UTP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PRO_v \"PRO\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PRO_v \"PRO\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pLEU_b \"pLEU[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pLEU_b \"pLEU[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Dodec_2_enoyl_ACPs_p \"Dodec_2_enoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Dodec_2_enoyl_ACPs_p \"Dodec_2_enoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aDATP_p \"dATP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aDATP_p \"dATP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_9451_p \"CPD-9451\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_9451_p \"CPD-9451\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_TRP_tRNAs_c \"Charged_TRP_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TRP_tRNAs_c \"Charged_TRP_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUC_c \"SUC\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUC_c \"SUC\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUC_m \"SUC\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUC_m \"SUC\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_ARG_tRNAs_c \"Charged_ARG_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_ARG_tRNAs_c \"Charged_ARG_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_METHYL_THF_c \"5-METHYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_METHYL_THF_c \"5-METHYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_10_FORMYL_THF_c \"10-FORMYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_10_FORMYL_THF_c \"10-FORMYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PRO_c \"PRO\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PRO_c \"PRO\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sPRO_b \"sPRO[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sPRO_b \"sPRO[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_TRP_tRNAs_c \"Charged_TRP_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_TRP_tRNAs_c \"Charged_TRP_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_D_ERYTHRO_IMIDAZOLE_GLYCEROL_P_p \"D-ERYTHRO-IMIDAZOLE-GLYCEROL-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_D_ERYTHRO_IMIDAZOLE_GLYCEROL_P_p \"D-ERYTHRO-IMIDAZOLE-GLYCEROL-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_METHYL_THF_p \"5-METHYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_METHYL_THF_p \"5-METHYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_HYDROXY_3_METHYL_GLUTARYL_COA_m \"3-HYDROXY-3-METHYL-GLUTARYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_HYDROXY_3_METHYL_GLUTARYL_COA_m \"3-HYDROXY-3-METHYL-GLUTARYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sALA_b \"sALA[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sALA_b \"sALA[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_N_ACETYL_GLUTAMYL_P_p \"N-ACETYL-GLUTAMYL-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_N_ACETYL_GLUTAMYL_P_p \"N-ACETYL-GLUTAMYL-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORIBULOSYL_FORMIMINO_AICAR_P_p \"PHOSPHORIBULOSYL-FORMIMINO-AICAR-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORIBULOSYL_FORMIMINO_AICAR_P_p \"PHOSPHORIBULOSYL-FORMIMINO-AICAR-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUC_x \"SUC\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUC_x \"SUC\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUPER_OXIDE_p \"SUPER-OXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUPER_OXIDE_p \"SUPER-OXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_P_BETA_D_RIBOSYL_AMINE_p \"5-P-BETA-D-RIBOSYL-AMINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_P_BETA_D_RIBOSYL_AMINE_p \"5-P-BETA-D-RIBOSYL-AMINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DELTA3_ISOPENTENYL_PP_p \"DELTA3-ISOPENTENYL-PP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DELTA3_ISOPENTENYL_PP_p \"DELTA3-ISOPENTENYL-PP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pASP_b \"pASP[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pASP_b \"pASP[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORYL_ETHANOLAMINE_m \"PHOSPHORYL-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORYL_ETHANOLAMINE_m \"PHOSPHORYL-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OH_PYR_x \"OH-PYR\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OH_PYR_x \"OH-PYR\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPHOSPHORYL_CHOLINE_c \"PHOSPHORYL-CHOLINE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPHOSPHORYL_CHOLINE_c \"PHOSPHORYL-CHOLINE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_KETO_ISOVALERATE_m \"2-KETO-ISOVALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_KETO_ISOVALERATE_m \"2-KETO-ISOVALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_KETO_ISOVALERATE_p \"2-KETO-ISOVALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_KETO_ISOVALERATE_p \"2-KETO-ISOVALERATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SUPER_OXIDE_c \"SUPER-OXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SUPER_OXIDE_c \"SUPER-OXIDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLUCURONATE_c \"GLUCURONATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLUCURONATE_c \"GLUCURONATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_D_6_P_GLUCONO_DELTA_LACTONE_c \"D-6-P-GLUCONO-DELTA-LACTONE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_D_6_P_GLUCONO_DELTA_LACTONE_c \"D-6-P-GLUCONO-DELTA-LACTONE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLUTARYL_COA_m \"GLUTARYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLUTARYL_COA_m \"GLUTARYL-COA\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aXANTHOSINE_5_PHOSPHATE_c \"aXANTHOSINE-5-PHOSPHATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aXANTHOSINE_5_PHOSPHATE_c \"aXANTHOSINE-5-PHOSPHATE[c]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AMMONIUM_c \"AMMONIUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AMMONIUM_c \"AMMONIUM\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXALACETIC_ACID_p \"OXALACETIC_ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXALACETIC_ACID_p \"OXALACETIC_ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHE_tRNAs_c \"PHE_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHE_tRNAs_c \"PHE_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CH3_MALONATE_S_ALD_m \"CH3-MALONATE-S-ALD\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CH3_MALONATE_S_ALD_m \"CH3-MALONATE-S-ALD\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_10_FORMYL_THF_p \"10-FORMYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_10_FORMYL_THF_p \"10-FORMYL-THF\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXALACETIC_ACID_m \"OXALACETIC_ACID[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXALACETIC_ACID_m \"OXALACETIC_ACID[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYCOLLATE_p \"GLYCOLLATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYCOLLATE_p \"GLYCOLLATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ALLYSINE_c \"ALLYSINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ALLYSINE_c \"ALLYSINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AMMONIUM_e \"AMMONIUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AMMONIUM_e \"AMMONIUM\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYCOLLATE_x \"GLYCOLLATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYCOLLATE_x \"GLYCOLLATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXALACETIC_ACID_c \"OXALACETIC_ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXALACETIC_ACID_c \"OXALACETIC_ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ILE_tRNAs_c \"ILE_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ILE_tRNAs_c \"ILE_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Hex_2_enoyl_ACPs_p \"Hex_2_enoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Hex_2_enoyl_ACPs_p \"Hex_2_enoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_MANNOSE_c \"MANNOSE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MANNOSE_c \"MANNOSE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Protein_tranlocation_cost_c \"Protein_tranlocation_cost[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD1F_133_p \"CPD1F-133\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD1F_133_p \"CPD1F-133\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLYCOLLATE_c \"GLYCOLLATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLYCOLLATE_c \"GLYCOLLATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DELTA3_ISOPENTENYL_PP_c \"DELTA3-ISOPENTENYL-PP\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DELTA3_ISOPENTENYL_PP_c \"DELTA3-ISOPENTENYL-PP\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LEU_c \"LEU\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LEU_c \"LEU\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sLEU_b \"sLEU[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sLEU_b \"sLEU[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_DEOXY_D_ARABINO_HEPTULOSONATE_7_P_p \"3-DEOXY-D-ARABINO-HEPTULOSONATE-7-P\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_DEOXY_D_ARABINO_HEPTULOSONATE_7_P_p \"3-DEOXY-D-ARABINO-HEPTULOSONATE-7-P\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aPHOSPHORIBOSYL_CARBOXY_AMINOIMIDAZOLE_p \"aPHOSPHORIBOSYL-CARBOXY-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aPHOSPHORIBOSYL_CARBOXY_AMINOIMIDAZOLE_p \"aPHOSPHORIBOSYL-CARBOXY-AMINOIMIDAZOLE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LEU_p \"LEU\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LEU_p \"LEU\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AMMONIUM_p \"AMMONIUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AMMONIUM_p \"AMMONIUM\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LYS_p \"LYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LYS_p \"LYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Decanoyl_ACPs_p \"Decanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Decanoyl_ACPs_p \"Decanoyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_12175_m \"CPD-12175[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_12175_m \"CPD-12175[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LEU_m \"LEU\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LEU_m \"LEU\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AMMONIUM_m \"AMMONIUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AMMONIUM_m \"AMMONIUM\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LYS_m \"LYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LYS_m \"LYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ASN_c \"ASN\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ASN_c \"ASN\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sASN_b \"sASN[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sASN_b \"sASN[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FeII_c \"FeII[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FeII_c \"FeII[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OXALACETIC_ACID_x \"OXALACETIC_ACID[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OXALACETIC_ACID_x \"OXALACETIC_ACID[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_MERCAPTO_PYRUVATE_m \"3-MERCAPTO-PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3_MERCAPTO_PYRUVATE_m \"3-MERCAPTO-PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LYS_v \"LYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LYS_v \"LYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_AMMONIUM_v \"AMMONIUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AMMONIUM_v \"AMMONIUM\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_D_6_P_GLUCONO_DELTA_LACTONE_p \"D-6-P-GLUCONO-DELTA-LACTONE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_D_6_P_GLUCONO_DELTA_LACTONE_p \"D-6-P-GLUCONO-DELTA-LACTONE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ORNITHINE_p \"L-ORNITHINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ORNITHINE_p \"L-ORNITHINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sGLU_b \"sGLU[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sGLU_b \"sGLU[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CDP_CHOLINE_m \"CDP-CHOLINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CDP_CHOLINE_m \"CDP-CHOLINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHO_ENOL_PYRUVATE_c \"PHOSPHO-ENOL-PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHO_ENOL_PYRUVATE_c \"PHOSPHO-ENOL-PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LYS_c \"LYS\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LYS_c \"LYS\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sLYS_b \"sLYS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sLYS_b \"sLYS[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_pGLY_b \"pGLY[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pGLY_b \"pGLY[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Acetoacetyl_ACPs_p \"Acetoacetyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Acetoacetyl_ACPs_p \"Acetoacetyl_ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCPD_4211_p \"CPD-4211[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCPD_4211_p \"CPD-4211[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ORNITHINE_m \"L-ORNITHINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ORNITHINE_m \"L-ORNITHINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ASPARTATE_SEMIALDEHYDE_p \"L-ASPARTATE-SEMIALDEHYDE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ASPARTATE_SEMIALDEHYDE_p \"L-ASPARTATE-SEMIALDEHYDE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLY_c \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLY_c \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_sGLY_b \"sGLY[b]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sGLY_b \"sGLY[b]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLY_v \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLY_v \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_ACETO_2_HYDROXY_BUTYRATE_p \"2-ACETO-2-HYDROXY-BUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_ACETO_2_HYDROXY_BUTYRATE_p \"2-ACETO-2-HYDROXY-BUTYRATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHORYL_ETHANOLAMINE_c \"PHOSPHORYL-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHORYL_ETHANOLAMINE_c \"PHOSPHORYL-ETHANOLAMINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLY_x \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLY_x \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aFUM_v \"aFUM\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aFUM_v \"aFUM\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_ORNITHINE_c \"L-ORNITHINE\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_ORNITHINE_c \"L-ORNITHINE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ASN_v \"ASN\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ASN_v \"ASN\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PHOSPHO_ENOL_PYRUVATE_p \"PHOSPHO-ENOL-PYRUVATE\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHO_ENOL_PYRUVATE_p \"PHOSPHO-ENOL-PYRUVATE\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLY_m \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLY_m \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_GLY_p \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_GLY_p \"GLY\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Charged_SER_tRNAs_c \"Charged_SER_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Charged_SER_tRNAs_c \"Charged_SER_tRNAs[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CDPDIACYLGLYCEROL_p \"CDPDIACYLGLYCEROL[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CDPDIACYLGLYCEROL_p \"CDPDIACYLGLYCEROL[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CDPDIACYLGLYCEROL_m \"CDPDIACYLGLYCEROL[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CDPDIACYLGLYCEROL_m \"CDPDIACYLGLYCEROL[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_1_PHOSPHATIDYL_GLYCEROL_P_p \"L-1-PHOSPHATIDYL-GLYCEROL-P[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_1_PHOSPHATIDYL_GLYCEROL_P_p \"L-1-PHOSPHATIDYL-GLYCEROL-P[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aL_1_PHOSPHATIDYL_GLYCEROL_P_p \"L-1-PHOSPHATIDYL-GLYCEROL-P[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aL_1_PHOSPHATIDYL_GLYCEROL_P_p \"L-1-PHOSPHATIDYL-GLYCEROL-P[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_1_PHOSPHATIDYL_GLYCEROL_P_m \"L-1-PHOSPHATIDYL-GLYCEROL-P[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_1_PHOSPHATIDYL_GLYCEROL_P_m \"L-1-PHOSPHATIDYL-GLYCEROL-P[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aL_1_PHOSPHATIDYL_GLYCEROL_P_m \"L-1-PHOSPHATIDYL-GLYCEROL-P[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aL_1_PHOSPHATIDYL_GLYCEROL_P_m \"L-1-PHOSPHATIDYL-GLYCEROL-P[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_1_PHOSPHATIDYL_GLYCEROL_p \"L-1-PHOSPHATIDYL-GLYCEROL[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_1_PHOSPHATIDYL_GLYCEROL_p \"L-1-PHOSPHATIDYL-GLYCEROL[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_1_PHOSPHATIDYL_GLYCEROL_m \"L-1-PHOSPHATIDYL-GLYCEROL[m]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_L_1_PHOSPHATIDYL_GLYCEROL_m \"L-1-PHOSPHATIDYL-GLYCEROL[m]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_2_Lysophosphatidylcholines_r \"2-Lysophosphatidylcholines[r]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2_Lysophosphatidylcholines_r \"2-Lysophosphatidylcholines[r]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_14553_c \"CPD-14553[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_14553_c \"CPD-14553[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_D_Galactosyl_12_diacyl_glycerols_p \"D-Galactosyl-12-diacyl-glycerols[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_D_Galactosyl_12_diacyl_glycerols_p \"D-Galactosyl-12-diacyl-glycerols[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Galactosyl_galactosyl_diacyl_glycerols_p \"Galactosyl-galactosyl-diacyl-glycerols[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Galactosyl_galactosyl_diacyl_glycerols_p \"Galactosyl-galactosyl-diacyl-glycerols[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_PALMITYL_COA_p \"PALMITYL-COA[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PALMITYL_COA_p \"PALMITYL-COA[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Triacylglycerols_p \"Triacylglycerols[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Triacylglycerols_p \"Triacylglycerols[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Fatty_Acids_p \"Fatty-Acids[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Long_Chain_Acyl_CoAs_p \"Long-Chain-Acyl-CoAs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Fatty_acyl_ACP_p \"Fatty-acid-ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_oxo_stearoyl_ACPs_p \"3-oxo-stearoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_R_3_hydroxystearoyl_ACPs_p \"R-3-hydroxystearoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Octadec_2_enoyl_ACPs_p \"Octadec-2-enoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_STEARIC_ACID_p \"STEARIC-ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_STEARIC_ACID_p \"STEARIC-ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_STEARIC_ACID_c \"STEARIC-ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_STEARIC_ACID_c \"STEARIC-ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_STEARIC_ACID_x \"STEARIC-ACID[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_STEARIC_ACID_x \"STEARIC-ACID[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Palmitoleoyl_ACP_p \"Palmitoleoyl-ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_9245_p \"CPD-9245[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_9245_p \"CPD-9245[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_9245_c \"CPD-9245[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_9245_c \"CPD-9245[c]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_9245_x \"CPD-9245[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_9245_x \"CPD-9245[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_17412_p \"CPD-17412[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_17412_p \"CPD-17412[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_17412_c \"CPD-17412[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_17412_c \"CPD-17412[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_17412_x \"CPD-17412[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_17412_x \"CPD-17412[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_17291_p \"CPD-17291[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_17291_p \"CPD-17291[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_17291_c \"CPD-17291[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_17291_c \"CPD-17291[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_17291_x \"CPD-17291[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_17291_x \"CPD-17291[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Stearoyl_ACPs_p \"Stearoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Oleoyl_ACPs_p \"Oleoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_hexadecadienoate_ACP_p \"hexadecadienoate ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_hexadecatrienoate_ACP_p \"hexadecatrienoate ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OLEATE_CPD_p \"OLEATE-CPD[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OLEATE_CPD_p \"OLEATE-CPD[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OLEATE_CPD_c \"OLEATE-CPD[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OLEATE_CPD_c \"OLEATE-CPD[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_OLEATE_CPD_x \"OLEATE-CPD[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_OLEATE_CPD_x \"OLEATE-CPD[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Octadecadienoyl_ACP_p \"Octadecadienoyl-ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Octadecadienoate_p \"Octadecadienoate[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Octadecadienoate_p \"Octadecadienoate[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Octadecadienoate_c \"Octadecadienoate[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Octadecadienoate_c \"Octadecadienoate[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Octadecadienoate_x \"Octadecadienoate[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Octadecadienoate_x \"Octadecadienoate[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Octadecatrienoyl_ACP_p \"Octadecatrienoyl-ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LINOLENIC_ACID_p \"LINOLENIC_ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LINOLENIC_ACID_p \"LINOLENIC_ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LINOLENIC_ACID_c \"LINOLENIC_ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LINOLENIC_ACID_c \"LINOLENIC_ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_LINOLENIC_ACID_x \"LINOLENIC_ACID[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_LINOLENIC_ACID_x \"LINOLENIC_ACID[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_oxo_arachidoyl_ACPs_p \"3-oxo-arachidoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_R_3_hydroxyarachidoyl_ACPs_p \"R-3-hydroxyarachidoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_trans_delta2_arachidoyl_ACPs_p \"trans-delta2-arachidoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Arachidoyl_ACPs_p \"Arachidoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Arachidoyl_ACPs_p \"Arachidoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_3_oxo_behenoyl_ACPs_p \"3-oxo-behenoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_R_3_hydroxybehenoyl_ACPs_p \"R-3-hydroxybehenoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_trans_delta2_behenoyl_ACPs_p \"trans-delta2-behenoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Behenoyl_ACPs_p \"Behenoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Behenoyl_ACPs_p \"Behenoyl-ACPs[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ARACHIDIC_ACID_p \"ARACHIDIC_ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ARACHIDIC_ACID_p \"ARACHIDIC_ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ARACHIDIC_ACID_c \"ARACHIDIC_ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ARACHIDIC_ACID_c \"ARACHIDIC_ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ARACHIDIC_ACID_x \"ARACHIDIC_ACID[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ARACHIDIC_ACID_x \"ARACHIDIC_ACID[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DOCOSANOATE_p \"DOCOSANOATE[p]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DOCOSANOATE_p \"DOCOSANOATE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DOCOSANOATE_c \"DOCOSANOATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DOCOSANOATE_c \"DOCOSANOATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_DOCOSANOATE_x \"DOCOSANOATE[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DOCOSANOATE_x \"DOCOSANOATE[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Eicosenoyl_ACP_p \"Eicosenoyl-ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_Eicosenoyl_ACP_p \"Eicosenoyl-ACP[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_16709_p \"CPD-16709[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_16709_p \"CPD-16709[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_16709_c \"CPD-16709[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_16709_c \"CPD-16709[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_16709_x \"CPD-16709[x]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_16709_x \"CPD-16709[x]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UDP_SULFOQUINOVOSE_p \"UDP-SULFOQUINOVOSE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UDP_SULFOQUINOVOSE_p \"UDP-SULFOQUINOVOSE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SULFOQUINOVOSYLDIACYLGLYCEROL_p \"SULFOQUINOVOSYLDIACYLGLYCEROL[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_UDP_GLUCOSE_p \"UDP_GLUCOSE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_UDP_GLUCOSE_p \"UDP_GLUCOSE[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Lysophosphatidylglycerols_r \"Lysophosphatidylglycerols[r]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_Fatty_Acids_c \"Fatty-Acids[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_L_1_phosphatidyl_inositols_r \"L-1-phosphatidyl-inositols[r]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_674_c \"CPD-674[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_674_c \"CPD-674[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_COUMARATE_c \"COUMARATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_COUMARATE_c \"COUMARATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_4_HYDROXYBENZALDEHYDE_c \"4-HYDROXYBENZALDEHYDE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4_HYDROXYBENZALDEHYDE_c \"4-HYDROXYBENZALDEHYDE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_a4_HYDROXYBENZALDEHYDE_c \"4-HYDROXYBENZALDEHYDE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_a4_HYDROXYBENZALDEHYDE_c \"4-HYDROXYBENZALDEHYDE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_7616_c \"CPD-7616[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_7616_c \"CPD-7616[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aCPD_7616_c \"CPD-7616[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aCPD_7616_c \"CPD-7616[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_VANILLIN_c \"VANILLIN[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_VANILLIN_c \"VANILLIN[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aVANILLIN_c \"VANILLIN[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aVANILLIN_c \"VANILLIN[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_P_COUMAROYL_COA_c \"P-COUMAROYL-COA[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_P_COUMAROYL_COA_c \"P-COUMAROYL-COA[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_412_c \"CPD-412[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_412_c \"CPD-412[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CAFFEOYLSHIKIMATE_c \"CAFFEOYLSHIKIMATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CAFFEOYLSHIKIMATE_c \"CAFFEOYLSHIKIMATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CAFFEOYL_COA_c \"CAFFEOYL-COA[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CAFFEOYL_COA_c \"CAFFEOYL-COA[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_CPD_676_c \"CPD-676[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_CPD_676_c \"CPD-676[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FERULIC_ACID_c \"FERULIC-ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FERULIC_ACID_c \"FERULIC-ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FERULIC_ACID_p \"FERULIC-ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FERULIC_ACID_p \"FERULIC-ACID[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_VANILLIN_p \"VANILLIN[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_VANILLIN_p \"VANILLIN[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aVANILLIN_p \"VANILLIN[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aVANILLIN_p \"VANILLIN[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FERULOYL_COA_c \"FERULOYL-COA[c]\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FERULOYL_COA_c \"FERULOYL-COA[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_FERULOYL_COA_p \"FERULOYL-COA[p]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FERULOYL_COA_p \"FERULOYL-COA[p]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETOVANILLONE_c \"ACETOVANILLONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETOVANILLONE_c \"ACETOVANILLONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aACETOVANILLONE_c \"ACETOVANILLONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aACETOVANILLONE_c \"ACETOVANILLONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_HYDROXY_ACETOVANILLONE_c \"5-HYDROXY-ACETOVANILLONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_HYDROXY_ACETOVANILLONE_c \"5-HYDROXY-ACETOVANILLONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_a5_HYDROXY_ACETOVANILLONE_c \"5-HYDROXY-ACETOVANILLONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_a5_HYDROXY_ACETOVANILLONE_c \"5-HYDROXY-ACETOVANILLONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_ACETOSYRINGONE_c \"ACETOSYRINGONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACETOSYRINGONE_c \"ACETOSYRINGONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aACETOSYRINGONE_c \"ACETOSYRINGONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aACETOSYRINGONE_c \"ACETOSYRINGONE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_5_HYDROXY_FERULIC_ACID_c \"5-HYDROXY-FERULIC-ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5_HYDROXY_FERULIC_ACID_c \"5-HYDROXY-FERULIC-ACID[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SINAPATE_c \"SINAPATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SINAPATE_c \"SINAPATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SYRINGALDEHYDE_c \"SYRINGALDEHYDE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SYRINGALDEHYDE_c \"SYRINGALDEHYDE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_aSYRINGALDEHYDE_c \"SYRINGALDEHYDE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aSYRINGALDEHYDE_c \"SYRINGALDEHYDE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SYRINGIC_ACID_c \"Syringic acid[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SYRINGIC_ACID_c \"Syringic acid[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_VANILLIC_ACID_c \"Vanillic acid[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_VANILLIC_ACID_c \"Vanillic acid[c]\">\n",
      "WARNING:cobra.io.sbml:Use of CHARGE in the notes element is discouraged, use fbc:charge instead: <Species M_SHIKIMATE_c \"SHIKIMATE[c]\">\n",
      "WARNING:cobra.io.sbml:Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_SHIKIMATE_c \"SHIKIMATE[c]\">\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_pi_t with default bounds for boundary metabolite: X_pi_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_CO2_t with default bounds for boundary metabolite: X_CO2_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_Mg_t with default bounds for boundary metabolite: X_Mg_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_SO4_t with default bounds for boundary metabolite: X_SO4_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_GLC_t with default bounds for boundary metabolite: X_GLC_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_NITRATE_t with default bounds for boundary metabolite: X_NITRATE_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_Ca_t with default bounds for boundary metabolite: X_Ca_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_H_t with default bounds for boundary metabolite: X_H_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_NH4_t with default bounds for boundary metabolite: X_NH4_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_H2O_t with default bounds for boundary metabolite: X_H2O_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_Biomass_t with default bounds for boundary metabolite: X_Biomass_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_Palmitate_b with default bounds for boundary metabolite: Palmitate_b.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_K_t with default bounds for boundary metabolite: X_K_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_Sucrose_t with default bounds for boundary metabolite: X_Sucrose_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_Phloem_contribution_t with default bounds for boundary metabolite: X_Phloem_contribution_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_O2_t with default bounds for boundary metabolite: X_O2_t.\n",
      "WARNING:cobra.io.sbml:Adding exchange reaction EX_X_Photon_t with default bounds for boundary metabolite: X_Photon_t.\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRO_PROTON_vc \"PRO_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Ca_tx \"Ca_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H2O_xc \"H2O_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sCIT_biomass \"sCIT_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETYLGLUTKIN_RXN_p \"ACETYLGLUTKIN-RXN:Acetylglutamate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2KG_OAA_mc \"2KG_OAA_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LEUCINE_TRNA_LIGASE_RXN_c \"LEUCINE--TRNA-LIGASE-RXN:Leucine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIAMINOPIMDECARB_RXN_p \"DIAMINOPIMDECARB-RXN:Diaminopimelate decarboxylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPARTATE_TRNA_LIGASE_RXN_c \"ASPARTATE--TRNA-LIGASE-RXN:Aspartate--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_F16ALDOLASE_RXN_p \"F16ALDOLASE-RXN:Fructose-bisphosphate aldolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7978_p \"RXN-7978:NIL\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Photon_tx \"Photon_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_METHYL_ACETO_ACETYL_COA_xc \"2-METHYL-ACETO-ACETYL-COA_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_F16ALDOLASE_RXN_c \"F16ALDOLASE-RXN:Fructose-bisphosphate aldolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9532_p \"RXN-9532:3-oxoacyl-[acyl-carrier protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_5642_c \"RXN-5642:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_ASCORBATE_PEROXIDASE_RXN_p \"L-ASCORBATE-PEROXIDASE-RXN:L-ascorbate peroxidase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_ASCORBATE_PEROXIDASE_RXN_m \"L-ASCORBATE-PEROXIDASE-RXN:L-ascorbate peroxidase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SER_PROTON_vc \"SER_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYRUVATE_PROTON_mc \"PYRUVATE_PROTON_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NADH_DEHYDROG_A_RXN_mi \"NADH-DEHYDROG-A-RXN:NADH dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_ALPHA_ALANINE_PROTON_vc \"L_ALPHA_ALANINE_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NADH_DEHYDROG_A_RXN_mc \"NADH-DEHYDROG-A-RXN:NADH dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETYL_COA_ACETYLTRANSFER_RXN_x \"ACETYL-COA-ACETYLTRANSFER-RXN:Acetyl-CoA C-acetyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pTHR_biomass \"pTHR_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Starch_biomass \"Starch_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_Pi_mc \"MAL_Pi_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALANINE_GLYOXYLATE_AMINOTRANSFERASE_RXN_x \"ALANINE--GLYOXYLATE-AMINOTRANSFERASE-RXN:Alanine--glyoxylate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9663_p \"RXN-9663:Enoyl-[acyl-carrier protein] reductase (NADPH, B-specific)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H_pc \"H_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H_mc \"H_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_METHYL_3_HYDROXY_BUTYRYL_COA_mc \"2-METHYL-3-HYDROXY-BUTYRYL-COA_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RIBULOSE_BISPHOSPHATE_CARBOXYLASE_RXN_p \"RIBULOSE-BISPHOSPHATE-CARBOXYLASE-RXN:Ribulose-bisphosphate carboxylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_IGPSYN_RXN_p \"IGPSYN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_5_METHYL_THF_pc \"5_METHYL_THF_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASN_PROTON_vc \"ASN_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_WATER_vc \"WATER_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9652_p \"RXN-9652:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FUMHYDR_RXN_m \"FUMHYDR-RXN:Fumarate hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_884_p \"RXN0-884:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HS_pc \"plastidic HS diffusion\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FUMHYDR_RXN_c \"FUMHYDR-RXN:Fumarate hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTAMINE_TRNA_LIGASE_RXN_c \"GLUTAMINE--TRNA-LIGASE-RXN:Glutamine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALANINE_AMINOTRANSFERASE_RXN_m \"ALANINE-AMINOTRANSFERASE-RXN:Alanine aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Nitrate_ec \"Nitrate_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYCOGENSYN_RXN_p \"GLYCOGENSYN-RXN:Starch (bacterial glycogen) synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NITRATE_vc \"NITRATE_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1841_v \"RXN-1841:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALANINE_AMINOTRANSFERASE_RXN_x \"ALANINE-AMINOTRANSFERASE-RXN:Alanine aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALSYN_RXN_x \"MALSYN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MYO_INOSITOL_1OR_4_MONOPHOSPHATASE_RXN_c \"MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN:Myo-inositol-1(or 4)-monophosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ORNITHINE_CITRULLINE_pc \"ORNITHINE_CITRULLINE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_2301_m \"RXN0-2301:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLT_xc \"GLT_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pGLU_biomass \"pGLU_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UREASE_RXN_c \"UREASE-RXN:Urease\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALANINE_AMINOTRANSFERASE_RXN_c \"ALANINE-AMINOTRANSFERASE-RXN:Alanine aminotransferase\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIAMINOPIMEPIM_RXN_p \"DIAMINOPIMEPIM-RXN:Diaminopimelate epimerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sFUM_biomass \"sFUM_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLURS_RXN_c \"GLURS-RXN:Glutamate--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISOBUTYRYL_COA_xc \"ISOBUTYRYL-COA_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2K_ADIPATE_mc \"2K-ADIPATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GABATRANSAM_RXN_m \"GABATRANSAM-RXN:4-aminobutyrate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_ACYLGLYCEROL_3_P_ACYLTRANSFER_RXN_p \"1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN:1-acylglycerol-3-phosphate O-acyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLY_PROTON_rev_vc \"GLY_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THREDEHYD_RXN_p \"THREDEHYD-RXN:Threonine dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MANNPISOM_RXN_c \"MANNPISOM-RXN:Mannose-6-phosphate isomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ATP_pc \"ATP_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PROPCOASYN_RXN_x \"PROPCOASYN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OAA_Pi_mc \"OAA_Pi_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACSERLY_RXN_c \"ACSERLY-RXN:Cysteine synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETOOHBUTSYN_RXN_p \"ACETOOHBUTSYN-RXN:Acetolactate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_ISOPROPYLMALATESYN_RXN_p \"2-ISOPROPYLMALATESYN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_ISOPROPYLMALISOM_RXN_p \"3-ISOPROPYLMALISOM-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_4_AMINO_BUTYRATE_PROTON_rev_vc \"4_AMINO_BUTYRATE_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUC1PADENYLTRANS_RXN_p \"GLUC1PADENYLTRANS-RXN:Glucose-1-phosphate adenylyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACONITATEHYDR_RXN_c \"ACONITATEHYDR-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PROTONATP_rev_vc \"PROTONATP_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALTODEXGLUCOSID_RXN_p \"MALTODEXGLUCOSID-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PGLYCDEHYDROG_RXN_p \"PGLYCDEHYDROG-RXN:Phosphoglycerate dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETOOHBUTREDUCTOISOM_RXN_p \"ACETOOHBUTREDUCTOISOM-RXN:Ketol-acid reductoisomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THR_PROTON_rev_vc \"THR_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACSERLY_RXN_p \"ACSERLY-RXN:Cysteine synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9661_p \"RXN-9661:Enoyl-[acyl-carrier protein] reductase (NADPH, B-specific)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACONITATEHYDR_RXN_m \"ACONITATEHYDR-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_6883_mi \"RXN-6883:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H_tx \"H_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTARYL_COA_DEHYDROG_RXN_m \"GLUTARYL-COA-DEHYDROG-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRPPAMIDOTRANS_RXN_p \"PRPPAMIDOTRANS-RXN:Amidophosphoribosyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_lycopene_biosynthesis_p \"HYPO lycopene biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_5_PERIOD_1_PERIOD_8_RXN_c \"1.5.1.8-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_6883_mc \"RXN-6883:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_13202_p \"RXN-13202:carbamoyl-phosphate synthetase I\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9650_p \"RXN-9650:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DHAP_Pi_pc \"DHAP_Pi_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H_im \"H_im\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CDPKIN_RXN_p \"CDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H2O_pc \"H2O_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7703_c \"RXN-7703:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CDPKIN_RXN_m \"CDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OAA_ISOCITRATE_mc \"OAA_ISOCITRATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3PGAREARR_RXN_p \"3PGAREARR-RXN:Phosphoglycerate mutase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_14903_m \"RXN-14903\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FGAMSYN_RXN_p \"FGAMSYN-RXN:phosphoribosylformylglycinamidine synthetase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_METHYL_3_HYDROXY_BUTYRYL_COA_xc \"2-METHYL-3-HYDROXY-BUTYRYL-COA_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASN_PROTON_rev_vc \"ASN_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISOCITRATE_DEHYDROGENASE_NAD_RXN_m \"ISOCITRATE-DEHYDROGENASE-NAD+-RXN:Isocitrate dehydrogenase (NAD+)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1TRANSKETO_RXN_p \"1TRANSKETO-RXN:Transketolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Sucrose_tx \"Sucrose_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ADP_pc \"ADP_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9536_p \"RXN-9536:3-oxoacyl-[acyl-carrier protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GAP_Pi_pc \"GAP_Pi_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_HYDROXYISOBUTYRATE_DEHYDROGENASE_RXN_m \"3-HYDROXYISOBUTYRATE-DEHYDROGENASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_4_HYDROXYPHENYLPYRUVATE_DIOXYGENASE_RXN_c \"4-HYDROXYPHENYLPYRUVATE-DIOXYGENASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MANNOSE_6_PHOSPHATE_6_REDUCTASE_RXN_c \"MANNOSE-6-PHOSPHATE-6-REDUCTASE-RXN_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_ISOCITRATE_mc \"MAL_ISOCITRATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_12541_c \"RXN_12541_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sALA_biomass \"sALA_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYS_PROTON_vc \"LYS_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_IMPCYCLOHYDROLASE_RXN_p \"IMPCYCLOHYDROLASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FERREDOXIN_NITRITE_REDUCTASE_RXN_p \"FERREDOXIN--NITRITE-REDUCTASE-RXN:Ferredoxin--nitrite reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPARTATEKIN_RXN_p \"ASPARTATEKIN-RXN:Aspartate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9523_p \"RXN-9523:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALTODEG_RXN_c \"MALTODEG-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARGINASE_RXN_m \"ARGINASE-RXN:Arginase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_DEHYDROQUINATE_DEHYDRATASE_RXN_p \"3-DEHYDROQUINATE-DEHYDRATASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISOBUTYRYL_COA_mc \"ISOBUTYRYL-COA_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_13161_m \"RXN-13161\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_2_PERIOD_1_PERIOD_13_RXN_p \"1.2.1.13-RXN:Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETALD_mc \"ACETALD_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GAP_3PGA_pc \"GAP_3PGA_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HOMOSERDEHYDROG_RXN_NADP_p \"HOMOSERDEHYDROG-RXN:Homoserine dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRP_TRNA_LIGASE_RXN_c \"TRYTOPHAN--TRNA-LIGASE-RXN:Tryptophan--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2KETO_4METHYL_PENTANOATE_DEHYDROG_RXN_m \"2KETO-4METHYL-PENTANOATE-DEHYDROG-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYTOCHROME_C_OXIDASE_RXN_mc \"CYTOCHROME-C-OXIDASE-RXN:Cytochrome-c oxidase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_1_PERIOD_1_PERIOD_178_RXN_x \"1.1.1.178-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYTOCHROME_C_OXIDASE_RXN_mi \"CYTOCHROME-C-OXIDASE-RXN:Cytochrome-c oxidase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OAA_CIT_mc \"OAA_CIT_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCCINATE_COA_LIGASE_GDP_FORMING_RXN_m \"SUCCINATE_COA_LIGASE_GDP_FORMING_RXN_m\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_5682_p \"RXN-5682:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RIBULP3EPIM_RXN_p \"RIBULP3EPIM-RXN:ribulose phosphate 3-epimerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_3_PERIOD_1_PERIOD_180_RXN_p \"2.3.1.180-RXN:Beta-ketoacyl-acyl-carrier-protein synthase III\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pILE_biomass \"pILE_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SER_PROTON_rev_vc \"SER_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GGPP_biosynthesis_p \"HYPO GGPP biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OAA_ACONITATE_mc \"OAA_ACONITATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ADPREDUCT_RXN_p \"ADPREDUCT-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pASP_biomass \"pASP_biomass\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HOMOSERDEHYDROG_RXN_NAD_p \"HOMOSERDEHYDROG-RXN:Homoserine dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AICARSYN_RXN_p \"AICARSYN-RXN:Adenylosuccinate lyase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SERINE_TRNA_LIGASE_RXN_c \"SERINE--TRNA-LIGASE-RXN:Serine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H2O_tx \"H2O_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TYR_PROTON_vc \"TYR_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5330_NADP_mi \"RXN0-5330:NADH dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCROSE_PROTON_vc \"SUCROSE_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CDPREDUCT_RXN_p \"CDPREDUCT-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYCOLLATE_pc \"GLYCOLLATE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYRUVATEORTHOPHOSPHATE_DIKINASE_RXN_p \"PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN:Pyruvate,phosphate dikinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3PGA_Pi_pc \"3PGA_Pi_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYRROLINECARBDEHYDROG_RXN_NADP_m \"PYRROLINECARBDEHYDROG-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MET_PROTON_rev_vc \"MET_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CATAL_RXN_x \"CATAL-RXN:Catalase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sGLU_biomass \"sGLU_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_IMP_DEHYDROG_RXN_c \"IMP-DEHYDROG-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AMPSYN_RXN_p \"AMPSYN-RXN:Adenylosuccinate lyase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9654_p \"RXN-9654:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RIBULP3EPIM_RXN_c \"RIBULP3EPIM-RXN:ribulose phosphate 3-epimerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYRUVATEORTHOPHOSPHATE_DIKINASE_RXN_c \"PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN:Pyruvate,phosphate dikinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALATE_DEHYDROGENASE_NADP_RXN_p \"MALATE-DEHYDROGENASE-NADP-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCCINATE_SEMIALDEHYDE_DEHYDROGENASE_RXN_m \"SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN:Succinate-semialdehyde dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DADPKIN_RXN_p \"DADPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HOMOGENTISATE_12_DIOXYGENASE_RXN_c \"HOMOGENTISATE-12-DIOXYGENASE-RXN:Homogentisate 1,2-dioxygenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYS_mc \"CYS_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5330_NADP_mc \"RXN0-5330:NADH dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_7_PERIOD_7_PERIOD_13_RXN_c \"2.7.7.13-RXN:Mannose-1-phosphate guanylyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NITRITE_pc \"NITRITE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACONITATEDEHYDR_RXN_m \"ACONITATEDEHYDR-RXN:Aconitate hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIACYLGLYCEROL_pr \"DIACYLGLYCEROL_pr\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUC_SO4_mc \"SUC_SO4_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sMAL_biomass \"sMAL_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HOMOCYSMETB12_RXN_p \"HOMOCYSMETB12-RXN:5-methyltetrahydrofolate--homocysteine S-methyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRIOSEPISOMERIZATION_RXN_c \"TRIOSEPISOMERIZATION-RXN:Triosephosphate isomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2KETO_3METHYLVALERATE_RXN_m \"2KETO-3METHYLVALERATE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_3522_p \"RXN-3522:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACONITATEDEHYDR_RXN_c \"ACONITATEDEHYDR-RXN:Aconitate hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HISTIDINE_TRNA_LIGASE_RXN_c \"HISTIDINE--TRNA-LIGASE-RXN:Histidine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRIOSEPISOMERIZATION_RXN_p \"TRIOSEPISOMERIZATION-RXN:Triosephosphate isomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MANNPGUANYLTRANGDP_RXN_c \"MANNPGUANYLTRANGDP_RXN_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_O2_ec \"O2_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Protein_Polymerisation_c \"Protein_Polymerisation_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5224_c \"RXN0-5224:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_4_PERIOD_2_PERIOD_1_PERIOD_61_RXN_p \"4.2.1.61-RXN:a 3-hydroxypalmitoyl-[acyl-carrier protein] dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Pi_ec \"Pi_ec\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_10_PERIOD_2_PERIOD_2_RXN_mc \"1.10.2.2-RXN:Ubiquinol--cytochrome c reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_VAL_PROTON_vc \"VAL_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ADENOSYLHOMOCYSTEINASE_RXN_c \"ADENOSYLHOMOCYSTEINASE-RXN:Adenosylhomocysteinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIHYDROOROT_RXN_p \"DIHYDROOROT-RXN:Dihydroorotase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRO_GLU_mc \"PRO_GLU_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_8_PERIOD_5_PERIOD_1_RXN_m \"1.8.5.1-RXN:Glutathione dehydrogenase (ascorbate)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_4_PERIOD_1_PERIOD_111_RXN_c \"2.4.1.111-RXN:Coniferyl-alcohol glucosyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5224_p \"RXN0-5224:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PROPIONYL_COA_mc \"PROPIONYL-COA_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_8_PERIOD_5_PERIOD_1_RXN_p \"1.8.5.1-RXN:Glutathione dehydrogenase (ascorbate)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FRU_PROTON_rev_vc \"FRU_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_METHYLGLUTACONYL_COA_HYDRATASE_RXN_m \"METHYLGLUTACONYL-COA-HYDRATASE-RXN:Methylglutaconyl-CoA hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5224_m \"RXN0-5224:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DUTP_PYROP_RXN_p \"DUTP-PYROP-RXN:dUTP pyrophosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_10_PERIOD_2_PERIOD_2_RXN_mi \"1.10.2.2-RXN:Ubiquinol--cytochrome c reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALCOHOL_DEHYDROG_RXN_c \"ALCOHOL-DEHYDROG-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pMET_biomass \"pMET_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CO2_pc \"CO2_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9527_p \"RXN-9527:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_ASPARTATE_xc \"L_ASPARTATE_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sGABA_biomass \"sGABA_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Phytol_biosynthesis_p \"HYPO phytol biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GDPREDUCT_RXN_p \"GDPREDUCT-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HISTCYCLOHYD_RXN_p \"HISTCYCLOHYD-RXN:Phosphoribosyl-AMP cyclohydrolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7677_p \"RXN-7677:Chlorophyllide-a oxygenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HIS_CITRULLINE_mc \"HIS_CITRULLINE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIHYDROXYMETVALDEHYDRAT_RXN_p \"DIHYDROXYMETVALDEHYDRAT-RXN:Dihydroxy-acid dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_S_ADENMETSYN_RXN_c \"S-ADENMETSYN-RXN:Methionine adenosyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCCCOASYN_RXN_m \"SUCCCOASYN-RXN:Succinate--CoA ligase (ADP-forming)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_11832_m \"RXN-11832\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_F16BDEPHOS_RXN_c \"F16BDEPHOS-RXN:Fructose-bisphosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LEU_PROTON_rev_vc \"LEU_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALLYSINE_DEHYDROG_RXN_c \"ALLYSINE-DEHYDROG-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Mehler_Reaction_p \"Mehler_Reaction_p\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UREA_mc \"UREA_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Ca_ec \"Ca_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_11832_p \"RXN-11832\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_2_PERIOD_1_PERIOD_2_RXN_p \"1.2.1.2-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LEU_mc \"LEU_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9516_p \"RXN-9516:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_F16BDEPHOS_RXN_p \"F16BDEPHOS-RXN:Fructose-bisphosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sASP_biomass \"sASP_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HOMOCYSMETB12_RXN_c \"HOMOCYSMETB12-RXN:5-methyltetrahydrofolate--homocysteine S-methyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Plastidial_ATP_Synthase_p \"Plastidial_ATP_Synthase_p\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_6384_x \"RXN-6384:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_2_PERIOD_1_PERIOD_2_RXN_m \"1.2.1.2-RXN:NIL\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NH3_pc \"NH3_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPARTATE_SEMIALDEHYDE_DEHYDROGENASE_RXN_p \"ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN:Aspartate-semialdehyde dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_14927_pc \"Phytenate transport\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_PERIOD_2_PERIOD_1_PERIOD_48_RXN_v \"3.2.1.48-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ATP_ADP_Pi_pc \"ATP_ADP_Pi_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NADH_KINASE_RXN_c \"NADH-KINASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETYL_COA_CARBOXYLTRANSFER_RXN_p \"ACETYL-COA-CARBOXYLTRANSFER-RXN:Acetyl-CoA carboxylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSPHOGLUCMUT_RXN_p \"PHOSPHOGLUCMUT-RXN:|Phosphoglucomutase|\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9549_p \"RXN-9549:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_METHYL_ACETO_ACETYL_COA_mc \"2-METHYL-ACETO-ACETYL-COA_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISOCIT_CLEAV_RXN_x \"ISOCIT-CLEAV-RXN:Isocitrate lyase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LEU_pc \"LEU_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_PERIOD_2_PERIOD_1_PERIOD_48_RXN_c \"3.2.1.48-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_SUC_mc \"MAL_SUC_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PEPDEPHOS_RXN_c \"PEPDEPHOS-RXN:Pyruvate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PEPDEPHOS_RXN_p \"PEPDEPHOS-RXN:Pyruvate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LEU_PROTON_vc \"LEU_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1781_v \"RXN-1781\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THREONINE_TRNA_LIGASE_RXN_c \"THREONINE--TRNA-LIGASE-RXN:Threonine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_HYDROXY_PROPIONATE_mc \"3_HYDROXY_PROPIONATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_METHYLACYL_COA_DEHYDROGENASE_RXN_m \"2-METHYLACYL-COA-DEHYDROGENASE-RXN:2-methylacyl-CoA dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_6PGLUCONOLACT_RXN_p \"6PGLUCONOLACT-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pLYS_biomass \"pLYS_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THREO_DS_ISO_CITRATE_xc \"THREO_DS_ISO_CITRATE_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CIT_PROTON_vc \"CIT_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_6PGLUCONOLACT_RXN_c \"6PGLUCONOLACT-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DSERDEAM_RXN_c \"DSERDEAM-RXN:D-serine ammonia-lyase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYS_pc \"LYS_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CIT_xc \"CIT_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISOCITDEH_RXN_m \"ISOCITDEH-RXN:Isocitrate dehydrogenase (NADP+)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHE_PROTON_rev_vc \"PHE_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTACONYL_COA_mc \"GLUTACONYL_COA_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARG_PROTON_vc \"ARG_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7984_p \"RXN-7984:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NADPHoxm_tx \"NADPHoxm_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PALMITATE_xc \"PALMITATE_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NH3_mc \"NH3_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PSERTRANSAM_RXN_p \"PSERTRANSAM-RXN:Phosphoserine aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_BRANCHED_CHAINAMINOTRANSFERILEU_RXN_p \"BRANCHED-CHAINAMINOTRANSFERILEU-RXN:Branched-chain amino acid aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FUM_pc \"FUM_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Ferredoxin_Plastoquinone_Reductase_p \"Ferredoxin_Plastoquinone_Reductase_p\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_BRANCHED_CHAINAMINOTRANSFERILEU_RXN_m \"BRANCHED-CHAINAMINOTRANSFERILEU-RXN:Branched-chain amino acid aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISOCITDEH_RXN_x \"ISOCITDEH-RXN:Isocitrate dehydrogenase (NADP+)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Cellulose_biomass \"Cellulose_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7679_p \"RXN-7679:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3PGAREARR_RXN_c \"3PGAREARR-RXN:Phosphoglycerate mutase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9658_p \"RXN-9658:Enoyl-[acyl-carrier protein] reductase (NADPH, B-specific)\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1826_p \"RXN-1826:starch phosphorylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSPHOGLUCMUT_RXN_c \"PHOSPHOGLUCMUT-RXN:|Phosphoglucomutase|\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYS_TRNA_LIGASE_RXN_c \"CYSTEINE--TRNA-LIGASE-RXN:Cysteine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LCYSDESULF_RXN_c \"LCYSDESULF-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FattyAcid_biomass \"FattyAcid_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISOCITDEH_RXN_c \"ISOCITDEH-RXN:Isocitrate dehydrogenase (NADP+)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9514_p \"RXN-9514:3-oxoacyl-[acyl-carrier protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PEPCARBOXYKIN_RXN_c \"PEPCARBOXYKIN-RXN:Phosphoenolpyruvate carboxykinase (ATP)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARGSUCCINSYN_RXN_p \"ARGSUCCINSYN-RXN:argininosuccinate synthetase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OAA_SO4_mc \"OAA_SO4_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CO2_tx \"CO2_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PREPHENATE_TRANSAMINE_RXN_p \"PREPHENATE-TRANSAMINE-RXN:glutamate-prephenate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CELLULOSE_SYNTHASE_UDP_FORMING_RXN_c \"CELLULOSE-SYNTHASE-UDP-FORMING-RXN:Cellulose synthase (UDP-forming)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_VAL_PROTON_rev_vc \"VAL_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Mg_biomass \"Mg_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSPHORYL_CHOLINE_mc \"PHOSPHORYL-CHOLINE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9660_p \"RXN-9660:Enoyl-[acyl-carrier protein] reductase (NADPH, B-specific)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIHYDROPICRED_RXN_NADP_p \"DIHYDROPICRED-RXN:Dihydrodipicolinate reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_6884_m \"RXN-6884:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALONYL_COA_ACP_TRANSACYL_RXN_p \"MALONYL-COA-ACP-TRANSACYL-RXN:[Acyl-carrier protein] S-malonyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCROSE_PROTON_rev_vc \"SUCROSE_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_O2_mc \"O2_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CIT_ISOCITRATE_mc \"CIT_ISOCITRATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYSINE_TRNA_LIGASE_RXN_c \"LYSINE--TRNA-LIGASE-RXN:Lysine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SULFATE_ADENYLYLTRANS_RXN_p \"SULFATE-ADENYLYLTRANS-RXN:Sulfate adenylyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H_xc \"H_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NITRATE_REDUCTASE_NADH_RXN_c \"NITRATE-REDUCTASE-NADH-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CO2_xc \"CO2_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THR_PROTON_vc \"THR_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_CITRULLINE_pc \"L_CITRULLINE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TIGLYLCOA_HYDROXY_RXN_m \"TIGLYLCOA-HYDROXY-RXN:Enoyl-CoA hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Glycerate_xc \"Glycerate_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTATHIONE_PEROXIDASE_RXN_p \"GLUTATHIONE-PEROXIDASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MEPROPCOA_FAD_RXN_m \"MEPROPCOA-FAD-RXN:2-methylacyl-CoA dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Mg_ec \"Mg_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALIC_NADP_RXN_p \"MALIC-NADP-RXN:Malate dehydrogenase (oxaloacetate decarboxylating) (NADP+)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DTMP_mc \"dTMP_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPARAGHYD_RXN_c \"ASPARAGHYD-RXN:Asparaginase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_DEHYDROQUINATE_SYNTHASE_RXN_p \"3-DEHYDROQUINATE-SYNTHASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_ASPARTATE_pc \"L_ASPARTATE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_1_PERIOD_1_PERIOD_255_RXN_c \"1.1.1.255-RXN_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DHAP_3PGA_pc \"DHAP_3PGA_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALIC_NADP_RXN_c \"MALIC-NADP-RXN:Malate dehydrogenase (oxaloacetate decarboxylating) (NADP+)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THF_pc \"THF_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MANNITOL_1_PHOSPHATASE_RXN_c \"MANNITOL-1-PHOSPHATASE-RXN_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pARG_biomass \"pARG_biomass\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_1_PERIOD_1_PERIOD_103_RXN_c \"2.1.1.103-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ANTHRANSYN_RXN_p \"ANTHRANSYN-RXN:Anthranilate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLY3KIN_RXN_p \"GLY3KIN-RXN:Glycerate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_14927_xc \"Phytenate transport\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FORMYLTHFDEFORMYL_RXN_p \"FORMYLTHFDEFORMYL-RXN:Formyltetrahydrofolate deformylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_7_PERIOD_7_PERIOD_34_RXN_c \"2.7.7.34-RXN:Glucose-1-phosphate guanylyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYS_PROTON_rev_vc \"CYS_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCCINATE_DEHYDROGENASE_UBIQUINONE_RXN_mi \"SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN:Succinate dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYRUVDEH_RXN_p \"PYRUVDEH-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYRUVDEH_RXN_m \"PYRUVDEH-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_O2_pc \"O2_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DCDPKIN_RXN_p \"DCDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UDP_GLUCURONATE_DECARBOXYLASE_RXN_c \"UDP-GLUCURONATE-DECARBOXYLASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5330_NAD_c \"RXN0-5330:NADH dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_2381_p \"RXN0-2381:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ORNITHINE_GLU_AMINOTRANSFERASE_RXN_m \"ORNITHINE-GLU-AMINOTRANSFERASE-RXN:Ornithine--oxo-acid aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYC3PDEHYDROGBIOSYN_RXN_c \"GLYC3PDEHYDROGBIOSYN-RXN:Glycerol-3-phosphate dehydrogenase (NAD(P)+)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SHIKIMATE_KINASE_RXN_p \"SHIKIMATE-KINASE-RXN:shikimate-kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISOLEUCINE_TRNA_LIGASE_RXN_c \"ISOLEUCINE--TRNA-LIGASE-RXN:Isoleucine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLC_PROTON_rev_vc \"GLC_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_METHYLACETOACETYLCOATHIOL_RXN_m \"METHYLACETOACETYLCOATHIOL-RXN:Acetyl-CoA C-acyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2KG_SUC_mc \"2KG_SUC_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHE_PROTON_vc \"PHE_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HIS_PROTON_vc \"HIS_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7678_NAD_p \"RXN-7678:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Pi_PROTON_mc \"Pi_PROTON_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2KG_ISOCITRATE_mc \"2KG_ISOCITRATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTACONYL_COA_xc \"GLUTACONYL_COA_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pGLY_biomass \"pGLY_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_2_PERIOD_1_PERIOD_25_RXN_m \"1.2.1.25-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_7_PERIOD_7_PERIOD_15_RXN_m \"2.7.7.15-RXN_m\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLY_PROTON_vc \"GLY_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_INORGPYROPHOSPHAT_RXN_x \"INORGPYROPHOSPHAT-RXN:Inorganic pyrophosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALEYLACETOACETATE_ISOMERASE_RXN_c \"MALEYLACETOACETATE-ISOMERASE-RXN:Maleylacetoacetate isomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYRROLINECARBREDUCT_RXN_NAD_c \"PYRROLINECARBREDUCT-RXN:Pyrroline-5-carboxylate reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FORMATETHFLIG_RXN_p \"FORMATETHFLIG-RXN:Formate--tetrahydrofolate ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OAA_SUC_mc \"OAA_SUC_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OROPRIBTRANS_RXN_p \"OROPRIBTRANS-RXN:Orotate phosphoribosyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THF_mc \"THF_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALATE_DEH_RXN_c \"MALATE-DEH-RXN:Malate dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUC1PURIDYLTRANS_RXN_c \"GLUC1PURIDYLTRANS-RXN:UTP--glucose-1-phosphate uridylyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MYO_INOSITOL_OXYGENASE_RXN_c \"MYO-INOSITOL-OXYGENASE-RXN:Myo-inositol oxygenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_7_PERIOD_7_PERIOD_14_RXN_m \"2.7.7.14-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYS_PROTON_vc \"CYS_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRP_pc \"TRP_pc\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HYDROXYMETHYLGLUTARYL_COA_LYASE_RXN_m \"HYDROXYMETHYLGLUTARYL-COA-LYASE-RXN:Hydroxymethylglutaryl-CoA lyase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_N_ACETYLGLUTPREDUCT_RXN_p \"N-ACETYLGLUTPREDUCT-RXN:N-acetyl-&amp;gamma;-glutamyl-phosphate reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPAMINOTRANS_RXN_m \"ASPAMINOTRANS-RXN:Aspartate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CIT_ACONITATE_mc \"CIT_ACONITATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPAMINOTRANS_RXN_p \"ASPAMINOTRANS-RXN:Aspartate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALATE_DEH_RXN_p \"MALATE-DEH-RXN:Malate dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SEDOBISALDOL_RXN_p \"SEDOBISALDOL-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARGSUCCINLYA_RXN_p \"ARGSUCCINLYA-RXN:Argininosuccinate lyase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_8_PERIOD_4_PERIOD_9_RXN_p \"1.8.4.9-RXN:Adenylyl-sulfate reductase (glutathione)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UDPREDUCT_RXN_p \"UDPREDUCT-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ATP_ADP_mc \"ATP_ADP_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALATE_DEH_RXN_m \"MALATE-DEH-RXN:Malate dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPAMINOTRANS_RXN_x \"ASPAMINOTRANS-RXN:Aspartate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_INORGPYROPHOSPHAT_RXN_c \"INORGPYROPHOSPHAT-RXN:Inorganic pyrophosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTATHIONE_REDUCT_NADPH_RXN_m \"GLUTATHIONE-REDUCT-NADPH-RXN:Glutathione reductase (NADPH)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTATHIONE_REDUCT_NADPH_RXN_p \"GLUTATHIONE-REDUCT-NADPH-RXN:Glutathione reductase (NADPH)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYCEROL_3P_pc \"GLYCEROL_3P_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYCEROL_3P_mc \"GLYCEROL_3P_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_INORGPYROPHOSPHAT_RXN_m \"INORGPYROPHOSPHAT-RXN:Inorganic pyrophosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPAMINOTRANS_RXN_c \"ASPAMINOTRANS-RXN:Aspartate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_INORGPYROPHOSPHAT_RXN_p \"INORGPYROPHOSPHAT-RXN:Inorganic pyrophosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9518_p \"RXN-9518:3-oxoacyl-[acyl-carrier protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALATE_DEH_RXN_x \"MALATE-DEH-RXN:Malate dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_HYDROXY_PROPIONATE_xc \"3_HYDROXY_PROPIONATE_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PGLUCISOM_RXN_c \"PGLUCISOM-RXN:Glucose-6-phosphate isomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIHYDROFOLATEREDUCT_RXN_m \"DIHYDROFOLATEREDUCT-RXN:Dihydrofolate reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLC_ec \"GLC_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9520_p \"RXN-9520:3-hydroxydecanoyl-[acyl-carrier protein] dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HEXOKINASE_RXN_MANNOSE_c \"HEXOKINASE-RXN_MANNOSE_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PGLUCISOM_RXN_p \"PGLUCISOM-RXN:Glucose-6-phosphate isomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_O2_tx \"O2_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DUMP_pc \"dUMP_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYCERATE_GLYCOLLATE_pc \"GLYCERATE_GLYCOLLATE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9653_p \"RXN-9653:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AMP_pc \"AMP_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SERINE_O_ACETTRAN_RXN_c \"SERINE-O-ACETTRAN-RXN:Serine O-acetyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GPH_RXN_p \"GPH-RXN:Phosphoglycolate phosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYRUVATE_pc \"PYRUVATE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_6902_m \"RXN-6902:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ILE_pc \"ILE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCROSE_PHOSPHATE_SYNTHASE_RXN_c \"SUCROSE-PHOSPHATE-SYNTHASE-RXN:Sucrose-phosphate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SERINE_GLYOXYLATE_AMINOTRANSFERASE_RXN_x \"SERINE-GLYOXYLATE-AMINOTRANSFERASE-RXN:Serine--glyoxylate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYS_ORNITHINE_mc \"LYS_ORNITHINE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SERINE_O_ACETTRAN_RXN_p \"SERINE-O-ACETTRAN-RXN:Serine O-acetyltransferase\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pSER_biomass \"pSER_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETOLACTREDUCTOISOM_RXN_p \"ACETOLACTREDUCTOISOM-RXN:Ketol-acid reductoisomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_4_PERIOD_2_PERIOD_1_PERIOD_59_RXN_p \"4.2.1.59-RXN:3-hydroxyoctanoyl-[acyl-carrier protein] dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DTMPKI_RXN_c \"DTMPKI-RXN:Thymidylate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Mitochondrial_ATP_Synthase_m \"Mitochondrial_ATP_Synthase_m\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Pi_tx \"Pi_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_X5P_Pi_pc \"X5P_Pi_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7737_p \"RXN-7737:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Ca_biomass \"Ca_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUPEROX_DISMUT_RXN_p \"SUPEROX-DISMUT-RXN:Superoxide dismutase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1381_p \"RXN-1381:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Biomass_tx \"Biomass_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7800_p \"RXN-7800:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUC_xc \"SUC_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THREONINE_ALDOLASE_RXN_c \"THREONINE-ALDOLASE-RXN:Threonine aldolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUPEROX_DISMUT_RXN_c \"SUPEROX-DISMUT-RXN:Superoxide dismutase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sSUCROSE_biomass \"sSUCROSE_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIHYDROPICRED_RXN_NAD_p \"DIHYDROPICRED-RXN:Dihydrodipicolinate reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ADENYL_KIN_RXN_c \"ADENYL-KIN-RXN:Adenylate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GAPOXNPHOSPHN_RXN_c \"GAPOXNPHOSPHN-RXN:Glyceraldehyde 3-phosphate dehydrogenase (phosphorylating)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9531_p \"RXN-9531:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7979_p \"RXN-7979:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_ISOPROPYLMALDEHYDROG_RXN_p \"3-ISOPROPYLMALDEHYDROG-RXN:3-isopropylmalate dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ILE_mc \"ILE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTACONYL_COA_DECARBOXYLASE_RXN_x \"GLUTACONYL-COA-DECARBOXYLASE-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLT_MAL_pc \"GLT_MAL_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ADENYL_KIN_RXN_p \"ADENYL-KIN-RXN:Adenylate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTAMIDOTRANS_RXN_p \"GLUTAMIDOTRANS-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ADENYL_KIN_RXN_m \"ADENYL-KIN-RXN:Adenylate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HYDROXYPYRUVATE_REDUCTASE_RXN_NAD_x \"HYDROXYPYRUVATE_REDUCTASE_RXN_NAD_x\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_1483_c \"RXN0-1483:Ferroxidase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_5643_c \"RXN-5643:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCCINATE_DEHYDROGENASE_UBIQUINONE_RXN_mc \"SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN:Succinate dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GAPOXNPHOSPHN_RXN_p \"GAPOXNPHOSPHN-RXN:Glyceraldehyde 3-phosphate dehydrogenase (phosphorylating)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRANSALDOL_RXN_p \"TRANSALDOL-RXN:Transaldolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MET_PROTON_vc \"MET_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PROPIONYL_COA_xc \"PROPIONYL-COA_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_HYDROXBUTYRYL_COA_DEHYDRATASE_RXN_x \"3-HYDROXBUTYRYL-COA-DEHYDRATASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THRESYN_RXN_p \"THRESYN-RXN:Threonine synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CO2_ec \"CO2_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_961_p \"RXN-961:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSPHORYL_ETHANOLAMINE_mc \"PHOSPHORYL-ETHANOLAMINE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GART_RXN_p \"GART-RXN:Phosphoribosylglycinamide formyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9662_p \"RXN-9662:Enoyl-[acyl-carrier protein] reductase (NADPH, B-specific)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2OXOGLUTARATEDEH_RXN_m \"2OXOGLUTARATEDEH-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ILE_PROTON_vc \"ILE_PROTON_vc\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_4_AMINO_BUTYRATE_PROTON_vc \"4_AMINO_BUTYRATE_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HISTIDPHOS_RXN_p \"HISTIDPHOS-RXN:Histidinol-phosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2KG_CIT_mc \"2KG_CIT_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Mg_tx \"Mg_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FRUCTOKINASE_RXN_c \"FRUCTOKINASE-RXN:Fructokinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HIS_ORNITHINE_mc \"HIS_ORNITHINE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_METHYLACYLYLCOA_HYDROXY_RXN_m \"METHYLACYLYLCOA-HYDROXY-RXN:Enoyl-CoA hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9651_p \"RXN-9651:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5260_m \"RXN0-5260:Glycerol-3-phosphate dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_ASPARTATE_GLU_mc \"L_ASPARTATE_GLU_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9540_p \"RXN-9540:3-oxoacyl-[acyl-carrier protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SEDOHEPTULOSE_BISPHOSPHATASE_RXN_p \"SEDOHEPTULOSE-BISPHOSPHATASE-RXN:Sedoheptulose-bisphosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYCINE_AMINOTRANSFERASE_RXN_x \"GLYCINE-AMINOTRANSFERASE-RXN:Glycine aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5330_NAD_mc \"RXN0-5330:NADH dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_CIT_vc \"MAL_CIT_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_CIT_rev_vc \"MAL_CIT_reverse_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SO4_ec \"SO4_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYCINE_TRNA_LIGASE_RXN_c \"GLYCINE--TRNA-LIGASE-RXN:Glycine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Pi_xc \"Pi_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYOHMETRANS_RXN_c \"GLYOHMETRANS-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYOHMETRANS_RXN_m \"GLYOHMETRANS-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5184_c \"RXN0-5184:Phosphorylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5330_NAD_mi \"RXN0-5330:NADH dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_11213_m \"RXN-11213\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYOHMETRANS_RXN_p \"GLYOHMETRANS-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pLEU_biomass \"pLEU_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UGD_RXN_c \"UGD-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HISTAMINOTRANS_RXN_p \"HISTAMINOTRANS-RXN:Histidinol-phosphate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HIS_pc \"HIS_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CA2_rev_vc \"CA2_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_O2_xc \"O2_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTDECARBOX_RXN_c \"GLUTDECARBOX-RXN:Glutamate decarboxylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_5641_c \"RXN-5641:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CARBAMATE_KINASE_RXN_p \"CARBAMATE-KINASE-RXN:Carbamate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRP_PROTON_rev_vc \"TRP_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Glycolate_xc \"Glycolate_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THR_pc \"THR_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DTDPKIN_RXN_c \"DTDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AIRCARBOXY_RXN_p \"AIRCARBOXY-RXN:Phosphoribosylaminoimidazole carboxylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PLASTOQUINOL_PLASTOCYANIN_REDUCTASE_RXN_p \"PLASTOQUINOL--PLASTOCYANIN-REDUCTASE-RXN:Plastoquinol--plastocyanin reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HISTPRATPHYD_RXN_p \"HISTPRATPHYD-RXN:Phosphoribosyl-ATP pyrophosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MET_pc \"MET_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9524_p \"RXN-9524:3-oxoacyl-[acyl-carrier protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OAA_MAL_mc \"OAA_MAL_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GCVMULTI_RXN_m \"GCVMULTI-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Xylan_biomass \"Xylan_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALANINE_TRNA_LIGASE_RXN_c \"ALANINE--TRNA-LIGASE-RXN:Alanine--tRNA ligase\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETYLORNTRANSAM_RXN_p \"ACETYLORNTRANSAM-RXN:Acetylornithine aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASNSYNA_RXN_c \"ASNSYNA-RXN:Aspartate--ammonia ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CONIFERIN_BETA_GLUCOSIDASE_RXN_c \"CONIFERIN-BETA-GLUCOSIDASE-RXN:Coniferin &amp;beta;-glucosidase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9657_p \"RXN-9657:Enoyl-[acyl-carrier protein] reductase (NADH)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pTRP_biomass \"pTRP_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_8001_p \"RXN-8001:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CIT_PROTON_rev_vc \"CIT_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2TRANSKETO_RXN_p \"2TRANSKETO-RXN:Transketolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHENYLALANINE_TRNA_LIGASE_RXN_c \"PHENYLALANINE--TRNA-LIGASE-RXN:Phenylalanine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUC_ISOCITRATE_mc \"SUC_ISOCITRATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pPHE_biomass \"pPHE_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRO_PROTON_rev_vc \"PRO_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_KETO_ADIPATE_DEHYDROG_RXN_m \"2-KETO-ADIPATE-DEHYDROG-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_SO4_mc \"MAL_SO4_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUCURONOKINASE_RXN_c \"GLUCURONOKINASE-RXN:Glucuronokinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTAMATE_SYNTHASE_FERREDOXIN_RXN_p \"GLUTAMATE-SYNTHASE-FERREDOXIN-RXN:Glutamate synthase (ferredoxin)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_ASPARTATE_PROTON_rev_vc \"L_ASPARTATE_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Phloem_output_tx \"Phloem output\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HMBPP_synthesis_p \"HYPO_HMBPP_synthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TYROSINE_TRNA_LIGASE_RXN_c \"TYROSINE--TRNA-LIGASE-RXN:Tyrosine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NITRATE_PROTON_rev_vc \"NITRATE_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUC_Pi_mc \"SUC_Pi_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Protein_Processing_c \"Protein_Processing_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PSII_RXN_p \"PSII-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NH4_ec \"NH4_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HIS_PROTON_rev_vc \"HIS_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_xc \"MAL_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9535_p \"RXN-9535:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLN_PROTON_rev_vc \"GLN_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISPH2_RXN_p \"ISPH2-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OAA_MAL_pc \"OAA_MAL_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTSEMIALDEHYDROG_RXN_c \"GLUTSEMIALDEHYDROG-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_A_B_oxidation_x \"HYPO Alpha-Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THIOREDOXIN_REDUCT_NADPH_RXN_p \"THIOREDOXIN-REDUCT-NADPH-RXN:Thioredoxin reductase (NADPH)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9104_c \"RXN-9104:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SHIKIMATE_5_DEHYDROGENASE_RXN_p \"SHIKIMATE-5-DEHYDROGENASE-RXN:Shikimate 5-dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACET_xc \"ACET_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_K_ec \"K_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7674_p \"RXN-7674:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CTPSYN_RXN_p \"CTPSYN-RXN:CTP synthetase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FRU_vc \"FRU_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9655_p \"RXN-9655:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_4_PERIOD_2_PERIOD_1_PERIOD_58_RXN_p \"4.2.1.58-RXN:Crotonoyl-[acyl-carrier protein] hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_18_PERIOD_1_PERIOD_2_RXN_p \"1.18.1.2-RXN:Ferredoxin--NADP(+) reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRO_mc \"PRO_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYSTEINE_AMINOTRANSFERASE_RXN_m \"CYSTEINE-AMINOTRANSFERASE-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUCOKIN_RXN_c \"GLUCOKIN-RXN:Glucokinase\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLT_PROTON_rev_vc \"GLT_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRPPSYN_RXN_p \"PRPPSYN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_VALINE_TRNA_LIGASE_RXN_c \"VALINE--TRNA-LIGASE-RXN:Valine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTAMINESYN_RXN_c \"GLUTAMINESYN-RXN:Glutamate--ammonia ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTAMINESYN_RXN_m \"GLUTAMINESYN-RXN:Glutamate--ammonia ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_5_PERIOD_1_PERIOD_20_RXN_c \"1.5.1.20-RXN:Methylenetetrahydrofolate reductase (NADPH)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTAMINESYN_RXN_p \"GLUTAMINESYN-RXN:Glutamate--ammonia ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HOMO_CYS_pc \"HOMO_CYS_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUCOKIN_RXN_p \"GLUCOKIN-RXN:Glucokinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PALMITATE_pc \"PALMITATE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DUMP_mc \"dUMP_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GUANYL_KIN_RXN_p \"GUANYL-KIN-RXN:Guanylate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_12002_p \"RXN-12002\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PEP_Pi_pc \"PEP_Pi_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_5781_r \"RXN-5781:Diacylglycerol cholinephosphotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_BRANCHED_CHAINAMINOTRANSFERLEU_RXN_m \"BRANCHED-CHAINAMINOTRANSFERLEU-RXN:Branched-chain amino acid aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_BRANCHED_CHAINAMINOTRANSFERLEU_RXN_p \"BRANCHED-CHAINAMINOTRANSFERLEU-RXN:Branched-chain amino acid aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PROTON_ATPase_c \"PROTON_ATPase_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIHYDROXYISOVALDEHYDRAT_RXN_p \"DIHYDROXYISOVALDEHYDRAT-RXN:Dihydroxy-acid dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CO2_mc \"CO2_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MDA_Fd_Ascorbate_p \"MDA-FD-Ascorbate_p\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Palmitate_biomass \"Palmitate_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CHORISMATEMUT_RXN_p \"CHORISMATEMUT-RXN:Chorismate mutase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUC_FUM_mc \"SUC_FUM_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLT_PROTON_vc \"GLT_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GUANYL_KIN_RXN_c \"GUANYL-KIN-RXN:Guanylate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRAISOM_RXN_p \"PRAISOM-RXN:Phosphoribosylanthranilate isomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MercaptoPyruvateSulfurtransferase_m \"MercaptoPyruvateSulfurtransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9533_p \"RXN-9533:3-hydroxyoctanoyl-[acyl-carrier protein] dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sSER_biomass \"sSER_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTAMATE_DEHYDROGENASE_RXN_m \"GLUTAMATE-DEHYDROGENASE-RXN:Glutamate dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARG_HIS_mc \"ARG_HIS_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCROSE_PHOSPHATASE_RXN_c \"SUCROSE-PHOSPHATASE-RXN:Sucrose-phosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARG_pc \"ARG_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PREPHENATEDEHYDROG_RXN_p \"PREPHENATEDEHYDROG-RXN:Prephenate dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AIRS_RXN_p \"AIRS-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTAMATE_SYNTHASE_NADH_RXN_p \"GLUTAMATE-SYNTHASE-NADH-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9528_p \"RXN-9528:3-oxoacyl-[acyl-carrier protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_BRANCHED_CHAINAMINOTRANSFERVAL_RXN_m \"BRANCHED-CHAINAMINOTRANSFERVAL-RXN:Branched-chain amino acid aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OROTATE_REDUCTASE_NADH_RXN_p \"OROTATE-REDUCTASE-NADH-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7676_p \"RXN-7676:Chlorophyllide-a oxygenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARG_PROTON_rev_vc \"ARG_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5114_p \"RXN0-5114:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ILE_PROTON_rev_vc \"ILE_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLC_vc \"GLC_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TYR_PROTON_rev_vc \"TYR_PROTON_rev_vc\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPCARBTRANS_RXN_p \"ASPCARBTRANS-RXN:Aspartate carbamoyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIHYDRODIPICSYN_RXN_p \"DIHYDRODIPICSYN-RXN:dihydrodipicolinate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_K_rev_vc \"K_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_VAL_mc \"VAL_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Plastoquinol_Oxidase_p \"Plastoquinol_Oxidase_p\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_10_FORMYL_THF_pc \"10_FORMYL_THF_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_IMIDPHOSDEHYD_RXN_p \"IMIDPHOSDEHYD-RXN:Imidazoleglycerol-phosphate dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_1_PERIOD_1_PERIOD_39_RXN_m \"MALIC-NAD-RXN:Malate dehydrogenase (oxaloacetate decarboxylating)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_PROTON_vc \"MAL_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_6383_x \"RXN-6383:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pVAL_biomass \"pVAL_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9648_p \"RXN-9648:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_6PGLUCONDEHYDROG_RXN_p \"6PGLUCONDEHYDROG-RXN:Phosphogluconate dehydrogenase (decarboxylating)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_METHIONINE_TRNA_LIGASE_RXN_c \"METHIONINE--TRNA-LIGASE-RXN:Methionine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FORMATE_mc \"FORMATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GDPKIN_RXN_m \"GDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_ACONITATE_mc \"MAL_ACONITATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H2O_ec \"H2O_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARG_CITRULLINE_mc \"ARG_CITRULLINE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GDPKIN_RXN_p \"GDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7678_NADP_p \"RXN-7678:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_ASPARTATE_PROTON_vc \"L_ASPARTATE_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_METHENYLTHFCYCLOHYDRO_RXN_c \"METHENYLTHFCYCLOHYDRO-RXN:Methenyltetrahydrofolate cyclohydrolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_3523_p \"RXN-3523:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pALA_biomass \"pALA_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TYR_pc \"TYR_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_BRANCHED_CHAINAMINOTRANSFERVAL_RXN_p \"BRANCHED-CHAINAMINOTRANSFERVAL-RXN:Branched-chain amino acid aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_G6P_Pi_pc \"G6P_Pi_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACET_mc \"ACET_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2KG_MAL_mc \"2KG_MAL_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TYROSINE_AMINOTRANSFERASE_RXN_p \"TYROSINE-AMINOTRANSFERASE-RXN:Aromatic amino acid transferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9539_p \"RXN-9539:3-oxoacyl-[acyl-carrier protein] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_VAL_pc \"VAL_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HOMOSERKIN_RXN_p \"HOMOSERKIN-RXN:Homoserine kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLN_GLU_pc \"GLN_GLU_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_6PGLUCONDEHYDROG_RXN_c \"6PGLUCONDEHYDROG-RXN:Phosphogluconate dehydrogenase (decarboxylating)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NADPHoxc_tx \"NADPHoxc_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_2_PERIOD_1_PERIOD_9_RXN_c \"1.2.1.9-RXN:Glyceraldehyde-3-phosphate dehydrogenase (NADP+)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ATPPHOSPHORIBOSYLTRANS_RXN_p \"ATPPHOSPHORIBOSYLTRANS-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_969_x \"RXN-969:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETOLACTSYN_RXN_p \"ACETOLACTSYN-RXN:Acetolactate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN1F_66_p \"RXN1F-66:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_15479_p \"RXN-15479:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pTYR_biomass \"pTYR_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AMP_ATP_xc \"AMP_ATP_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PEPCARBOX_RXN_c \"PEPCARBOX-RXN:Phosphoenolpyruvate carboxylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACET_pc \"ACET_pc\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MG2_rev_vc \"MG2_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSPHORIBULOKINASE_RXN_p \"PHOSPHORIBULOKINASE-RXN:Phosphoribulokinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2KG_MAL_pc \"2KG_MAL_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLY_xc \"GLY_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHE_pc \"PHE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUC_CIT_mc \"SUC_CIT_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2PGADEHYDRAT_RXN_p \"2PGADEHYDRAT-RXN:Phosphopyruvate hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GDPKIN_RXN_c \"GDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9659_p \"RXN-9659:Enoyl-[acyl-carrier protein] reductase (NADPH, B-specific)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1827_p \"RXN-1827:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CITSYN_RXN_x \"CITSYN-RXN:Citrate (si)-synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRO_TRNA_LIGASE_RXN_c \"PROLINE--TRNA-LIGASE-RXN:Proline--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H2O_mc \"H2O_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2PGADEHYDRAT_RXN_c \"2PGADEHYDRAT-RXN:Phosphopyruvate hydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FORMATE_pc \"FORMATE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_1_PERIOD_5_PERIOD_1_PERIOD_9_RXN_c \"1.5.1.9-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRTRANS_RXN_p \"PRTRANS-RXN:Anthranilate phosphoribosyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DAHPSYN_RXN_p \"DAHPSYN-RXN:2-dehydro-3-deoxyphosphoheptonate aldolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYSPH_RXN_p \"CYSPH-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Glycerol_biomass \"Glycerol_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_5_PERIOD_1_PERIOD_19_RXN_p \"2.5.1.19-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_AMINOADIPATE_AMINOTRANSFERASE_RXN_c \"2-AMINOADIPATE-AMINOTRANSFERASE-RXN:2-aminoadipate aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ORNCARBAMTRANSFER_RXN_p \"ORNCARBAMTRANSFER-RXN:Ornithine carbamoyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_IPP_biosynthesis_c \"HYPO IPP biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PREPHENATE_DEHYDROGENASE_NADP_RXN_p \"PREPHENATE_DEHYDROGENASE_NADP_RXN_p\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HISTOLDEHYD_RXN_p \"HISTOLDEHYD-RXN:Histidinol dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_5330_NADP_c \"RXN0-5330:NADH dehydrogenase (ubiquinone)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HISTALDEHYD_RXN_p \"HISTALDEHYD-RXN:Histidinol dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_14903_mi \"RXN-14903\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTAMATE_N_ACETYLTRANSFERASE_RXN_p \"GLUTAMATE-N-ACETYLTRANSFERASE-RXN:Glutamate N-acetyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PROTON_PPi_rev_vc \"PROTON_PPi_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9958_NAD_m \"RXN-9958\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLN_GLU_mc \"GLN_GLU_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NADPH_Dehydrogenase_p \"NADPH_Dehydrogenase_p\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CITSYN_RXN_m \"CITSYN-RXN:Citrate (si)-synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OROTPDECARB_RXN_p \"OROTPDECARB-RXN:Orotidine-5&#039;-phosphate decarboxylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUC_ACONITATE_mc \"SUC_ACONITATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_K_biomass \"K_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYRROLINECARBREDUCT_RXN_NADP_c \"PYRROLINECARBREDUCT-RXN:Pyrroline-5-carboxylate reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Nitrate_tx \"Nitrate_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FUM_PROTON_vc \"FUM_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9537_p \"RXN-9537:3-hydroxyoctanoyl-[acyl-carrier protein] dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SER_xc \"SER_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRP_PROTON_vc \"TRP_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Photon_ep \"Photon_ep\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AICARTRANSFORM_RXN_p \"AICARTRANSFORM-RXN:Phosphoribosylaminoimidazolecarboxamide formyltransferase\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SULFITE_OXIDASE_RXN_m \"SULFITE-OXIDASE-RXN:Sulfite oxidase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CELLULOSE_SYNTHASE_GDP_FORMING_RXN_c \"CELLULOSE-SYNTHASE-GDP-FORMING-RXN:Cellulose synthase (GDP-forming)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sGLN_biomass \"sGLN_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SO4_tx \"SO4_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7985_p \"RXN-7985:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RIB5PISOM_RXN_p \"RIB5PISOM-RXN:Ribose 5-phosphate epimerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_7_PERIOD_1_PERIOD_90_RXN_c \"2.7.1.90-RXN:Diphosphate--fructose-6-phosphate 1-phosphotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ORNITHINE_CITRULLINE_mc \"ORNITHINE_CITRULLINE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pPRO_biomass \"pPRO_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NH4_tx \"NH4_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ADENYLOSUCCINATE_SYNTHASE_RXN_p \"ADENYLOSUCCINATE-SYNTHASE-RXN:adenylosuccinate synthetase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FERRIC_CHELATE_REDUCTASE_RXN_c \"FERRIC-CHELATE-REDUCTASE-RXN:Ferric-chelate reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OAA_xc \"OAA_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ATPase_tx \"ATPase_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UDPKIN_RXN_c \"UDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NADPHoxp_tx \"NADPHoxp_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_4_AMINO_BUTYRATE_mc \"4_AMINO_BUTYRATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_6PFRUCTPHOS_RXN_c \"6PFRUCTPHOS-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_HYDROXYISOBUTYRYL_COA_HYDROLASE_RXN_m \"3-HYDROXYISOBUTYRYL-COA-HYDROLASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN66_3_c \"RXN66-3:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN66_3_m \"RXN66-3:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UDPKIN_RXN_p \"UDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_10773_c \"RXN-10773\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pASN_biomass \"pASN_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Sucrose_ec \"Sucrose_ec\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLY_mc \"GLY_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DGDPKIN_RXN_p \"DGDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DUDPKIN_RXN_p \"DUDPKIN-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_8991_p \"RXN-8991:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETATE_COA_LIGASE_RXN_p \"ACETATE--COA-LIGASE-RXN:acetate--CoA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ETHANOLAMINEPHOSPHOTRANSFERASE_RXN_r \"ETHANOLAMINEPHOSPHOTRANSFERASE-RXN:Ethanolaminephosphotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sSUC_biomass \"sSUC_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN0_2382_p \"RXN0-2382:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Protein_Translocation_c \"Protein_Translocation_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THYMIDYLATESYN_RXN_m \"THYMIDYLATESYN-RXN:Thymidylate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_L_ALPHA_ALANINE_PROTON_rev_vc \"L_ALPHA_ALANINE_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ATP_CITRATE_PRO_S_LYASE_RXN_c \"ATP-CITRATE-PRO-S--LYASE-RXN:ATP-citrate (pro-S-)-lyase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2KG_ACONITATE_mc \"2KG_ACONITATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AMP_DEAMINASE_RXN_c \"AMP-DEAMINASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FUMARYLACETOACETASE_RXN_c \"FUMARYLACETOACETASE-RXN:Fumarylacetoacetase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SO4_pc \"SO4_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NH4_vc \"NH4_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLC_pc \"GLC_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_PROTON_rev_vc \"MAL_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CARBOXYCYCLOHEXADIENYL_DEHYDRATASE_RXN_p \"CARBOXYCYCLOHEXADIENYL-DEHYDRATASE-RXN:Carboxycyclohexadienyl dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASPARAGINE_TRNA_LIGASE_RXN_c \"ASPARAGINE--TRNA-LIGASE-RXN:Asparagine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLU6PDEHYDROG_RXN_p \"GLU6PDEHYDROG-RXN:Glucose-6-phosphate 1-dehydrogenase\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_METHYLENE_THF_mc \"METHYLENE_THF_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GMP_SYN_GLUT_RXN_c \"GMP-SYN-GLUT-RXN:GMP synthetase (glutamine-hydrolysing)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLU6PDEHYDROG_RXN_c \"GLU6PDEHYDROG-RXN:Glucose-6-phosphate 1-dehydrogenase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETATE_COA_LIGASE_RXN_x \"ACETATE--COA-LIGASE-RXN:acetate--CoA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARGININE_TRNA_LIGASE_RXN_c \"ARGININE--TRNA-LIGASE-RXN:Arginine--tRNA ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_15130_p \"RXN-15130:Cystathionine &amp;gamma;-lyase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ADENOSINE_KINASE_RXN_c \"ADENOSINE-KINASE-RXN:Adenosine kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AraCore_Biomass_tx \"AraCoreBiomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSGLYPHOS_RXN_p \"PHOSGLYPHOS-RXN:Phosphoglycerate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_7_PERIOD_7_PERIOD_44_RXN_c \"2.7.7.44-RXN:Glucuronate-1-phosphate uridylyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pGLN_biomass \"pGLN_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCCINYL_COA_HYDROLASE_RXN_m \"SUCCINYL-COA-HYDROLASE-RXN:Succinyl-CoA hydrolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pHIS_biomass \"pHIS_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_BHBDCLOS_RXN_x \"BHBDCLOS-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_K_tx \"K_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SULFITE_REDUCTASE_FERREDOXIN_RXN_p \"SULFITE-REDUCTASE-FERREDOXIN-RXN:Sulfite reductase (ferredoxin)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUTKIN_RXN_c \"GLUTKIN-RXN:Glutamate 5-kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TYROSINE_AMINOTRANSFERASE_RXN_c \"TYROSINE-AMINOTRANSFERASE-RXN:Tyrosine aminotransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_unlProtHYPO_c \"unlProtHYPO_c\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MYO_INOSITOL_1_PHOSPHATE_SYNTHASE_RXN_c \"MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN:myo-inositol-1-phosphate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pCYS_biomass \"pCYS_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_HYDROXYPROPIONATE_DEHYDROGENASE_RXN_m \"3-HYDROXYPROPIONATE-DEHYDROGENASE-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYS_PROTON_rev_vc \"LYS_PROTON_rev_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_KETOGLUTARATE_xc \"2_KETOGLUTARATE_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLY_pc \"GLY_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_12486_c \"RXN-12486\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSPHATIDATE_PHOSPHATASE_RXN_p \"PHOSPHATIDATE-PHOSPHATASE-RXN:Phosphatidate phosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SAICARSYN_RXN_p \"SAICARSYN-RXN:Phosphoribosylaminoimidazole-succinocarboxamide synthetase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SER_mc \"SER_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_2141_p \"RXN-2141:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARG_ORNITHINE_mc \"ARG_ORNITHINE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GMP_pc \"GMP_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCROSE_SYNTHASE_RXN_c \"SUCROSE-SYNTHASE-RXN:Sucrose synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_14351_pc \"RXN_14351_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARG_LYS_mc \"ARG_LYS_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYRIBONUCSYN_RXN_p \"GLYRIBONUCSYN-RXN:Phosphoribosylamine--glycine ligase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN66_1_c \"RXN66-1:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ETHANOLAMINE_KINASE_RXN_c \"ETHANOLAMINE-KINASE-RXN:Ethanolamine kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ISOCITRATE_ACONITATE_mc \"ISOCITRATE_ACONITATE_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSGLYPHOS_RXN_c \"PHOSGLYPHOS-RXN:Phosphoglycerate kinase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CHORISMATE_SYNTHASE_RXN_p \"CHORISMATE-SYNTHASE-RXN:Chorismate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_CIT_mc \"MAL_CIT_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SPONTPRO_RXN_m \"SPONTPRO-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_METHYLENE_THF_pc \"METHYLENE_THF_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_3521_p \"RXN-3521:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYSTATHIONINE_BETA_LYASE_RXN_p \"CYSTATHIONINE-BETA-LYASE-RXN:Cystathionine &amp;beta;-lyase\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_6PFRUCTPHOS_RXN_p \"6PFRUCTPHOS-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRIBFAICARPISOM_RXN_p \"PRIBFAICARPISOM-RXN:N-(5&#039;-phospho-D-ribosylformimino)-5-amino-1-(5&#039;&#039;-phosphoribosyl)-4- imidazole carboxamide isomerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_METHYLCROTONYL_COA_CARBOXYLASE_RXN_m \"METHYLCROTONYL-COA-CARBOXYLASE-RXN:Methylcrotonyl-CoA carboxylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ATP_AMP_mc \"ATP_AMP_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_METHYLENETHFDEHYDROG_NADP_RXN_c \"METHYLENETHFDEHYDROG-NADP-RXN:Methylenetetrahydrofolate dehydrogenase (NADP+)\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLN_PROTON_vc \"GLN_PROTON_vc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SPONTPRO_RXN_c \"SPONTPRO-RXN:NIL\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARG_mc \"ARG_mc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Phytol_degradation_p \"HYPO Phytol -greater_than Phytenate\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLC_tx \"GLC_tx\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SER_pc \"SER_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sARG_biomass \"sARG_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sHIS_biomass \"sHIS_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sLYS_biomass \"sLYS_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sTHR_biomass \"sTHR_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sASN_biomass \"sASN_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sCYS_biomass \"sCYS_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sGLY_biomass \"sGLY_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sPRO_biomass \"sPRO_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sVAL_biomass \"sVAL_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sILE_biomass \"sILE_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sLEU_biomass \"sLEU_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sMET_biomass \"sMET_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sPHE_biomass \"sPHE_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sTYR_biomass \"sTYR_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sTRP_biomass \"sTRP_biomass\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DIACYLGLYCEROL_O_ACYLTRANSFERASE_RXN_p \"DIACYLGLYCEROL-O-ACYLTRANSFERASE-RXN:diacylglycerol acyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CDPDIGLYSYN_RXN_p \"CDPDIGLYSYN-RXN:phosphatidate cytidylyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CDPDIGLYSYN_RXN_m \"CDPDIGLYSYN-RXN:phosphatidate cytidylyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSPHAGLYPSYN_RXN_p \"PHOSPHAGLYPSYN-RXN:Phosphatidylglycerol phosphate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSPHAGLYPSYN_RXN_m \"PHOSPHAGLYPSYN-RXN:Phosphatidylglycerol phosphate synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PGPPHOSPHA_RXN_p \"PGPPHOSPHA-RXN:Phosphatidylglycerophosphate phosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PGPPHOSPHA_RXN_m \"PGPPHOSPHA-RXN:Phosphatidylglycerophosphate phosphatase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_3_PERIOD_1_PERIOD_23_RXN_p \"2.3.1.23-RXN:Lysophosphatidylcholine acyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHOSPHOLIPASE_A2_RXN_c \"PHOSPHOLIPASE-A2-RXN:Phospholipase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UDPGLUCEPIM_RXN_c \"UDPGLUCEPIM-RXN:UDP-glucose 4-epimerase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_4_PERIOD_1_PERIOD_46_RXN_p \"2.4.1.46-RXN:UDP-galactose:DAG galactosyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1225_p \"RXN-1225:digalactosyldiacylglycerol synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9623_p \"RXN-9623:\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9632_p \"RXN-9632:3-ketoacyl-[acp] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9633_p \"RXN-9633:3-oxoacyl-[acyl-carrier-protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9634_p \"RXN-9634:3-hydroxyacyl-[acyl-carrier-protein] dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9635_p \"RXN-9635:Octadec-2-enoyl-ACP reductase [NADH]\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_9548_p \"RXN-9548:stearoyl ACP hydrolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_palmitoyl_ACP_desaturase_p \"palmitoyl-ACP desaturase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hexadecenoate_biosynthesis_p \"hexadecenoate_biosynthesis\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_palmitoleoyl_ACP_desaturase_p \"palmitoleoyl-ACP desaturase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hexadecadienoate_biosynthesis_p \"hexadecadienoate biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hexadecadienoate_ACP_desaturase_p \"hexadecadienoate ACP desaturase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hexadecatrienoate_biosynthesis_p \"hexadecatrienoate biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_7903_p \"RXN-7903:stearoyl-ACP desaturase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_3_PERIOD_1_PERIOD_2_PERIOD_14_RXN_p \"3.1.2.14-RXN:Oleoyl-ACP hydrolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Oleoyl_ACP_desaturase_p \"Oleoyl-ACP desaturase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Octadecadienoyl_ACP_hydrolase_p \"Octadecadienoyl-ACP hydrolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Octadecadienoyl_ACP_desaturase_p \"Octadecadienoyl-ACP desaturase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Octadecatrienoyl_ACP_hydrolase_p \"Octadecatrienoyl-ACP hydrolase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN1G_368_p \"RXN1G-368:3-ketoacyl-[acp] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN1G_349_p \"RXN1G-349:3-oxoacyl-[acyl-carrier-protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN1G_320_p \"RXN1G-320:3-hydroxyacyl-[acyl-carrier-protein] dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN1G_395_p \"RXN1G-395:Trans-delta-2-arachidoyl ACP reductase [NADH]\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN1G_445_p \"RXN1G-445:3-ketoacyl-[acp] synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN1G_469_p \"RXN1G-469:3-oxoacyl-[acyl-carrier-protein] reductase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN1G_363_p \"RXN1G-363:3-hydroxyacyl-[acyl-carrier-protein] dehydratase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN1G_488_p \"RXN1G-488:Trans-delta-2-behenoyl ACP reductase [NADH]\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_arachidate_biosynthesis_p \"arachidate biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_docosanoate_biosynthesis_p \"docosanoate biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Arachidoyl_ACP_desaturase_p \"Arachidoyl-ACP desaturase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gadoleic_acid_biosynthesis_p \"gadoleic acid biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1223_p \"RXN-1223:UDP-sulfoquinovose synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1224_p \"RXN-1224:UDP-sulfoquinovose synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLUC1PURIDYLTRANS_RXN_p \"GLUC1PURIDYLTRANS-RXN:UTP--glucose-1-phosphate uridylyltransferase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LPG_biosynthesis_c \"Lysophosphatidylglycerol biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Fatty_Acids_pc \"Fatty_Acids_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_7_PERIOD_8_PERIOD_11_RXN_r \"2.7.8.11-RXN:phosphatidylinositol synthase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHE_NH4_Lyase_c \"Phenylalanine_Ammonia_Lyase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRANS_CINNAMATE_4_MONOOXYGENASE_RXN_c \"TRANS-CINNAMATE-4-MONOOXYGENASE-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_8871_c \"RXN-8871\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_8872_c \"RXN-8872\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_8873_c \"RXN-8873\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_4_COUMARATE_COA_LIGASE_RXN_c \"4-COUMARATE--COA-LIGASE-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_2_PERIOD_3_PERIOD_1_PERIOD_133_RXN_c \"2.3.1.133-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_2581_c \"RXN-2581\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_2621_c \"RXN-2621\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1103_c \"RXN-1103\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1104_c \"RXN-1104\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FERULIC_ACID_pc \"FERULIC_ACID_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1104_p \"RXN-1104\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_VANILLIN_pc \"VANILLIN_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_6_PERIOD_2_PERIOD_1_PERIOD_34_RXN_p \"6.2.1.34-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_6_PERIOD_2_PERIOD_1_PERIOD_34_RXN_c \"6.2.1.34-RXN\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETOVANILLONE_SYNTHASE_c \"ACETOVANILLONE SYNTHASE\">\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETOVANILLONE_HYDROXYLASE_c \"Acetovanillone 5-Hydroxylase\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACETOSYRINGONE_BIOSYNTHESIS_c \"Acetosyringone biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_1121_c \"RXN-1121\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RXN_3422_c \"RXN-3422\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SYRINGALDEHYDE_BIOSYNTHESIS_c \"HYPO Syringaldehyde biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SYRINGICACID_BIOSYNTHESIS_c \"HYPO Syringicacid biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_VANILLICACID_BIOSYNTHESIS_c \"HYPO Vanillicacid biosynthesis\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_STEARIC_ACID_pc \"STEARIC_ACID_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_STEARIC_ACID_xc \"STEARIC_ACID_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_Stearate_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OLEATE_CPD_pc \"OLEATE_CPD_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_OLEATE_CPD_xc \"OLEATE_CPD_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_OLEATE_CPD_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Octadecadienoate_pc \"Octadecadienoate_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Octadecadienoate_xc \"Octadecadienoate_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_Octadecadienoate_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LINOLENIC_ACID_pc \"LINOLENIC_ACID_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LINOLENIC_ACID_xc \"LINOLENIC_ACID_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_LINOLENIC_ACID_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARACHIDIC_ACID_pc \"ARACHIDIC_ACID_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARACHIDIC_ACID_xc \"ARACHIDIC_ACID_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_Arachidicacid_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_16709_pc \"CPD_16709_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_16709_xc \"CPD_16709_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_CPD_16709_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DOCOSANOATE_pc \"DOCOSANOATE_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DOCOSANOATE_xc \"DOCOSANOATE_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_DOCOSANOATE_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_9245_pc \"CPD_9245_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_9245_xc \"CPD_9245_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_CPD_9245_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_17412_pc \"CPD_17412_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_17412_xc \"CPD_17412_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_CPD_17412_x \"Beta-Oxidation\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_17291_pc \"CPD_17291_pc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CPD_17291_xc \"CPD_17291_xc\">\n",
      "WARNING:cobra.io.sbml:Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_Beta_Oxidation_CPD_17291_x \"Beta-Oxidation\">\n",
      "ERROR:cobra.io.sbml:No objective coefficients in model. Unclear what should be optimized\n"
     ]
    }
   ],
   "source": [
    "fname = \"C:\\\\Users\\\\FFAR\\\\Downloads\\\\plantcoremetabolism-model\\\\PlantCoreMetabolism_v1_3_2.xml\"\n",
    "model = io.read_sbml_model(fname)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-3"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.metabolites.get_by_id(\"L_1_PHOSPHATIDYL_GLYCEROL_P_m\").charge"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "\n",
    "df = pd.read_csv(\"Data/biomass_sorghum.csv\")\n",
    "\n",
    "FA=[\"PALMITATE_p\",\"CPD_9245_p\",\"CPD_17412_p\",\"CPD_17291_p\",\"STEARIC_ACID_p\",\"OLEATE_CPD_p\",\n",
    "    \"Octadecadienoate_p\",\"LINOLENIC_ACID_p\",\"ARACHIDIC_ACID_p\",\"CPD_16709_p\",\"DOCOSANOATE_p\"]\n",
    "FACP = {\"PALMITATE_p\":\"Palmitoyl_ACPs_p\",\n",
    "        \"CPD_9245_p\":\"Palmitoleoyl_ACP_p\",\n",
    "        \"CPD_17412_p\":\"hexadecadienoate_ACP_p\",\n",
    "        \"CPD_17291_p\":\"hexadecatrienoate_ACP_p\",\n",
    "        \"STEARIC_ACID_p\":\"Stearoyl_ACPs_p\",\n",
    "        \"OLEATE_CPD_p\":\"Oleoyl_ACPs_p\",\n",
    "        \"Octadecadienoate_p\":\"Octadecadienoyl_ACP_p\",\n",
    "        \"LINOLENIC_ACID_p\":\"Octadecatrienoyl_ACP_p\",\n",
    "        \"ARACHIDIC_ACID_p\":\"Arachidoyl_ACPs_p\",\n",
    "        \"CPD_16709_p\":\"Eicosenoyl_ACP_p\",\n",
    "        \"DOCOSANOATE_p\":\"Behenoyl_ACPs_p\"}\n",
    "\n",
    "\n",
    "PLs = [\"ACYL_SN_GLYCEROL_3P_p\",\n",
    "       \"L_PHOSPHATIDATE_p\",\"L_PHOSPHATIDATE_m\",\"DIACYLGLYCEROL_p\",\n",
    "       \"DIACYLGLYCEROL_r\",\"Triacylglycerols_p\",\"PHOSPHATIDYL_CHOLINE_r\",\n",
    "       \"L_1_PHOSPHATIDYL_ETHANOLAMINE_r\",\"L_1_PHOSPHATIDYL_GLYCEROL_p\",\n",
    "       \"L_1_PHOSPHATIDYL_GLYCEROL_P_p\",\"L_1_PHOSPHATIDYL_GLYCEROL_P_m\",\n",
    "       \"L_1_PHOSPHATIDYL_GLYCEROL_m\",\"2_Lysophosphatidylcholines_r\",\n",
    "       \"Lysophosphatidylglycerols_r\",\"CDPDIACYLGLYCEROL_p\",\"CDPDIACYLGLYCEROL_m\",\n",
    "           \"D_Galactosyl_12_diacyl_glycerols_p\",\"Galactosyl_galactosyl_diacyl_glycerols_p\"]\n",
    "\n",
    "\n",
    "for met in PLs:\n",
    "    met=model.metabolites.get_by_id(met)\n",
    "    met.formula=\"\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Use biomass composition to generate biomass equations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "def generateMissingFormula(model,debug=False):\n",
    "    loop_counter = 0\n",
    "    former = 0\n",
    "    for met in model.metabolites:\n",
    "        if met.formula == \"\" or met.formula == \"NA\":\n",
    "            former = former +1\n",
    "    latter = 1\n",
    "    while True:\n",
    "        loop_counter = loop_counter+1\n",
    "        if debug:\n",
    "            print(\"Loop = \"+str(loop_counter))\n",
    "        former = latter\n",
    "        for rxn in model.reactions:\n",
    "            count = 0\n",
    "            for met in rxn.metabolites:\n",
    "                if met.formula==\"\" or met.formula==\"NA\" or met.formula == None:\n",
    "                    if met.formula == \"NA\" or met.formula == None:\n",
    "                        met.formula = \"\"\n",
    "                    count = count + 1\n",
    "            if count == 1:\n",
    "                unb = rxn.check_mass_balance()\n",
    "                eqn = rxn.reaction\n",
    "                eqn = \" \"+eqn+\" \"\n",
    "                for met in rxn.metabolites.keys():\n",
    "                    formula = met.formula\n",
    "                    if formula == None:\n",
    "                        formula = \"0\"\n",
    "                        NF_list.add(rxn.id)\n",
    "                    eqn=eqn.replace(\" \"+met.id+\" \",\"(\"+formula+\")\")\n",
    "                if debug:\n",
    "                    print(eqn)\n",
    "                    print(unb)\n",
    "                for met in rxn.metabolites:\n",
    "                    if met.formula == \"\":\n",
    "                        tempForm = \"\"\n",
    "                        for a in sorted(unb.keys()):\n",
    "                            if a==\"charge\" or round(unb[a],2)==0:\n",
    "                                continue\n",
    "                            num = float(abs(unb[a]))\n",
    "                            if str(round(num))==str(num):\n",
    "                                tempForm = tempForm+a+str(int(round(num)))\n",
    "                            else:\n",
    "                                tempForm = tempForm+a+str(num)\n",
    "                                #print(a)\n",
    "                                #print(round(num)==num)\n",
    "                                #print(round(num))\n",
    "                                #print(num)\n",
    "                                #print(type(round(num)))\n",
    "                                #print(type(num))\n",
    "                        met.formula = tempForm\n",
    "                        if debug:\n",
    "                            print(met.id)\n",
    "                            print(tempForm)\n",
    "        latter = 0\n",
    "        for met in model.metabolites:\n",
    "            if met.formula == \"\" or met.formula == \"NA\":\n",
    "                latter = latter +1\n",
    "        if former == latter:\n",
    "            break\n",
    "        \n",
    "        "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run stem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "cobra\\core\\metabolite.py:104 UserWarning: 17.000000000000004 is not an integer (in formula C37.0H66.0N7.0O17.000000000000004P3.0S1.0)\n",
      "cobra\\core\\metabolite.py:104 UserWarning: 79.00000000000001 is not an integer (in formula C44.0H79.00000000000001N3.0O15.000000000000002P2.0)\n",
      "cobra\\core\\metabolite.py:104 UserWarning: 15.000000000000002 is not an integer (in formula C44.0H79.00000000000001N3.0O15.000000000000002P2.0)\n",
      "cobra\\core\\metabolite.py:104 UserWarning: 36.86 is not an integer (in formula C36.86H70.81000000000002O12.61P1.94)\n",
      "cobra\\core\\metabolite.py:104 UserWarning: 70.81000000000002 is not an integer (in formula C36.86H70.81000000000002O12.61P1.94)\n",
      "cobra\\core\\metabolite.py:104 UserWarning: 12.61 is not an integer (in formula C36.86H70.81000000000002O12.61P1.94)\n",
      "cobra\\core\\metabolite.py:104 UserWarning: 1.94 is not an integer (in formula C36.86H70.81000000000002O12.61P1.94)\n"
     ]
    },
    {
     "ename": "KeyError",
     "evalue": "'Protein_b'",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-6-888d48b1909a>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m     32\u001b[0m     \u001b[1;32mif\u001b[0m \u001b[0mmet\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mFA\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     33\u001b[0m         \u001b[1;32mcontinue\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 34\u001b[1;33m     \u001b[0mrxn\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0madd_metabolites\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m{\u001b[0m\u001b[0mstem_model\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmetabolites\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_by_id\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mmet\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m-\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m*\u001b[0m\u001b[0mfloat\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mdf\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m\"Unnamed: 0\"\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m==\u001b[0m\u001b[0mmet\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mk\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m}\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     35\u001b[0m \u001b[0mrxn\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mlower_bound\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     36\u001b[0m \u001b[0mrxn\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mupper_bound\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m1000\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m~\\Anaconda3\\lib\\site-packages\\cobra\\core\\dictlist.py\u001b[0m in \u001b[0;36mget_by_id\u001b[1;34m(self, id)\u001b[0m\n\u001b[0;32m     56\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0mget_by_id\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mid\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     57\u001b[0m         \u001b[1;34m\"\"\"return the element with a matching id\"\"\"\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 58\u001b[1;33m         \u001b[1;32mreturn\u001b[0m \u001b[0mlist\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m__getitem__\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_dict\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mid\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     59\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     60\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0mlist_attr\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mattribute\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mKeyError\u001b[0m: 'Protein_b'"
     ]
    }
   ],
   "source": [
    "from cobra import flux_analysis\n",
    "stem_model = model.copy()\n",
    "\n",
    "k = \"stem\"\n",
    "RXN1 = Reaction(\"Fatty_acid_mix_\"+k)\n",
    "RXN2 = Reaction(\"Fatty_acid_ACP_\"+k)\n",
    "tot = 0\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    #print met\n",
    "    if met in FA:\n",
    "        RXN1.add_metabolites({stem_model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "        RXN2.add_metabolites({stem_model.metabolites.get_by_id(FACP[met]):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "        tot = tot+(float(df[df[\"Unnamed: 0\"]==met][k]))\n",
    "if tot==0:\n",
    "    RXN1.add_metabolites({stem_model.metabolites.PALMITATE_p:-1})\n",
    "    RXN2.add_metabolites({stem_model.metabolites.Palmitoyl_ACPs_p:-1})\n",
    "    tot = 1\n",
    "RXN1.add_metabolites({stem_model.metabolites.Fatty_Acids_p:tot})\n",
    "RXN1.lower_bound = 1000\n",
    "RXN1.upper_bound = 0\n",
    "stem_model.add_reaction(RXN1)\n",
    "\n",
    "RXN2.add_metabolites({stem_model.metabolites.Fatty_acyl_ACP_p:tot})\n",
    "RXN2.lower_bound = 1000\n",
    "RXN2.upper_bound = 0\n",
    "stem_model.add_reaction(RXN2)\n",
    "\n",
    "generateMissingFormula(stem_model)\n",
    "\n",
    "rxn = Reaction(\"Biomass_stem_tx\")\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    if met in FA:\n",
    "        continue\n",
    "    rxn.add_metabolites({stem_model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "rxn.lower_bound = 0\n",
    "rxn.upper_bound = 1000\n",
    "stem_model.add_reaction(rxn)\n",
    "\n",
    "\n",
    "stem_model.reactions.GLC_tx.upper_bound = 0\n",
    "stem_model.reactions.GLC_tx.lower_bound = 0\n",
    "stem_model.reactions.Sucrose_tx.upper_bound = 1\n",
    "stem_model.reactions.Sucrose_tx.lower_bound = 1\n",
    "stem_model.reactions.Photon_tx.upper_bound = 0\n",
    "stem_model.reactions.Photon_tx.lower_bound = 0\n",
    "stem_model.reactions.Biomass_stem_tx.objective_coefficient=1\n",
    "\n",
    "flux_analysis.parsimonious.pfba(stem_model)\n",
    "print(\"Biomass flux =\"+str(stem_model.reactions.Biomass_stem_tx.flux))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "stem_model.reactions.Biomass_stem_tx.reaction"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run root"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra import flux_analysis\n",
    "root_model = model.copy()\n",
    "\n",
    "k = \"root\"\n",
    "RXN1 = Reaction(\"Fatty_acid_mix_\"+k)\n",
    "RXN2 = Reaction(\"Fatty_acid_ACP_\"+k)\n",
    "tot = 0\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    #print met\n",
    "    if met in FA:\n",
    "        RXN1.add_metabolites({root_model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "        RXN2.add_metabolites({root_model.metabolites.get_by_id(FACP[met]):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "        tot = tot+(float(df[df[\"Unnamed: 0\"]==met][k]))\n",
    "if tot==0:\n",
    "    RXN1.add_metabolites({root_model.metabolites.PALMITATE_p:-1})\n",
    "    RXN2.add_metabolites({root_model.metabolites.Palmitoyl_ACPs_p:-1})\n",
    "    tot = 1\n",
    "RXN1.add_metabolites({root_model.metabolites.Fatty_Acids_p:tot})\n",
    "RXN1.lower_bound = 0\n",
    "RXN1.upper_bound = 3000\n",
    "root_model.add_reaction(RXN1)\n",
    "    \n",
    "RXN2.add_metabolites({root_model.metabolites.Fatty_acyl_ACP_p:tot})\n",
    "RXN2.lower_bound = 0\n",
    "RXN2.upper_bound = 3000\n",
    "root_model.add_reaction(RXN2)\n",
    "\n",
    "\n",
    "generateMissingFormula(root_model)\n",
    "\n",
    "rxn = Reaction(\"Biomass_root_tx\")\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    if met in FA:\n",
    "        continue\n",
    "    rxn.add_metabolites({root_model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "rxn.lower_bound = 0\n",
    "rxn.upper_bound = 1000\n",
    "root_model.add_reaction(rxn)\n",
    "\n",
    "root_model.reactions.GLC_tx.upper_bound = 0\n",
    "root_model.reactions.GLC_tx.lower_bound = 0\n",
    "root_model.reactions.Sucrose_tx.upper_bound = 1\n",
    "root_model.reactions.Sucrose_tx.lower_bound = 1\n",
    "root_model.reactions.Photon_tx.upper_bound = 0\n",
    "root_model.reactions.Photon_tx.lower_bound = 0\n",
    "root_model.reactions.Biomass_root_tx.objective_coefficient=1\n",
    "flux_analysis.parsimonious.pfba(root_model)\n",
    "print(\"Biomass flux =\"+str(root_model.reactions.Biomass_root_tx.flux))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "stem_model.reactions.Biomass_stem_tx.reaction"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run seed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra import flux_analysis\n",
    "seed_model = model.copy()\n",
    "\n",
    "k = \"seed\"\n",
    "RXN1 = Reaction(\"Fatty_acid_mix_\"+k)\n",
    "RXN2 = Reaction(\"Fatty_acid_ACP_\"+k)\n",
    "tot = 0\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    #print met\n",
    "    if met in FA:\n",
    "        RXN1.add_metabolites({seed_model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "        RXN2.add_metabolites({seed_model.metabolites.get_by_id(FACP[met]):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "        tot = tot+(float(df[df[\"Unnamed: 0\"]==met][k]))\n",
    "if tot==0:\n",
    "    RXN1.add_metabolites({seed_model.metabolites.PALMITATE_p:-1})\n",
    "    RXN2.add_metabolites({seed_model.metabolites.Palmitoyl_ACPs_p:-1})\n",
    "    tot = 1\n",
    "RXN1.add_metabolites({seed_model.metabolites.Fatty_Acids_p:tot})\n",
    "RXN1.lower_bound = 0\n",
    "RXN1.upper_bound = 0\n",
    "seed_model.add_reaction(RXN1)\n",
    "    \n",
    "RXN2.add_metabolites({seed_model.metabolites.Fatty_acyl_ACP_p:tot})\n",
    "RXN2.lower_bound = 0\n",
    "RXN2.upper_bound = 0\n",
    "seed_model.add_reaction(RXN2)\n",
    "\n",
    "\n",
    "generateMissingFormula(seed_model)\n",
    "\n",
    "rxn = Reaction(\"Biomass_seed_tx\")\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    if met in FA:\n",
    "        continue\n",
    "    rxn.add_metabolites({seed_model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "rxn.lower_bound = 0\n",
    "rxn.upper_bound = 1000\n",
    "seed_model.add_reaction(rxn)\n",
    "\n",
    "seed_model.reactions.GLC_tx.upper_bound = 0\n",
    "seed_model.reactions.GLC_tx.lower_bound = 0\n",
    "seed_model.reactions.Sucrose_tx.upper_bound = 1\n",
    "seed_model.reactions.Sucrose_tx.lower_bound = 1\n",
    "seed_model.reactions.Photon_tx.upper_bound = 0\n",
    "seed_model.reactions.Photon_tx.lower_bound = 0\n",
    "seed_model.reactions.Biomass_seed_tx.objective_coefficient=1\n",
    "sol=flux_analysis.parsimonious.pfba(seed_model)\n",
    "print(\"Biomass flux =\"+str(seed_model.reactions.Biomass_seed_tx.flux))\n",
    "\n",
    "    \n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "seed_model.reactions.Biomass_seed_tx.reaction"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Generate diel leaf model\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "def generateMultiphaseModel(model,tags):\n",
    "    models=dict()\n",
    "    for i in range(0,len(tags)):\n",
    "        temp=model.copy()\n",
    "        for met in temp.metabolites:\n",
    "            met.id = met.id+str(i+1)\n",
    "            met.compartment = met.compartment+str(i+1)\n",
    "            met.name = met.name+\" \"+tags[i]\n",
    "        for rxn in temp.reactions:\n",
    "            rxn.id = rxn.id+str(i+1)\n",
    "            rxn.name = rxn.name+\" \"+tags[i]\n",
    "        if i==0:\n",
    "            modelOut = temp.copy()\n",
    "        else:\n",
    "            modelOut = modelOut+temp\n",
    "            for met in temp.metabolites:\n",
    "                if met.id not in modelOut.metabolites:\n",
    "                    met2 = met.copy()\n",
    "                    #print(met2.id)\n",
    "                    modelOut.add_metabolites(met2)\n",
    "        for comp in temp.compartments:\n",
    "            modelOut.compartments={str(comp):model.compartments[comp[0:len(comp)-1]]+\" \"+tags[i]}\n",
    "    return modelOut\n",
    "\n",
    "\n",
    "def addLinkers(model,baseMets,from_phase,to_phase,reversible=True):\n",
    "    from cobra.core import Reaction\n",
    "    for met in baseMets.keys():\n",
    "        baseMet = met\n",
    "    rxn = Reaction(baseMet+\"_linker\"+from_phase+to_phase)\n",
    "    rxn.name = rxn.id\n",
    "    baseMets = baseMets[baseMet]\n",
    "    for baseMetID in baseMets.keys():\n",
    "        met1 = model.metabolites.get_by_id(baseMetID+from_phase)\n",
    "        met2 = model.metabolites.get_by_id(baseMetID+to_phase)\n",
    "        rxn.add_metabolites({met1:-1*baseMets[baseMetID],met2:1*baseMets[baseMetID]})\n",
    "    rxn.upper_bound = 1000\n",
    "    if reversible:\n",
    "        rxn.lower_bound = -1000\n",
    "    else:\n",
    "        rxn.lower_bound = 0\n",
    "    model.add_reaction(rxn)\n",
    "    return model\n",
    "    \n",
    "\n",
    "def identifyFractionalMets(model):\n",
    "    import re\n",
    "    fractionMets=dict()\n",
    "    for rxn in model.reactions:\n",
    "        for met in rxn.metabolites.keys():\n",
    "            prefix=\"\"\n",
    "            a=re.search(\"^a{1,3}\",met.id)\n",
    "            anion=\"\"\n",
    "            if a:\n",
    "                anion=a.group(0)\n",
    "                prefix=anion\n",
    "            b=re.search(\"^b{1,3}\",met.id)\n",
    "            basic=\"\"\n",
    "            if b:\n",
    "                basic=b.group(0)\n",
    "                prefix=basic\n",
    "            if (not prefix == \"\"):\n",
    "                mainMet=model.metabolites.get_by_id(met.id[len(prefix):])\n",
    "                fractionMets[met.id]=mainMet.id\n",
    "                #fractionMets[met.id]=prefix\n",
    "    return fractionMets\n",
    "\n",
    "\n",
    "# def mergeCompartments(model,comp1,comp2):\n",
    "#     temp = model.copy()\n",
    "#     for met in model.metabolites:\n",
    "#         if met.compartment==comp2:\n",
    "#             M_orig = met.id.replace(comp2,comp1)\n",
    "#             if M_orig in model.metabolites:\n",
    "#                 M_orig = model.metabolites.get_by_id(M_orig)\n",
    "#                 for rxn in M_orig.reactions:\n",
    "#                     M2 = model.metabolites.get_by_id(M_orig.id)\n",
    "#                     coeff = rxn.metabolites[M_orig]\n",
    "#                     rxn.add_metabolites({M_orig:-1*coeff,M2:coeff})\n",
    "                    \n",
    "def addUpperAndLowerBoundsFromFile(model,filename):\n",
    "    import pandas as pd\n",
    "    df = pd.read_csv(filename,sep=\"\\t\")\n",
    "    \n",
    "    for rxn in df[\"reaction\"]:\n",
    "        rxn = model.reactions.get_by_id(str(rxn))\n",
    "        rxn.lower_bound = float(df[df[\"reaction\"]==rxn.id][\"lower-bound\"])\n",
    "        rxn.upper_bound = float(df[df[\"reaction\"]==rxn.id][\"upper-bound\"])\n",
    "    \n",
    "    return model\n",
    "\n",
    "\n",
    "def generateC4leafModel(model,constraintsFile):\n",
    "    tags = [\"mesophyll day\",\"mesophyll night\",\"bundlesheath day\",\"bundlesheath night\"]\n",
    "    C4_model = generateMultiphaseModel(model,tags)\n",
    "\n",
    "    mets1 = [\"STARCH_p\",\"MAL_v\",\"FUM_v\",\"CIT_v\",\"NITRATE_v\",\"SUCROSE_v\",\"GLC_v\",\"FRU_v\"]\n",
    "    for met in mets1:\n",
    "        if met == \"MAL_v\":\n",
    "            mets = {met:{\"MAL_v\":0.7,\"aMAL_v\":0.3}}\n",
    "        elif met == \"FUM_v\":\n",
    "            mets = {met:{\"FUM_v\":0.92,\"aFUM_v\":0.08}}\n",
    "        elif met == \"CIT_v\":\n",
    "            mets = {met:{\"CIT_v\":0.5,\"aCIT_v\":0.5}}\n",
    "        else:\n",
    "            mets = {met:{met:1}}\n",
    "        C4_model = addLinkers(C4_model,mets,\"1\",\"2\")\n",
    "        C4_model = addLinkers(C4_model,mets,\"3\",\"4\")\n",
    "\n",
    "    mets2 = [\"ASN_v\",\"GLT_v\",\"L_ALPHA_ALANINE_v\",\"LEU_v\",\"bHIS_v\",\"MET_v\",\"LYS_v\",\"THR_v\",\"VAL_v\",\"PHE_v\",\n",
    "            \"4_AMINO_BUTYRATE_v\",\"SER_v\",\"ARG_v\",\"GLN_v\",\"GLY_v\",\"L_ASPARTATE_v\",\"ILE_v\",\"PRO_v\",\"CYS_v\",\n",
    "            \"TRP_v\",\"TYR_v\"]\n",
    "    for met in mets2:\n",
    "        mets = {met:{met:1}}\n",
    "        C4_model = addLinkers(C4_model,mets,\"1\",\"2\",reversible=False)\n",
    "        C4_model = addLinkers(C4_model,mets,\"3\",\"4\",reversible=False)\n",
    "\n",
    "\n",
    "    mets3 = [\"MAL_c\",\"PYRUVATE_c\",\"ASN_c\",\"GLT_c\",\"L_ALPHA_ALANINE_c\",\"LEU_c\",\n",
    "            \"MET_c\",\"LYS_c\",\"HIS_c\",\"THR_c\",\"VAL_c\",\"PHE_c\",\"4_AMINO_BUTYRATE_c\",\"SER_c\",\"ARG_c\",\"GLN_c\",\n",
    "            \"GLY_c\",\"L_ASPARTATE_c\",\"ILE_c\",\"PRO_c\",\"CYS_c\",\"TRP_c\",\"TYR_c\",\"G3P_c\",\"GAP_c\",\"Pi_c\",\n",
    "            \"PHOSPHO_ENOL_PYRUVATE_c\"] #\"SUCROSE_c\",\"MALTOSE_p\",\n",
    "    for met in mets3:\n",
    "        if met==\"Pi_c\":\n",
    "            mets = {met:{\"Pi_c\":0.7,\"aPi_c\":0.3}}\n",
    "        else:\n",
    "            mets = {met:{met:1}}\n",
    "        C4_model = addLinkers(C4_model,mets,\"1\",\"3\")\n",
    "        C4_model = addLinkers(C4_model,mets,\"2\",\"4\")\n",
    "\n",
    "\n",
    "    C4_model = addUpperAndLowerBoundsFromFile(C4_model,constraintsFile)   \n",
    "\n",
    "    #Nitrate ratio day:night\n",
    "    met = Metabolite(\"Nitrate_pseudo\")\n",
    "    met.name = \"Nitrate_pseudo\"\n",
    "    met.compartment = \"f\"\n",
    "    met.charge = 0\n",
    "    for i in (1,3):\n",
    "        C4_model.reactions.get_by_id(str(\"Nitrate_tx\" + str(i))).add_metabolites({met : 2})\n",
    "    for i in (2,4):\n",
    "        C4_model.reactions.get_by_id(str(\"Nitrate_tx\" + str(i))).add_metabolites({met : -3})\n",
    "\n",
    "    #Rubisco oxygenase\n",
    "    for i in range(1,5):\n",
    "        met = Metabolite(\"Rubisco_pseudo\" + str(i))\n",
    "        met.name = \"Rubisco_pseudo\" + str(i)\n",
    "        met.compartment = \"f\"\n",
    "        met.charge = 0\n",
    "        C4_model.reactions.get_by_id(str(\"RIBULOSE_BISPHOSPHATE_CARBOXYLASE_RXN_p\" + str(i))).add_metabolites({met : 1})\n",
    "        C4_model.reactions.get_by_id(str(\"RXN_961_p\" + str(i))).add_metabolites({met : -20})\n",
    "\n",
    "\n",
    "    #Maintainence costs\n",
    "    for i in range(1,5):\n",
    "        C4_model.reactions.get_by_id(str(\"ATPase_tx\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"ATPase_tx\" + str(i))).lower_bound = 19.5\n",
    "        met = Metabolite(str(\"Maint_pseudo\" + str(i)))\n",
    "        met.name = str(\"Maint_pseudo\" + str(i))\n",
    "        met.compartment = \"f\"\n",
    "        met.charge = 0\n",
    "        C4_model.reactions.get_by_id(str(\"ATPase_tx\" + str(i))).add_metabolites({met : 1})\n",
    "        C4_model.reactions.get_by_id(str(\"NADPHoxc_tx\" + str(i))).add_metabolites({met : -3})\n",
    "        C4_model.reactions.get_by_id(str(\"NADPHoxm_tx\" + str(i))).add_metabolites({met : -3})\n",
    "        C4_model.reactions.get_by_id(str(\"NADPHoxp_tx\" + str(i))).add_metabolites({met : -3})\n",
    "\n",
    "\n",
    "\n",
    "    for i in range(3,5):\n",
    "        for met in model.metabolites:\n",
    "            if \"CARBON_DIOXIDE\" in met.id or \"OXYGEN_MOLECULE\" in met.id or \"Photon\" in met.id:\n",
    "                continue\n",
    "            if met.compartment == \"e\"+str(i):\n",
    "                rxn = Reaction(met.id+\"_e\"+str(i-2)+str(i))\n",
    "                rxn.add_metabolites({met:1,C4_model.metabolites.get_by_id(met.id.replace(met.compartment,\"e\"+str(i-2))):-1})\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "    met1 = Metabolite(\"X_Phloem_contribution_day\",name=\"Phloem output during the day\",compartment=\"b1\")\n",
    "    C4_model.reactions.get_by_id(\"Phloem_output_tx1\").remove_from_model()\n",
    "    C4_model.reactions.get_by_id(\"Phloem_output_tx3\").add_metabolites({met1:1})\n",
    "    met2 = Metabolite(\"X_Phloem_contribution_night\",name=\"Phloem output during at night\",compartment=\"b1\")\n",
    "    C4_model.reactions.get_by_id(\"Phloem_output_tx2\").remove_from_model()\n",
    "    C4_model.reactions.get_by_id(\"Phloem_output_tx4\").add_metabolites({met2:1})\n",
    "\n",
    "    rxn = Reaction(\"diel_biomass\")\n",
    "    rxn.add_metabolites({met1:-0.75,met2:-0.25})\n",
    "    rxn.lower_bound = 0\n",
    "    rxn.upper_bound = 1000\n",
    "    C4_model.add_reaction(rxn)\n",
    "    rxn.objective_coefficient=1\n",
    "    return C4_model\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "leaf_model_source = generateC4leafModel(model,\"Sorghum_Leaf_Constraints.txt\")\n",
    "\n",
    "leaf_model_source.reactions.Photon_tx1.upper_bound = 600\n",
    "leaf_model_source.reactions.Photon_tx3.upper_bound = 400\n",
    "\n",
    "sol = flux_analysis.parsimonious.pfba(leaf_model_source)\n",
    "print(\"Phloem output = \")\n",
    "print(leaf_model_source.reactions.diel_biomass.flux)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for i in range(1,5):\n",
    "    for rxn in [\"CO2_tx\",\"O2_tx\",\"PSII_RXN_p\",\"RIBULOSE_BISPHOSPHATE_CARBOXYLASE_RXN_p\",\n",
    "                \"PEPCARBOXYKIN_RXN_c\",\"1_PERIOD_1_PERIOD_1_PERIOD_39_RXN_m\",\"MALIC_NADP_RXN_p\",\n",
    "                \"MALIC_NADP_RXN_c\"]:\n",
    "        print(rxn+str(i)+\" flux = \"+str(sol.fluxes[rxn+str(i)]))\n",
    "    print(\"------\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "leaf_model = model.copy()\n",
    "\n",
    "\n",
    "k = \"leaf\"\n",
    "RXN1 = Reaction(\"Fatty_acid_mix_\"+k)\n",
    "RXN2 = Reaction(\"Fatty_acid_ACP_\"+k)\n",
    "tot = 0\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    #print met\n",
    "    if met in FA:\n",
    "        RXN1.add_metabolites({leaf_model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "        RXN2.add_metabolites({leaf_model.metabolites.get_by_id(FACP[met]):-1*float(df[df[\"Unnamed: 0\"]==met][k])})\n",
    "        tot = tot+(float(df[df[\"Unnamed: 0\"]==met][k]))\n",
    "if tot==0:\n",
    "    RXN1.add_metabolites({leaf_model.metabolites.PALMITATE_p:-1})\n",
    "    RXN2.add_metabolites({leaf_model.metabolites.Palmitoyl_ACPs_p:-1})\n",
    "    tot = 1\n",
    "RXN1.add_metabolites({leaf_model.metabolites.Fatty_Acids_p:tot})\n",
    "RXN1.lower_bound = 0\n",
    "RXN1.upper_bound = 0\n",
    "leaf_model.add_reaction(RXN1)\n",
    "    \n",
    "RXN2.add_metabolites({leaf_model.metabolites.Fatty_acyl_ACP_p:tot})\n",
    "RXN2.lower_bound = 0\n",
    "RXN2.upper_bound = 0\n",
    "leaf_model.add_reaction(RXN2)\n",
    "\n",
    "\n",
    "generateMissingFormula(leaf_model)\n",
    "\n",
    "rxn = Reaction(\"Biomass_leaf_tx\")\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    if met in FA:\n",
    "        continue\n",
    "    rxn.add_metabolites({leaf_model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][\"stem\"])})\n",
    "rxn.lower_bound = 0\n",
    "rxn.upper_bound = 1000\n",
    "leaf_model.add_reaction(rxn)\n",
    "\n",
    "leaf_model_sink = generateC4leafModel(leaf_model,\"Sorghum_Leaf_Constraints.txt\")\n",
    "\n",
    "\n",
    "met = Metabolite(\"X_Biomass_contribution_day\")\n",
    "leaf_model_sink.reactions.Biomass_leaf_tx1.add_metabolites({met:1})\n",
    "leaf_model_sink.reactions.Biomass_leaf_tx3.add_metabolites({met:1})\n",
    "leaf_model_sink.metabolites.X_Phloem_contribution_day.remove_from_model()\n",
    "leaf_model_sink.reactions.diel_biomass.add_metabolites({met:-0.75})\n",
    "\n",
    "met = Metabolite(\"X_Biomass_contribution_night\")\n",
    "leaf_model_sink.reactions.Biomass_leaf_tx2.add_metabolites({met:1})\n",
    "leaf_model_sink.reactions.Biomass_leaf_tx4.add_metabolites({met:1})\n",
    "leaf_model_sink.metabolites.X_Phloem_contribution_night.remove_from_model()\n",
    "leaf_model_sink.reactions.diel_biomass.add_metabolites({met:-0.25})\n",
    "\n",
    "leaf_model_sink.reactions.diel_biomass.objective_coefficient=1\n",
    "sol = flux_analysis.parsimonious.pfba(leaf_model_sink)\n",
    "print(\"Biomass accumulation = \")\n",
    "print(leaf_model_sink.reactions.diel_biomass.flux)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "leaf_model_sink.reactions.Biomass_leaf_tx4.reaction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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