3) configure models (cQuellen2024).ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "ad39e96e-12b4-491a-9e36-421e708cc1a4",
   "metadata": {
    "is_executing": true,
    "tags": []
   },
   "outputs": [],
   "source": [
    "import cobra\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "9f9d556b-3137-488a-ae0d-5ffee607245b",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cobrapy version 0.29.0\n",
      "pandas version 2.2.2\n"
     ]
    }
   ],
   "source": [
    "print('cobrapy version', cobra.__version__)\n",
    "print('pandas version', pd.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "e24f2c1f-c15f-4775-8331-4f9232e3a227",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Model does not contain SBML fbc package information.\n",
      "SBML package 'layout' not supported by cobrapy, information is not parsed\n",
      "SBML package 'render' not supported by cobrapy, information is not parsed\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_h_c \"h[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_h_e \"h[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_atp_c \"atp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glc_D_c \"glc-D[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_adp_c \"adp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_g6p_c \"g6p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_f6p_c \"f6p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fdp_c \"fdp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_h2o_c \"h2o[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pi_c \"pi[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dhap_c \"dhap[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_g3p_c \"g3p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_nad_c \"nad[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_13dpg_c \"13dpg[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_nadh_c \"nadh[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_nadph_c \"nadph[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_nadp_c \"nadp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3pg_c \"3pg[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2pg_c \"2pg[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pep_c \"pep[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pyr_c \"pyr[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_lac_L_c \"lac-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_amp_c \"amp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_mal_L_c \"mal-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_co2_c \"co2[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_accoa_c \"accoa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_actp_c \"actp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_coa_c \"coa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ac_c \"ac[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_q8_c \"q8[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_q8h2_c \"q8h2[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_for_c \"for[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_oaa_c \"oaa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cit_c \"cit[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acn_c \"acn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_icit_c \"icit[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_akg_c \"akg[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_succoa_c \"succoa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_suc_c \"suc[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fum_c \"fum[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glx_c \"glx[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gtp_c \"gtp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gdp_c \"gdp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hco3_c \"hco3[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_6pgl_c \"6pgl[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_6pgc_c \"6pgc[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ru5p_D_c \"ru5p-D[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_r5p_c \"r5p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_xu5p_D_c \"xu5p-D[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_s7p_c \"s7p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_e4p_c \"e4p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_o2_c \"o2[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_trdox_c \"trdox[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_trdrd_c \"trdrd[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_h2s_c \"h2s[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_so3_c \"so3[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glyc3p_c \"glyc3p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pro_L_c \"pro-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_1pyr5c_c \"1pyr5c[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_no3_c \"no3[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_no2_c \"no2[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_malcoa_c \"malcoa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ACP_c \"ACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acACP_c \"acACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_malACP_c \"malACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_actACP_c \"actACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_C140ACP_c \"C140ACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_C150ACP_c \"C150ACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_C160ACP_c \"C160ACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_C180ACP_c \"C180ACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_C161ACP_c \"C161ACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_C181ACP_c \"C181ACP[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_AGL3P_c \"AGL3P[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pa_EC_c \"pa-EC[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cdpdag_EC_c \"cdpdag-EC[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cmp_c \"cmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pgp_EC_c \"pgp-EC[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ser_L_c \"ser-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ps_EC_c \"ps-EC[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pg_EC_c \"pg-EC[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_prpp_c \"prpp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gln_L_c \"gln-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glu_L_c \"glu-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ppi_c \"ppi[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pram_c \"pram[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gly_c \"gly[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gar_c \"gar[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_10fthf_c \"10fthf[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fgam_c \"fgam[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_thf_c \"thf[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fpram_c \"fpram[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_air_c \"air[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5aizc_c \"5aizc[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_asp_L_c \"asp-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_25aics_c \"25aics[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aicar_c \"aicar[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fprica_c \"fprica[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_imp_c \"imp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dcamp_c \"dcamp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_xmp_c \"xmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gmp_c \"gmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dadp_c \"dadp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_datp_c \"datp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dgdp_c \"dgdp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dgtp_c \"dgtp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5caiz_c \"5caiz[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cdp_c \"cdp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dcdp_c \"dcdp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_udp_c \"udp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dudp_c \"dudp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dtdp_c \"dtdp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dttp_c \"dttp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dtmp_c \"dtmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dump_c \"dump[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_mlthf_c \"mlthf[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dhf_c \"dhf[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dutp_c \"dutp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dctp_c \"dctp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_nh3_c \"nh3[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ctp_c \"ctp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_orot_c \"orot[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_orot5p_c \"orot5p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_utp_c \"utp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ump_c \"ump[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dhor_S_c \"dhor-S[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cbasp_c \"cbasp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cbp_c \"cbp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ins_c \"ins[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hxan_c \"hxan[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_adn_c \"adn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ade_c \"ade[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_r1p_c \"r1p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gua_c \"gua[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dgmp_c \"dgmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dgsn_c \"dgsn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gsn_c \"gsn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_xtsn_c \"xtsn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_xan_c \"xan[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cytd_c \"cytd[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_uri_c \"uri[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ura_c \"ura[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_thymd_c \"thymd[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_val_L_c \"val-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3mob_c \"3mob[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ala_L_c \"ala-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ala_D_c \"ala-D[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_alac_S_c \"alac-S[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_23dhmb_c \"23dhmb[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4pasp_c \"4pasp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aspsa_c \"aspsa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_23dhdp_c \"23dhdp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_thdp_c \"thdp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sl2a6o_c \"sl2a6o[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sl26da_c \"sl26da[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_26dap_LL_c \"26dap-LL[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_26dap_M_c \"26dap-M[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_lys_L_c \"lys-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acglu_c \"acglu[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acorn_c \"acorn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_orn_c \"orn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acg5p_c \"acg5p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acg5sa_c \"acg5sa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_citr_L_c \"citr-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_argsuc_c \"argsuc[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_arg_L_c \"arg-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_asn_L_c \"asn-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hom_L_c \"hom-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_phom_c \"phom[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_thr_L_c \"thr-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2obut_c \"2obut[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2ahbut_c \"2ahbut[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_23dhmp_c \"23dhmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3mop_c \"3mop[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ile_L_c \"ile-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3c3hmp_c \"3c3hmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2ippm_c \"2ippm[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3c2hmp_c \"3c2hmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4mop_c \"4mop[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_leu_L_c \"leu-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3c4mop_c \"3c4mop[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glu5p_c \"glu5p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glu5sa_c \"glu5sa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3php_c \"3php[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pser_L_c \"pser-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_chor_c \"chor[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pphn_c \"pphn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_34hpp_c \"34hpp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_tyr_L_c \"tyr-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3ig3p_c \"3ig3p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_trp_L_c \"trp-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_anth_c \"anth[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pran_c \"pran[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2cpr5p_c \"2cpr5p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acser_c \"acser[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cys_L_c \"cys-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_phpyr_c \"phpyr[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_phe_L_c \"phe-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5mthf_c \"5mthf[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hcys_L_c \"hcys-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_met_L_c \"met-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cyst_L_c \"cyst-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_achms_c \"achms[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ahcys_c \"ahcys[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_amet_c \"amet[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_prbatp_c \"prbatp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_prbamp_c \"prbamp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_prfp_c \"prfp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_prlp_c \"prlp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_eig3p_c \"eig3p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_imacp_c \"imacp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hisp_c \"hisp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_histd_c \"histd[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_his_L_c \"his-L[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_man6p_c \"man6p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_man1p_c \"man1p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gdpman_c \"gdpman[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glyc_c \"glyc[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acgam1p_c \"acgam1p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_uacgam_c \"uacgam[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gam6p_c \"gam6p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gam1p_c \"gam1p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_g1p_c \"g1p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_udpg_c \"udpg[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ALAALA_c \"ALAALA[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glu_D_c \"glu-D[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_uaccg_c \"uaccg[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_uamr_c \"uamr[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pnto_R_c \"pnto-R[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4ppan_c \"4ppan[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4ppcys_c \"4ppcys[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pan4p_c \"pan4p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dpcoa_c \"dpcoa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_methf_c \"methf[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dnad_c \"dnad[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_nicrnt_c \"nicrnt[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ncam_c \"ncam[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_nac_c \"nac[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2dhp_c \"2dhp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pant_R_c \"pant-R[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ala_B_c \"ala-B[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_25drapp_c \"25drapp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5apru_c \"5apru[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5aprbu_c \"5aprbu[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_db4p_c \"db4p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4r5au_c \"4r5au[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dmlz_c \"dmlz[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ribflv_c \"ribflv[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fmn_c \"fmn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fad_c \"fad[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ahdt_c \"ahdt[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dhpmp_c \"dhpmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dhnpt_c \"dhnpt[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_6hmhpt_c \"6hmhpt[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4adcho_c \"4adcho[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4abz_c \"4abz[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_6hmhptpp_c \"6hmhptpp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dhpt_c \"dhpt[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2dda7p_c \"2dda7p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3dhq_c \"3dhq[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3dhsk_c \"3dhsk[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_skm_c \"skm[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_skm5p_c \"skm5p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_3psme_c \"3psme[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_tre6p_c \"tre6p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_tre_c \"tre[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_adpglc_c \"adpglc[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glycogen_c \"glycogen[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_suc6p_c \"suc6p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fru_c \"fru[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_f1p_c \"f1p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glc_D_e \"glc-D[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ac_e \"ac[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_co2_e \"co2[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_o2_e \"o2[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_h2o_e \"h2o[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_lac_L_e \"lac-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_so3_e \"so3[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_suc_e \"suc[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glu_L_e \"glu-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_nh3_e \"nh3[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pi_e \"pi[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gln_L_e \"gln-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_na_c \"na[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_na_e \"na[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ala_L_e \"ala-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_val_L_e \"val-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_lys_L_e \"lys-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cit_e \"cit[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_leu_L_e \"leu-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_tyr_L_e \"tyr-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_trp_L_e \"trp-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pro_L_e \"pro-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ile_L_e \"ile-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_met_L_e \"met-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ser_L_e \"ser-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_thr_L_e \"thr-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_arg_L_e \"arg-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PROTEIN_c \"PROTEIN[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_DNA_c \"DNA[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_RNA_c \"RNA[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PHOSPHOLIPID_c \"PHOSPHOLIPID[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PEPTIDOGLYCAN_c \"PEPTIDOGLYCAN[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ARABINOGALACTAN_c \"ARABINOGALACTAN[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_MYCOLICACID_c \"MYCOLICACID[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_damp_c \"damp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dcmp_c \"dcmp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_udpgal_c \"udpgal[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_udpara_c \"udpara[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_FREEMYCOLICACID_c \"FREEMYCOLICACID[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TMCM_c \"TMCM[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_TDCM_c \"TDCM[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PIT_c \"PIT[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_PIM_c \"PIM[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_lac_D_c \"lac-D[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_h2o2_c \"h2o2[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_malts_c \"malts[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fadh2_c \"fadh2[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_duri_c \"duri[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dcyt_c \"dcyt[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dad_2_c \"dad-2[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_trnaglu_c \"trnaglu[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glutrna_c \"glutrna[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glu1sa_c \"glu1sa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_5aop_c \"5aop[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ppbng_c \"ppbng[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hmbil_c \"hmbil[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_uppg3_c \"uppg3[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cpppg3_c \"cpppg3[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pppg9_c \"pppg9[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ppp9_c \"ppp9[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fe2_c \"fe2[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pheme_c \"pheme[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_frdp_c \"frdp[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hemeO_c \"hemeO[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ichor_c \"ichor[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2shchc_c \"2shchc[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sucbz_c \"sucbz[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sbzcoa_c \"sbzcoa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dhna_c \"dhna[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_2dmmq8_c \"2dmmq8[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acald_c \"acald[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_etoh_c \"etoh[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glyc_R_c \"glyc-R[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acgam6p_c \"acgam6p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_rib_D_c \"rib-D[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_xyl_D_c \"xyl-D[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gal_c \"gal[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gal1p_c \"gal1p[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glcn_c \"glcn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ppa_c \"ppa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4abut_c \"4abut[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sucsal_c \"sucsal[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_aps_c \"aps[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_paps_c \"paps[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pap_c \"pap[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_urea_c \"urea[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_kapa_c \"kapa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dann_c \"dann[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_dtbt_c \"dtbt[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_btn_c \"btn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_itn_c \"itn[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_itn_e \"itn[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_urea_e \"urea[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_no3_e \"no3[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_phe_L_e \"phe-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fru_e \"fru[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_man_e \"man[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_sucr_e \"sucr[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_tre_e \"tre[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_rib_D_e \"rib-D[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_xyl_D_e \"xyl-D[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ura_e \"ura[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_orn_e \"orn[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glcn_e \"glcn[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_4abut_e \"4abut[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ncam_e \"ncam[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_no2_e \"no2[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pant_R_e \"pant-R[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_btn_e \"btn[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glyc_e \"glyc[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_etoh_e \"etoh[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gal_e \"gal[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_glyc_R_e \"glyc-R[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ppa_e \"ppa[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_for_e \"for[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_lac_D_e \"lac-D[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_asn_L_e \"asn-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_asp_L_e \"asp-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gly_e \"gly[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_cys_L_e \"cys-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_his_L_e \"his-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ppi_e \"ppi[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pyr_e \"pyr[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_acgam_e \"acgam[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fe2_e \"fe2[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_fum_e \"fum[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_mal_L_e \"mal-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hom_L_e \"hom-L[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gam_e \"gam[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_gam_c \"gam[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ara_e \"ara[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_ara_c \"ara[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hcys_c \"hcys[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_hma_c \"hma[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pca_e \"pca[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_pca_c \"pca[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_m3cm_c \"m3cm[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_m2c5da_c \"m2c5da[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_m3oel_c \"m3oel[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_m3oa_c \"m3oa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_m3ocoa_c \"m3ocoa[c]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_malt_e \"malt[e]\">\n",
      "Use of FORMULA in the notes element is discouraged, use fbc:chemicalFormula instead: <Species M_malt_c \"malt[c]\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glk \"glk\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glk \"glk\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pgi \"pgi\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pgi \"pgi\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pfkA \"pfkA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pfkA \"pfkA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_fbp \"fbp\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_fbp \"fbp\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_fda \"fda\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_fda \"fda\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_tpiA \"tpiA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_tpiA \"tpiA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gapA \"gapA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gapA \"gapA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gapB \"gapB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gapB \"gapB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pgk \"pgk\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pgk \"pgk\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pgm \"pgm\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pgm \"pgm\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_eno \"eno\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_eno \"eno\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyk \"pyk\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyk \"pyk\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ldh \"ldh\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ldh \"ldh\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pps \"pps\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pps \"pps\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_mez \"mez\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_mez \"mez\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pta \"pta\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pta \"pta\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ackA \"ackA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ackA \"ackA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pqo \"pqo\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pqo \"pqo\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_fdhF \"fdhF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_fdhF \"fdhF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pdh \"pdh\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pdh \"pdh\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gltA \"gltA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gltA \"gltA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_acnA \"acnA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_acnA \"acnA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_acnB \"acnB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_acnB \"acnB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_icd \"icd\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_icd \"icd\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_odhA \"odhA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_odhA \"odhA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sucD \"sucD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_sucD \"sucD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sdhCAB \"sdhCAB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_sdhCAB \"sdhCAB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_fumC \"fumC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_fumC \"fumC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_mdh \"mdh\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_mdh \"mdh\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aceA \"aceA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aceA \"aceA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aceB \"aceB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aceB \"aceB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pckG \"pckG\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pckG \"pckG\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ppc \"ppc\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ppc \"ppc\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyc \"pyc\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyc \"pyc\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HCO3E \"HCO3E\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_HCO3E \"HCO3E\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_zwf \"zwf\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_zwf \"zwf\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_opcA \"opcA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_opcA \"opcA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gnd \"gnd\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gnd \"gnd\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_rpi \"rpi\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_rpi \"rpi\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_rpe \"rpe\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_rpe \"rpe\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_tkt_1 \"tkt_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_tkt_1 \"tkt_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_tal \"tal\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_tal \"tal\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_tkt_2 \"tkt_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_tkt_2 \"tkt_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cyto_bd_complex \"cyto-bd-complex\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cyto_bd_complex \"cyto-bd-complex\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ATPase \"ATPase\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ATPase \"ATPase\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ndh \"ndh\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ndh \"ndh\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_trxB \"trxB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_trxB \"trxB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cysI \"cysI\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cysI \"cysI\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ppnK \"ppnK\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ppnK \"ppnK\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_mqo \"mqo\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_mqo \"mqo\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_lldD \"lldD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_lldD \"lldD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glpD \"glpD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glpD \"glpD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_putA \"putA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_putA \"putA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_narGHIJ \"narGHIJ\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_narGHIJ \"narGHIJ\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_accDA \"accDA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_accDA \"accDA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_fas_IA_1 \"fas-IA_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_fas_IA_1 \"fas-IA_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_fas_IB_1 \"fas-IB_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_fas_IB_1 \"fas-IB_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_KAS14 \"KAS14\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_KAS14 \"KAS14\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FASC140 \"FASC140\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FASC140 \"FASC140\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FASC150 \"FASC150\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FASC150 \"FASC150\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FASC160 \"FASC160\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FASC160 \"FASC160\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FASC180 \"FASC180\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FASC180 \"FASC180\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FASC161 \"FASC161\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FASC161 \"FASC161\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FASC181 \"FASC181\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FASC181 \"FASC181\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gpsA \"gpsA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gpsA \"gpsA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pacs \"pacs\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pacs \"pacs\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_plsC \"plsC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_plsC \"plsC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pgsA2 \"pgsA2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pgsA2 \"pgsA2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cdsB \"cdsB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cdsB \"cdsB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_7_8_a \"r2_7_8_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_7_8_a \"r2_7_8_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_prsA \"prsA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_prsA \"prsA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purF \"purF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purF \"purF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purD \"purD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purD \"purD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purN \"purN\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purN \"purN\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purLQS \"purLQS\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purLQS \"purLQS\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purM \"purM\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purM \"purM\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purC \"purC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purC \"purC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purB_1 \"purB_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purB_1 \"purB_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purH_1 \"purH_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purH_1 \"purH_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purH_2 \"purH_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purH_2 \"purH_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purA \"purA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purA \"purA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purB_2 \"purB_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purB_2 \"purB_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_guaB1 \"guaB1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_guaB1 \"guaB1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_guaA \"guaA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_guaA \"guaA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ndk_2 \"ndk_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ndk_2 \"ndk_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gmk_1 \"gmk_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gmk_1 \"gmk_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ndk_1 \"ndk_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ndk_1 \"ndk_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ndk_3 \"ndk_3\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ndk_3 \"ndk_3\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purE \"purE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purE \"purE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_adk_1 \"adk_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_adk_1 \"adk_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nrdD_2 \"nrdD_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nrdD_2 \"nrdD_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_purK \"purK\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_purK \"purK\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nrdF_10 \"nrdF_10\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nrdF_10 \"nrdF_10\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nrdF_4 \"nrdF_4\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nrdF_4 \"nrdF_4\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ndk_12 \"ndk_12\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ndk_12 \"ndk_12\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_tmk \"tmk\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_tmk \"tmk\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_thyA \"thyA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_thyA \"thyA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dut \"dut\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dut \"dut\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ndk_6 \"ndk_6\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ndk_6 \"ndk_6\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dcd_2 \"dcd_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dcd_2 \"dcd_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ndk_5 \"ndk_5\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ndk_5 \"ndk_5\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ndk_11 \"ndk_11\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ndk_11 \"ndk_11\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrE_1 \"pyrE_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrE_1 \"pyrE_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrG_2gln \"pyrG_2gln\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrG_2gln \"pyrG_2gln\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ndk_10 \"ndk_10\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ndk_10 \"ndk_10\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrH \"pyrH\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrH \"pyrH\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrF \"pyrF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrF \"pyrF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrD \"pyrD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrD \"pyrD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrE_2 \"pyrE_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrE_2 \"pyrE_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrC \"pyrC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrC \"pyrC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrB \"pyrB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrB \"pyrB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_2 \"nucA_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_2 \"nucA_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_4_2_8_1 \"r2_4_2_8_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_4_2_8_1 \"r2_4_2_8_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r3_2_2_1_1 \"r3_2_2_1_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r3_2_2_1_1 \"r3_2_2_1_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r3_2_2_1_2 \"r3_2_2_1_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r3_2_2_1_2 \"r3_2_2_1_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_4_2_8_3 \"r2_4_2_8_3\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_4_2_8_3 \"r2_4_2_8_3\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_amn \"amn\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_amn \"amn\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_4_2_8_2 \"r2_4_2_8_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_4_2_8_2 \"r2_4_2_8_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_11 \"nucA_11\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_11 \"nucA_11\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r3_2_2_1_4 \"r3_2_2_1_4\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r3_2_2_1_4 \"r3_2_2_1_4\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_4 \"nucA_4\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_4 \"nucA_4\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r3_2_2_1_3 \"r3_2_2_1_3\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r3_2_2_1_3 \"r3_2_2_1_3\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_5 \"nucA_5\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_5 \"nucA_5\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_6 \"nucA_6\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_6 \"nucA_6\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cmk_2 \"cmk_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cmk_2 \"cmk_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrR \"pyrR\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrR \"pyrR\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_7 \"nucA_7\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_7 \"nucA_7\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gltBD \"gltBD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gltBD \"gltBD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gdh \"gdh\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gdh \"gdh\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glnA \"glnA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glnA \"glnA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NCgl0388 \"NCgl0388\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NCgl0388 \"NCgl0388\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_alr \"alr\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_alr \"alr\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvE_val \"ilvE_val\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvE_val \"ilvE_val\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvBN_val \"ilvBN_val\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvBN_val \"ilvBN_val\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvC_val \"ilvC_val\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvC_val \"ilvC_val\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvD_val \"ilvD_val\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvD_val \"ilvD_val\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aspB \"aspB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aspB \"aspB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_lysC \"lysC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_lysC \"lysC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_asd \"asd\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_asd \"asd\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dapA \"dapA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dapA \"dapA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dapB \"dapB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dapB \"dapB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dapD \"dapD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dapD \"dapD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dapC \"dapC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dapC \"dapC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dapE \"dapE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dapE \"dapE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dapF \"dapF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dapF \"dapF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ddh \"ddh\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ddh \"ddh\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_lysA \"lysA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_lysA \"lysA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_argR \"argR\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_argR \"argR\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_carA \"carA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_carA \"carA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_argJ \"argJ\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_argJ \"argJ\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_argB \"argB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_argB \"argB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_argC \"argC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_argC \"argC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_argD \"argD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_argD \"argD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_argF \"argF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_argF \"argF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_argH \"argH\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_argH \"argH\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_argG \"argG\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_argG \"argG\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NCgl2116 \"NCgl2116\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NCgl2116 \"NCgl2116\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ltsA \"ltsA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ltsA \"ltsA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_thrB \"thrB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_thrB \"thrB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_thrC \"thrC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_thrC \"thrC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvA_ile \"ilvA_ile\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvA_ile \"ilvA_ile\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvBN_ile \"ilvBN_ile\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvBN_ile \"ilvBN_ile\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvC_ile \"ilvC_ile\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvC_ile \"ilvC_ile\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvE_ile \"ilvE_ile\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvE_ile \"ilvE_ile\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvD_ile \"ilvD_ile\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvD_ile \"ilvD_ile\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_leuA \"leuA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_leuA \"leuA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_leuE \"leuE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_leuE \"leuE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_leuCD \"leuCD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_leuCD \"leuCD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ilvE \"ilvE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ilvE \"ilvE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_leuB \"leuB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_leuB \"leuB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_leuP \"leuP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_leuP \"leuP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_proB \"proB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_proB \"proB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_proA \"proA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_proA \"proA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_proC \"proC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_proC \"proC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_rGLUGSAL \"rGLUGSAL\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_rGLUGSAL \"rGLUGSAL\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_serA \"serA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_serA \"serA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_serB \"serB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_serB \"serB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_serC \"serC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_serC \"serC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sdaA \"sdaA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_sdaA \"sdaA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_csm \"csm\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_csm \"csm\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_tyrA \"tyrA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_tyrA \"tyrA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_6_1_57 \"r2_6_1_57\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_6_1_57 \"r2_6_1_57\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_trpB \"trpB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_trpB \"trpB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_trpEG \"trpEG\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_trpEG \"trpEG\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_trpD \"trpD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_trpD \"trpD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_trpC \"trpC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_trpC \"trpC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_trpA \"trpA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_trpA \"trpA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cysKM \"cysKM\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cysKM \"cysKM\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cysE \"cysE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cysE \"cysE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NCgl0215 \"NCgl0215\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NCgl0215 \"NCgl0215\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pheA \"pheA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pheA \"pheA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glyA \"glyA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glyA \"glyA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_metH \"metH\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_metH \"metH\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aecD \"aecD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aecD \"aecD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_metB \"metB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_metB \"metB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_metX \"metX\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_metX \"metX\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_metY \"metY\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_metY \"metY\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sahH \"sahH\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_sahH \"sahH\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_metK \"metK\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_metK \"metK\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hisG \"hisG\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hisG \"hisG\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hisI \"hisI\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hisI \"hisI\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hisE \"hisE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hisE \"hisE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hisA \"hisA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hisA \"hisA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hisFH \"hisFH\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hisFH \"hisFH\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hisB \"hisB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hisB \"hisB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hisC \"hisC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hisC \"hisC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hisN \"hisN\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hisN \"hisN\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hisD \"hisD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hisD \"hisD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_6_1_13 \"r2_6_1_13\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_6_1_13 \"r2_6_1_13\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_manA \"manA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_manA \"manA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pmmA \"pmmA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pmmA \"pmmA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_rmlA2 \"rmlA2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_rmlA2 \"rmlA2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glpK \"glpK\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glpK \"glpK\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glmU \"glmU\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glmU \"glmU\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glmS \"glmS\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glmS \"glmS\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pmmB_2 \"pmmB_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pmmB_2 \"pmmB_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_3_1_157 \"r2_3_1_157\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_3_1_157 \"r2_3_1_157\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_galU1 \"galU1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_galU1 \"galU1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dppt \"dppt\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dppt \"dppt\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ddl \"ddl\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ddl \"ddl\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_murI \"murI\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_murI \"murI\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_murB \"murB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_murB \"murB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_murA \"murA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_murA \"murA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_mt \"mt\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_mt \"mt\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_coaA \"coaA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_coaA \"coaA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PPNCL2 \"PPNCL2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PPNCL2 \"PPNCL2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PPCDC \"PPCDC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PPCDC \"PPCDC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_coaE \"coaE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_coaE \"coaE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_coaD \"coaD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_coaD \"coaD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MTHFR2 \"MTHFR2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_MTHFR2 \"MTHFR2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_folD2 \"folD2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_folD2 \"folD2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FTHFD \"FTHFD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FTHFD \"FTHFD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nadE \"nadE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nadE \"nadE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r6_3_5_1 \"r6_3_5_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r6_3_5_1 \"r6_3_5_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_7_7_18 \"r2_7_7_18\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_7_7_18 \"r2_7_7_18\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r3_5_1_19 \"r3_5_1_19\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r3_5_1_19 \"r3_5_1_19\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_4_2_11 \"r2_4_2_11\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_4_2_11 \"r2_4_2_11\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_panB \"panB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_panB \"panB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_panE \"panE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_panE \"panE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_panD \"panD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_panD \"panD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_panC \"panC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_panC \"panC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ribA \"ribA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ribA \"ribA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ribG \"ribG\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ribG \"ribG\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NCgl1535 \"NCgl1535\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NCgl1535 \"NCgl1535\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_rib_1 \"rib_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_rib_1 \"rib_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ribH \"ribH\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ribH \"ribH\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_rib_2 \"rib_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_rib_2 \"rib_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_rib_3 \"rib_3\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_rib_3 \"rib_3\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_rib_4 \"rib_4\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_rib_4 \"rib_4\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ribF \"ribF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ribF \"ribF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_folE \"folE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_folE \"folE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_phoB \"phoB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_phoB \"phoB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_folX \"folX\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_folX \"folX\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_folK \"folK\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_folK \"folK\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_folA \"folA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_folA \"folA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_folD1 \"folD1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_folD1 \"folD1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r6_3_5_8 \"r6_3_5_8\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r6_3_5_8 \"r6_3_5_8\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r4_1_3_58 \"r4_1_3_58\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r4_1_3_58 \"r4_1_3_58\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_sulI \"sulI\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_sulI \"sulI\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hom \"hom\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hom \"hom\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aroG \"aroG\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aroG \"aroG\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aroB \"aroB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aroB \"aroB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aroQ \"aroQ\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aroQ \"aroQ\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aroE \"aroE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aroE \"aroE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aroK \"aroK\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aroK \"aroK\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aroA \"aroA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aroA \"aroA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aroC \"aroC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aroC \"aroC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_otsB \"otsB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_otsB \"otsB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_otsA \"otsA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_otsA \"otsA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glgC \"glgC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glgC \"glgC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pmmB \"pmmB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pmmB \"pmmB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glgA \"glgA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glgA \"glgA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_scrB \"scrB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_scrB \"scrB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pfkB \"pfkB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pfkB \"pfkB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLC_t_PEP \"GLC_t_PEP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLC_t_PEP \"GLC_t_PEP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AC_d \"AC_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_AC_d \"AC_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CO2_d \"CO2_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_CO2_d \"CO2_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_O2_d \"O2_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_O2_d \"O2_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_H2O_d \"H2O_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LAC_L_d \"LAC-L_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LAC_L_d \"LAC-L_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_so3_d \"so3_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_so3_d \"so3_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUC_d \"SUC_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLU_d \"GLU_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NH3_t_H \"NH3_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NH3_t_H \"NH3_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PI_t_H \"PI_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PI_t_H \"PI_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLU_t_H \"GLU_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLU_t_H \"GLU_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLN_t_NA \"GLN_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLN_t_NA \"GLN_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALA_t_NA \"ALA_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ALA_t_NA \"ALA_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_VAL_t_NA \"VAL_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_VAL_t_NA \"VAL_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYS_t_H \"LYS_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LYS_t_H \"LYS_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CIT_t_H \"CIT_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LEU_t_NA \"LEU_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LEU_t_NA \"LEU_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TYR_t_ATP \"TYR_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_TYR_t_ATP \"TYR_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRP_t_ATP \"TRP_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_TRP_t_ATP \"TRP_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PRO_t_NA \"PRO_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PRO_t_NA \"PRO_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ILE_t_NA \"ILE_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ILE_t_NA \"ILE_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MET_t_ATP \"MET_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_MET_t_ATP \"MET_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SER_t_NA \"SER_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_SER_t_NA \"SER_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THR_t_H \"THR_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_THR_t_H \"THR_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARG_t_H \"ARG_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ARG_t_H \"ARG_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_biomass_a \"biomass_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_biomass_a \"biomass_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PROTEIN_a \"PROTEIN_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PROTEIN_a \"PROTEIN_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DNA_a \"DNA_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_DNA_a \"DNA_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RNA_a \"RNA_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_RNA_a \"RNA_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARBGALN_a \"ARBGALN_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ARBGALN_a \"ARBGALN_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PTDGLYN_a \"PTDGLYN_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PTDGLYN_a \"PTDGLYN_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FMYCAC_a \"FMYCAC_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FMYCAC_a \"FMYCAC_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MYCAC_a \"MYCAC_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_MYCAC_a \"MYCAC_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PLIP_a \"PLIP_a\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PLIP_a \"PLIP_a\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cmt \"cmt\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cmt \"cmt\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cmt_3 \"cmt_3\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cmt_3 \"cmt_3\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_fas_IA_MA \"fas-IA_MA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_fas_IA_MA \"fas-IA_MA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_7_8_b \"r2_7_8_b\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_7_8_b \"r2_7_8_b\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_7_8_c \"r2_7_8_c\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_7_8_c \"r2_7_8_c\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cdsA \"cdsA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cdsA \"cdsA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_odx \"odx\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_odx \"odx\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dld2 \"dld2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dld2 \"dld2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_bc1_aa3_complex \"bc1-aa3-complex\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_bc1_aa3_complex \"bc1-aa3-complex\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_katA \"katA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_katA \"katA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_putA1 \"putA1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_putA1 \"putA1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aspA \"aspA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aspA \"aspA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glgP1 \"glgP1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glgP1 \"glgP1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALA_B_deg \"ALA-B_deg\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ALA_B_deg \"ALA-B_deg\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aspn \"aspn\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aspn \"aspn\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_metF \"metF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_metF \"metF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ocd \"ocd\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ocd \"ocd\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_thyX \"thyX\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_thyX \"thyX\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pyrG_1 \"pyrG_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pyrG_1 \"pyrG_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dcd_1 \"dcd_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dcd_1 \"dcd_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_umk \"umk\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_umk \"umk\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_adk_2 \"adk_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_adk_2 \"adk_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cmk_3 \"cmk_3\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cmk_3 \"cmk_3\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gmk_2 \"gmk_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gmk_2 \"gmk_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nrdD_1 \"nrdD_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nrdD_1 \"nrdD_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_1 \"nucA_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_1 \"nucA_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_3 \"nucA_3\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_3 \"nucA_3\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_8 \"nucA_8\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_8 \"nucA_8\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_9 \"nucA_9\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_9 \"nucA_9\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nucA_10 \"nucA_10\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nucA_10 \"nucA_10\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ushA \"ushA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ushA \"ushA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r3_1_5_1 \"r3_1_5_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r3_1_5_1 \"r3_1_5_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NCgl0233_NCgl1244 \"NCgl0233_NCgl1244\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NCgl0233_NCgl1244 \"NCgl0233_NCgl1244\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hemA \"hemA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hemA \"hemA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hemL \"hemL\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hemL \"hemL\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hemB \"hemB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hemB \"hemB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hemC \"hemC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hemC \"hemC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hemD \"hemD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hemD \"hemD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hemE \"hemE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hemE \"hemE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hemN \"hemN\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hemN \"hemN\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hemG \"hemG\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hemG \"hemG\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_hemH \"hemH\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_hemH \"hemH\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ctaB \"ctaB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ctaB \"ctaB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_menF \"menF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_menF \"menF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_menD \"menD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_menD \"menD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_menC \"menC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_menC \"menC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_menE \"menE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_menE \"menE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_menB \"menB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_menB \"menB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_menA \"menA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_menA \"menA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_menG \"menG\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_menG \"menG\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_adhA \"adhA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_adhA \"adhA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_dhaS_1 \"dhaS_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_dhaS_1 \"dhaS_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_glxK \"glxK\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_glxK \"glxK\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nagA \"nagA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nagA \"nagA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_rbsK1 \"rbsK1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_rbsK1 \"rbsK1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PutARA \"PutARA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PutARA \"PutARA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_xylB \"xylB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_xylB \"xylB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_iolC \"iolC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_iolC \"iolC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_r2_7_1_6 \"r2_7_1_6\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_r2_7_1_6 \"r2_7_1_6\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_galE \"galE\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_galE \"galE\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gntK \"gntK\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gntK \"gntK\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_prpDBC \"prpDBC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_prpDBC \"prpDBC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALA_D_deg \"ALA-D_deg\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ALA_D_deg \"ALA-D_deg\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_msmA \"msmA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_msmA \"msmA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gabT \"gabT\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gabT \"gabT\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gabD2 \"gabD2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_gabD2 \"gabD2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cysND \"cysND\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cysND \"cysND\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cysH_1 \"cysH_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cysH_1 \"cysH_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cysC \"cysC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cysC \"cysC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cysH_2 \"cysH_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cysH_2 \"cysH_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_unk_34 \"unk_34\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_unk_34 \"unk_34\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ureA \"ureA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ureA \"ureA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_nagB \"nagB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_nagB \"nagB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_acpS \"acpS\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_acpS \"acpS\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_folC \"folC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_folC \"folC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_bioF \"bioF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_bioF \"bioF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_bioA \"bioA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_bioA \"bioA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_bioD \"bioD\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_bioD \"bioD\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_bioB \"bioB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_bioB \"bioB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_cadA \"cadA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_cadA \"cadA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ITN_d \"ITN_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UREA_d \"UREA_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_UREA_d \"UREA_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NO3_d \"NO3_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NO3_d \"NO3_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THR_d \"THR_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_THR_d \"THR_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHE_d \"PHE_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PHE_d \"PHE_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TYR_d \"TYR_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_TYR_d \"TYR_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ILE_d \"ILE_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ILE_d \"ILE_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NH3_d \"NH3_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NH3_d \"NH3_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FRU_t_PEP \"FRU_t_PEP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FRU_t_PEP \"FRU_t_PEP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAN_t_PEP \"MAN_t_PEP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_MAN_t_PEP \"MAN_t_PEP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUCR_t_PEP \"SUCR_t_PEP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_SUCR_t_PEP \"SUCR_t_PEP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_TRE_t_PEP \"TRE_t_PEP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_TRE_t_PEP \"TRE_t_PEP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PI_t_ATP \"PI_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PI_t_ATP \"PI_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLU_t_ATP \"GLU_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLU_t_ATP \"GLU_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_RIB_t_ATP \"RIB_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_RIB_t_ATP \"RIB_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_XYL_t_ATP \"XYL_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_XYL_t_ATP \"XYL_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_URA_t_ATP \"URA_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_URA_t_ATP \"URA_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NH3_t_ATP \"NH3_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NH3_t_ATP \"NH3_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_so3_t_ATP \"so3_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_so3_t_ATP \"so3_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLC_t_ATP \"GLC_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLC_t_ATP \"GLC_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THR_t_ATP \"THR_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_THR_t_ATP \"THR_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PHE_t_ATP \"PHE_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PHE_t_ATP \"PHE_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ILE_t_ATP \"ILE_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ILE_t_ATP \"ILE_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ORN_t_ATP \"ORN_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ORN_t_ATP \"ORN_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UREA_t_ATP \"UREA_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_UREA_t_ATP \"UREA_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NO3_t_H \"NO3_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NO3_t_H \"NO3_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLCN_t_H \"GLCN_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLCN_t_H \"GLCN_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GABA_t_H \"GABA_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GABA_t_H \"GABA_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_UREA_t_H \"UREA_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_UREA_t_H \"UREA_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_AC_t_H \"AC_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_AC_t_H \"AC_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NA_t_H \"NA_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NA_t_H \"NA_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PI_t_NA \"PI_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PI_t_NA \"PI_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLU_t_NA \"GLU_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLU_t_NA \"GLU_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_THR_t_NA \"THR_t_NA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_THR_t_NA \"THR_t_NA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NCAM_d \"NCAM_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NCAM_d \"NCAM_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_NO2_d \"NO2_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_NO2_d \"NO2_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MET_d \"MET_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_MET_d \"MET_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PANT_R_d \"PANT-R_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PANT_R_d \"PANT-R_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_BTN_d \"BTN_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_BTN_d \"BTN_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYS_t_ALA \"LYS_t_ALA\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LYS_t_ALA \"LYS_t_ALA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYS_t_VAL \"LYS_t_VAL\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LYS_t_VAL \"LYS_t_VAL\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYS_t_LEU \"LYS_t_LEU\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LYS_t_LEU \"LYS_t_LEU\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_VAL_d \"VAL_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_VAL_d \"VAL_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LEU_d \"LEU_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LEU_d \"LEU_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYC_d \"GLYC_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLYC_d \"GLYC_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ETOH_d \"ETOH_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ETOH_d \"ETOH_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LAC_L_t_H \"LAC-L_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LAC_L_t_H \"LAC-L_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GAL_d \"GAL_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GAL_d \"GAL_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLYC_R_d \"GLYC-R_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLYC_R_d \"GLYC-R_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PPA_t_H \"PPA_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PPA_t_H \"PPA_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FOR_t_H \"FOR_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FOR_t_H \"FOR_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LAC_D_t_H \"LAC-D_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LAC_D_t_H \"LAC-D_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASN_d \"ASN_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ASN_d \"ASN_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ASP_d \"ASP_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ASP_d \"ASP_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GLY_d \"GLY_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GLY_d \"GLY_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_CYS_d \"CYS_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_CYS_d \"CYS_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HIS_d \"HIS_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_HIS_d \"HIS_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PPI_d \"PPI_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PPI_d \"PPI_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PYR_d \"PYR_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PYR_d \"PYR_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FRU_d \"FRU_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FRU_d \"FRU_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACGAM_t_PEP \"ACGAM_t_PEP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ACGAM_t_PEP \"ACGAM_t_PEP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FE2_t_ATP \"FE2_t_ATP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FE2_t_ATP \"FE2_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FUM_t_H \"FUM_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_FUM_t_H \"FUM_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_t_H \"MAL_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_MAL_t_H \"MAL_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_SUC_t_H \"SUC_t_H\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_SUC_t_H \"SUC_t_H\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_HOM_d \"HOM_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_hom_L_e \"EX_hom_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ALA_d \"ALA_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MAL_d \"MAL_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_FUM_d \"FUM_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_pi_e \"EX_pi(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_4abut_e \"EX_4abut(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_ac_e \"EX_ac(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_acgam_e \"EX_acgam(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_ala_L_e \"EX_ala_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_arg_L_e \"EX_arg_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_asn_L_e \"EX_asn_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_asp_L_e \"EX_asp_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_cit_e \"EX_cit(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_co2_e \"EX_co2(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_cys_L_e \"EX_cys_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_etoh_e \"EX_etoh(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_fe2_e \"EX_fe2(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_for_e \"EX_for(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_fru_e \"EX_fru(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_fum_e \"EX_fum(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_gal_e \"EX_gal(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_glc_e \"EX_glc(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_glcn_e \"EX_glcn(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_gln_L_e \"EX_gln_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_glu_L_e \"EX_glu_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_gly_e \"EX_gly(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_glyc_e \"EX_glyc(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_h2o_e \"EX_h2o(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_his_L_e \"EX_his_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_ile_L_e \"EX_ile_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_lac_D_e \"EX_lac_D(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_lac_L_e \"EX_lac_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_leu_L_e \"EX_leu_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_lys_L_e \"EX_lys_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_mal_L_e \"EX_mal_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_man_e \"EX_man(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_met_L_e \"EX_met_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_na1_e \"EX_na1(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_nh3_e \"EX_nh3(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_no2_e \"EX_no2(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_no3_e \"EX_no3(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_o2_e \"EX_o2(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_orn_e \"EX_orn(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_phe_L_e \"EX_phe_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_ppi_e \"EX_ppi(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_pnto_R_e \"EX_pnto_R(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_pro_L_e \"EX_pro_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_pyr_e \"EX_pyr(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_rib_D_e \"EX_rib_D(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_ser_L_e \"EX_ser_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_so3_e \"EX_so3(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_suc_e \"EX_suc(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_sucr_e \"EX_sucr(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_thr_L_e \"EX_thr_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_tre_e \"EX_tre(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_trp_L_e \"EX_trp_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_tyr_L_e \"EX_tyr_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_ura_e \"EX_ura(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_urea_e \"EX_urea(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_val_L_e \"EX_val_L(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_xyl_D_e \"EX_xyl_D(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_ncam_e \"EX_ncam(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_btn_e \"EX_btn(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_ppa_e \"EX_ppa(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ACC_glycogen_c \"ACC_glycogen_c\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_itn_e \"EX_itn(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pi_buf \"pi_buf\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_combineComplexes \"combineComplexes\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_leakage \"leakage\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_slipe \"slipe\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GAM_d \"GAM_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_gam2gam6p \"gam2gam6p\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_GAM_t_PEP \"GAM_t_PEP\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_GAM_t_PEP \"GAM_t_PEP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_gam_e \"EX_gam(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_ara_e \"EX_ara(e)\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_ARA_d \"ARA_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_ARA_d \"ARA_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aradh \"aradh\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aradh \"aradh\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_LYS_d \"LYS_d\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_LYS_d \"LYS_d\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_thfC_1 \"thfC_1\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_thfC_1 \"thfC_1\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_actA \"actA\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_metB_2 \"metB_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_metB_2 \"metB_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_aecD_2 \"aecD_2\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_aecD_2 \"aecD_2\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_pca \"EX_pca\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pcaK \"pcaK\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pcaK \"pcaK\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pcaGH \"pcaGH\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pcaGH \"pcaGH\">\n",
      "Malformed gene_reaction_rule '(pcaG and pca H)' for (pcaG and pca H)\n",
      "Traceback (most recent call last):\n",
      "  File \"/home/jadebeck/base/lib/python3.12/site-packages/cobra/core/gene.py\", line 350, in from_string\n",
      "    tree = ast_parse(escaped_str, \"<string>\", \"eval\")\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.12/ast.py\", line 52, in parse\n",
      "    return compile(source, filename, mode, flags,\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"<string>\", line 1\n",
      "    (pcaG and pca H)\n",
      "     ^^^^^^^^^^^^^^\n",
      "SyntaxError: invalid syntax. Perhaps you forgot a comma?\n",
      "\n",
      "During handling of the above exception, another exception occurred:\n",
      "\n",
      "Traceback (most recent call last):\n",
      "  File \"/home/jadebeck/base/lib/python3.12/site-packages/cobra/core/gene.py\", line 365, in from_string\n",
      "    tree = ast_parse(escaped_str, \"<string>\", \"eval\")\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"/usr/lib/python3.12/ast.py\", line 52, in parse\n",
      "    return compile(source, filename, mode, flags,\n",
      "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
      "  File \"<string>\", line 1\n",
      "    (pcaG and pca H)\n",
      "     ^^^^^^^^^^^^^^\n",
      "SyntaxError: invalid syntax. Perhaps you forgot a comma?\n",
      "GPR will be empty\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pcaB \"pcaB\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pcaB \"pcaB\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pcaC \"pcaC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pcaC \"pcaC\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pcaL \"pcaL\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pcaL \"pcaL\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pcaIJ \"pcaIJ\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pcaIJ \"pcaIJ\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_pcaF \"pcaF\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_pcaF \"pcaF\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_coa \"EX_coa\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_malt \"EX_malt\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_MALT_t_ATP \"MALT_t_ATP\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_malQ \"malQ\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_DNA_b \"DNA_b\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_DNA_b \"DNA_b\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_PROTEIN_b \"PROTEIN_b\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_PROTEIN_b \"PROTEIN_b\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_C140 \"EX_C140\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_C150 \"EX_C150\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_C160 \"EX_C160\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_C180 \"EX_C180\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_C161 \"EX_C161\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_EX_C181 \"EX_C181\">\n",
      "Encoding LOWER_BOUND and UPPER_BOUND in KineticLaw is discouraged, use fbc:fluxBounds instead: <Reaction R_quiC \"quiC\">\n",
      "Use of GENE ASSOCIATION or GENE_ASSOCIATION in the notes element is discouraged, use fbc:gpr instead: <Reaction R_quiC \"quiC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glk \"glk\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pgi \"pgi\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pfkA \"pfkA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_fbp \"fbp\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_fda \"fda\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_tpiA \"tpiA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gapA \"gapA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gapB \"gapB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pgk \"pgk\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pgm \"pgm\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_eno \"eno\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyk \"pyk\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ldh \"ldh\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pps \"pps\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_mez \"mez\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pta \"pta\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ackA \"ackA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pqo \"pqo\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_fdhF \"fdhF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pdh \"pdh\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gltA \"gltA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_acnA \"acnA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_acnB \"acnB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_icd \"icd\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_odhA \"odhA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_sucD \"sucD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_sdhCAB \"sdhCAB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_fumC \"fumC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_mdh \"mdh\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aceA \"aceA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aceB \"aceB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pckG \"pckG\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ppc \"ppc\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyc \"pyc\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_HCO3E \"HCO3E\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_zwf \"zwf\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_opcA \"opcA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gnd \"gnd\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_rpi \"rpi\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_rpe \"rpe\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_tkt_1 \"tkt_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_tal \"tal\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_tkt_2 \"tkt_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cyto_bd_complex \"cyto-bd-complex\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ATPase \"ATPase\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ndh \"ndh\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_trxB \"trxB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cysI \"cysI\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ppnK \"ppnK\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_mqo \"mqo\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_lldD \"lldD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glpD \"glpD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_putA \"putA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_narGHIJ \"narGHIJ\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_accDA \"accDA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_fas_IA_1 \"fas-IA_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_fas_IB_1 \"fas-IB_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_KAS14 \"KAS14\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FASC140 \"FASC140\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FASC150 \"FASC150\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FASC160 \"FASC160\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FASC180 \"FASC180\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FASC161 \"FASC161\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FASC181 \"FASC181\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gpsA \"gpsA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pacs \"pacs\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_plsC \"plsC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pgsA2 \"pgsA2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cdsB \"cdsB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_7_8_a \"r2_7_8_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_prsA \"prsA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purF \"purF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purD \"purD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purN \"purN\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purLQS \"purLQS\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purM \"purM\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purC \"purC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purB_1 \"purB_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purH_1 \"purH_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purH_2 \"purH_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purA \"purA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purB_2 \"purB_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_guaB1 \"guaB1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_guaA \"guaA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ndk_2 \"ndk_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gmk_1 \"gmk_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ndk_1 \"ndk_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ndk_3 \"ndk_3\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purE \"purE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_adk_1 \"adk_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nrdD_2 \"nrdD_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_purK \"purK\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nrdF_10 \"nrdF_10\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nrdF_4 \"nrdF_4\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ndk_12 \"ndk_12\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_tmk \"tmk\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_thyA \"thyA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dut \"dut\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ndk_6 \"ndk_6\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dcd_2 \"dcd_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ndk_5 \"ndk_5\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ndk_11 \"ndk_11\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrE_1 \"pyrE_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrG_2gln \"pyrG_2gln\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ndk_10 \"ndk_10\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrH \"pyrH\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrF \"pyrF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrD \"pyrD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrE_2 \"pyrE_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrC \"pyrC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrB \"pyrB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_2 \"nucA_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_4_2_8_1 \"r2_4_2_8_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r3_2_2_1_1 \"r3_2_2_1_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r3_2_2_1_2 \"r3_2_2_1_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_4_2_8_3 \"r2_4_2_8_3\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_amn \"amn\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_4_2_8_2 \"r2_4_2_8_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_11 \"nucA_11\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r3_2_2_1_4 \"r3_2_2_1_4\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_4 \"nucA_4\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r3_2_2_1_3 \"r3_2_2_1_3\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_5 \"nucA_5\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_6 \"nucA_6\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cmk_2 \"cmk_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrR \"pyrR\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_7 \"nucA_7\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gltBD \"gltBD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gdh \"gdh\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glnA \"glnA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NCgl0388 \"NCgl0388\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_alr \"alr\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvE_val \"ilvE_val\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvBN_val \"ilvBN_val\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvC_val \"ilvC_val\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvD_val \"ilvD_val\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aspB \"aspB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_lysC \"lysC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_asd \"asd\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dapA \"dapA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dapB \"dapB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dapD \"dapD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dapC \"dapC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dapE \"dapE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dapF \"dapF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ddh \"ddh\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_lysA \"lysA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_argR \"argR\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_carA \"carA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_argJ \"argJ\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_argB \"argB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_argC \"argC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_argD \"argD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_argF \"argF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_argH \"argH\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_argG \"argG\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NCgl2116 \"NCgl2116\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ltsA \"ltsA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_thrB \"thrB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_thrC \"thrC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvA_ile \"ilvA_ile\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvBN_ile \"ilvBN_ile\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvC_ile \"ilvC_ile\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvE_ile \"ilvE_ile\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvD_ile \"ilvD_ile\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_leuA \"leuA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_leuE \"leuE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_leuCD \"leuCD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ilvE \"ilvE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_leuB \"leuB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_leuP \"leuP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_proB \"proB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_proA \"proA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_proC \"proC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_rGLUGSAL \"rGLUGSAL\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_serA \"serA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_serB \"serB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_serC \"serC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_sdaA \"sdaA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_csm \"csm\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_tyrA \"tyrA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_6_1_57 \"r2_6_1_57\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_trpB \"trpB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_trpEG \"trpEG\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_trpD \"trpD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_trpC \"trpC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_trpA \"trpA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cysKM \"cysKM\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cysE \"cysE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NCgl0215 \"NCgl0215\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pheA \"pheA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glyA \"glyA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_metH \"metH\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aecD \"aecD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_metB \"metB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_metX \"metX\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_metY \"metY\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_sahH \"sahH\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_metK \"metK\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hisG \"hisG\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hisI \"hisI\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hisE \"hisE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hisA \"hisA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hisFH \"hisFH\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hisB \"hisB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hisC \"hisC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hisN \"hisN\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hisD \"hisD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_6_1_13 \"r2_6_1_13\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_manA \"manA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pmmA \"pmmA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_rmlA2 \"rmlA2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glpK \"glpK\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glmU \"glmU\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glmS \"glmS\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pmmB_2 \"pmmB_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_3_1_157 \"r2_3_1_157\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_galU1 \"galU1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dppt \"dppt\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ddl \"ddl\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_murI \"murI\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_murB \"murB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_murA \"murA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_mt \"mt\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_coaA \"coaA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PPNCL2 \"PPNCL2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PPCDC \"PPCDC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_coaE \"coaE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_coaD \"coaD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_MTHFR2 \"MTHFR2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_folD2 \"folD2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FTHFD \"FTHFD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nadE \"nadE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r6_3_5_1 \"r6_3_5_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_7_7_18 \"r2_7_7_18\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r3_5_1_19 \"r3_5_1_19\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_4_2_11 \"r2_4_2_11\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_panB \"panB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_panE \"panE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_panD \"panD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_panC \"panC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ribA \"ribA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ribG \"ribG\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NCgl1535 \"NCgl1535\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_rib_1 \"rib_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ribH \"ribH\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_rib_2 \"rib_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_rib_3 \"rib_3\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_rib_4 \"rib_4\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ribF \"ribF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_folE \"folE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_phoB \"phoB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_folX \"folX\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_folK \"folK\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_folA \"folA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_folD1 \"folD1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r6_3_5_8 \"r6_3_5_8\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r4_1_3_58 \"r4_1_3_58\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_sulI \"sulI\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hom \"hom\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aroG \"aroG\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aroB \"aroB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aroQ \"aroQ\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aroE \"aroE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aroK \"aroK\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aroA \"aroA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aroC \"aroC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_otsB \"otsB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_otsA \"otsA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glgC \"glgC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pmmB \"pmmB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glgA \"glgA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_scrB \"scrB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pfkB \"pfkB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLC_t_PEP \"GLC_t_PEP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_AC_d \"AC_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_CO2_d \"CO2_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_O2_d \"O2_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_H2O_d \"H2O_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LAC_L_d \"LAC-L_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_so3_d \"so3_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_SUC_d \"SUC_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLU_d \"GLU_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NH3_t_H \"NH3_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PI_t_H \"PI_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLU_t_H \"GLU_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLN_t_NA \"GLN_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ALA_t_NA \"ALA_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_VAL_t_NA \"VAL_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LYS_t_H \"LYS_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_CIT_t_H \"CIT_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LEU_t_NA \"LEU_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_TYR_t_ATP \"TYR_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_TRP_t_ATP \"TRP_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PRO_t_NA \"PRO_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ILE_t_NA \"ILE_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_MET_t_ATP \"MET_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_SER_t_NA \"SER_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_THR_t_H \"THR_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ARG_t_H \"ARG_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_biomass_a \"biomass_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PROTEIN_a \"PROTEIN_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_DNA_a \"DNA_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_RNA_a \"RNA_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ARBGALN_a \"ARBGALN_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PTDGLYN_a \"PTDGLYN_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FMYCAC_a \"FMYCAC_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_MYCAC_a \"MYCAC_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PLIP_a \"PLIP_a\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cmt \"cmt\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cmt_3 \"cmt_3\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_fas_IA_MA \"fas-IA_MA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_7_8_b \"r2_7_8_b\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_7_8_c \"r2_7_8_c\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cdsA \"cdsA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_odx \"odx\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dld2 \"dld2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_bc1_aa3_complex \"bc1-aa3-complex\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_katA \"katA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_putA1 \"putA1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aspA \"aspA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glgP1 \"glgP1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ALA_B_deg \"ALA-B_deg\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aspn \"aspn\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_metF \"metF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ocd \"ocd\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_thyX \"thyX\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pyrG_1 \"pyrG_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dcd_1 \"dcd_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_umk \"umk\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_adk_2 \"adk_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cmk_3 \"cmk_3\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gmk_2 \"gmk_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nrdD_1 \"nrdD_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_1 \"nucA_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_3 \"nucA_3\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_8 \"nucA_8\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_9 \"nucA_9\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nucA_10 \"nucA_10\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ushA \"ushA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r3_1_5_1 \"r3_1_5_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NCgl0233_NCgl1244 \"NCgl0233_NCgl1244\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hemA \"hemA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hemL \"hemL\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hemB \"hemB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hemC \"hemC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hemD \"hemD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hemE \"hemE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hemN \"hemN\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hemG \"hemG\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_hemH \"hemH\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ctaB \"ctaB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_menF \"menF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_menD \"menD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_menC \"menC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_menE \"menE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_menB \"menB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_menA \"menA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_menG \"menG\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_adhA \"adhA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_dhaS_1 \"dhaS_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_glxK \"glxK\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nagA \"nagA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_rbsK1 \"rbsK1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PutARA \"PutARA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_xylB \"xylB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_iolC \"iolC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_r2_7_1_6 \"r2_7_1_6\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_galE \"galE\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gntK \"gntK\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_prpDBC \"prpDBC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ALA_D_deg \"ALA-D_deg\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_msmA \"msmA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gabT \"gabT\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gabD2 \"gabD2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cysND \"cysND\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cysH_1 \"cysH_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cysC \"cysC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cysH_2 \"cysH_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_unk_34 \"unk_34\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ureA \"ureA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_nagB \"nagB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_acpS \"acpS\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_folC \"folC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_bioF \"bioF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_bioA \"bioA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_bioD \"bioD\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_bioB \"bioB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_cadA \"cadA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ITN_d \"ITN_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_UREA_d \"UREA_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NO3_d \"NO3_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_THR_d \"THR_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PHE_d \"PHE_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_TYR_d \"TYR_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ILE_d \"ILE_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NH3_d \"NH3_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FRU_t_PEP \"FRU_t_PEP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_MAN_t_PEP \"MAN_t_PEP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_SUCR_t_PEP \"SUCR_t_PEP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_TRE_t_PEP \"TRE_t_PEP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PI_t_ATP \"PI_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLU_t_ATP \"GLU_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_RIB_t_ATP \"RIB_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_XYL_t_ATP \"XYL_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_URA_t_ATP \"URA_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NH3_t_ATP \"NH3_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_so3_t_ATP \"so3_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLC_t_ATP \"GLC_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_THR_t_ATP \"THR_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PHE_t_ATP \"PHE_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ILE_t_ATP \"ILE_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ORN_t_ATP \"ORN_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_UREA_t_ATP \"UREA_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NO3_t_H \"NO3_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLCN_t_H \"GLCN_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GABA_t_H \"GABA_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_UREA_t_H \"UREA_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_AC_t_H \"AC_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NA_t_H \"NA_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PI_t_NA \"PI_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLU_t_NA \"GLU_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_THR_t_NA \"THR_t_NA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NCAM_d \"NCAM_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_NO2_d \"NO2_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_MET_d \"MET_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PANT_R_d \"PANT-R_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_BTN_d \"BTN_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LYS_t_ALA \"LYS_t_ALA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LYS_t_VAL \"LYS_t_VAL\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LYS_t_LEU \"LYS_t_LEU\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_VAL_d \"VAL_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LEU_d \"LEU_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLYC_d \"GLYC_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ETOH_d \"ETOH_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LAC_L_t_H \"LAC-L_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GAL_d \"GAL_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLYC_R_d \"GLYC-R_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PPA_t_H \"PPA_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FOR_t_H \"FOR_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LAC_D_t_H \"LAC-D_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ASN_d \"ASN_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ASP_d \"ASP_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GLY_d \"GLY_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_CYS_d \"CYS_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_HIS_d \"HIS_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PPI_d \"PPI_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PYR_d \"PYR_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FRU_d \"FRU_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ACGAM_t_PEP \"ACGAM_t_PEP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FE2_t_ATP \"FE2_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FUM_t_H \"FUM_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_MAL_t_H \"MAL_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_SUC_t_H \"SUC_t_H\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_HOM_d \"HOM_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_hom_L_e \"EX_hom_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ALA_d \"ALA_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_MAL_d \"MAL_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_FUM_d \"FUM_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_pi_e \"EX_pi(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_4abut_e \"EX_4abut(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_ac_e \"EX_ac(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_acgam_e \"EX_acgam(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_ala_L_e \"EX_ala_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_arg_L_e \"EX_arg_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_asn_L_e \"EX_asn_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_asp_L_e \"EX_asp_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_cit_e \"EX_cit(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_co2_e \"EX_co2(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_cys_L_e \"EX_cys_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_etoh_e \"EX_etoh(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_fe2_e \"EX_fe2(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_for_e \"EX_for(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_fru_e \"EX_fru(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_fum_e \"EX_fum(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_gal_e \"EX_gal(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_glc_e \"EX_glc(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_glcn_e \"EX_glcn(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_gln_L_e \"EX_gln_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_glu_L_e \"EX_glu_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_gly_e \"EX_gly(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_glyc_e \"EX_glyc(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_h2o_e \"EX_h2o(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_his_L_e \"EX_his_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_ile_L_e \"EX_ile_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_lac_D_e \"EX_lac_D(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_lac_L_e \"EX_lac_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_leu_L_e \"EX_leu_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_lys_L_e \"EX_lys_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_mal_L_e \"EX_mal_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_man_e \"EX_man(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_met_L_e \"EX_met_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_na1_e \"EX_na1(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_nh3_e \"EX_nh3(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_no2_e \"EX_no2(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_no3_e \"EX_no3(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_o2_e \"EX_o2(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_orn_e \"EX_orn(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_phe_L_e \"EX_phe_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_ppi_e \"EX_ppi(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_pnto_R_e \"EX_pnto_R(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_pro_L_e \"EX_pro_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_pyr_e \"EX_pyr(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_rib_D_e \"EX_rib_D(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_ser_L_e \"EX_ser_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_so3_e \"EX_so3(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_suc_e \"EX_suc(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_sucr_e \"EX_sucr(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_thr_L_e \"EX_thr_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_tre_e \"EX_tre(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_trp_L_e \"EX_trp_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_tyr_L_e \"EX_tyr_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_ura_e \"EX_ura(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_urea_e \"EX_urea(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_val_L_e \"EX_val_L(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_xyl_D_e \"EX_xyl_D(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_ncam_e \"EX_ncam(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_btn_e \"EX_btn(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_ppa_e \"EX_ppa(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ACC_glycogen_c \"ACC_glycogen_c\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_itn_e \"EX_itn(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pi_buf \"pi_buf\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_combineComplexes \"combineComplexes\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_leakage \"leakage\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_slipe \"slipe\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GAM_d \"GAM_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_gam2gam6p \"gam2gam6p\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_GAM_t_PEP \"GAM_t_PEP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_gam_e \"EX_gam(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_ara_e \"EX_ara(e)\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_ARA_d \"ARA_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aradh \"aradh\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_LYS_d \"LYS_d\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_thfC_1 \"thfC_1\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_actA \"actA\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_metB_2 \"metB_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_aecD_2 \"aecD_2\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_pca \"EX_pca\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pcaK \"pcaK\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pcaGH \"pcaGH\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pcaB \"pcaB\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pcaC \"pcaC\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pcaL \"pcaL\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pcaIJ \"pcaIJ\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_pcaF \"pcaF\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_coa \"EX_coa\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_malt \"EX_malt\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_MALT_t_ATP \"MALT_t_ATP\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_malQ \"malQ\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_DNA_b \"DNA_b\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_PROTEIN_b \"PROTEIN_b\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_C140 \"EX_C140\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_C150 \"EX_C150\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_C160 \"EX_C160\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_C180 \"EX_C180\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_C161 \"EX_C161\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_EX_C181 \"EX_C181\">\n",
      "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead: <Reaction R_quiC \"quiC\">\n"
     ]
    }
   ],
   "source": [
    "original_model= cobra.io.read_sbml_model('models/iEZ481_2024.xml')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "3345dd9f-8a3f-4e6e-a7da-3ab96a944009",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Read LP format model from file /tmp/tmp376i76rh.lp\n",
      "Reading time = 0.00 seconds\n",
      ": 413 rows, 1116 columns, 4450 nonzeros\n"
     ]
    }
   ],
   "source": [
    "# reset model without having to parse xml\n",
    "model = original_model.copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "bbf852f6-0063-499e-96f4-6f519435d428",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "model.solver = 'glpk'\n",
    "# GLPK has trouble, try gurobi\n",
    "# model.solver = 'gurobi' "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8f804e2d-365a-4c47-b96f-cb14cbd0677f",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "type(model.solver)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "eec0173b-64b9-44e2-8533-24c0d9b2d95b",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Example setting boundaries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "667e67f4-d4b6-47cb-900b-f9b8137169c0",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# example getting reaction by id (note the lower case o)\n",
    "model.reactions.get_by_id(\"EX_o2_e\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "dd049e69-09f9-4923-97fb-ba436a758fdf",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "model.reactions.get_by_id(\"EX_o2_e\").lower_bound = -30"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "349351d3-5a20-425f-9bc3-a7ec95324434",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "model.reactions.get_by_id(\"EX_o2_e\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "01aaa052-815c-4b64-ab2f-1d3b0871447e",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Standard settings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e6d925dd-0269-4e2e-bf86-5e816934bbbb",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "## Manual translations\n",
    "ub = 0 # default ub\n",
    "lb = 0 # default lb\n",
    "\n",
    "# M=changeRxnBounds(M,'EX_o2_e',-30,'l');\n",
    "model.reactions.get_by_id(\"EX_o2_e\").lower_bound = -30\n",
    "# M=changeRxnBounds(M,'PI_t_NA',0,'b');\n",
    "model.reactions.get_by_id(\"PI_t_NA\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"PI_t_NA\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'PI_t_ATP',0,'b');\n",
    "model.reactions.get_by_id(\"PI_t_ATP\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"PI_t_ATP\").upper_bound = ub\n",
    "\n",
    "## Caution: The expressions below were translated from matlab by chatgpt. I asked chatgpt to comment the originals\n",
    "## above but they should be re-checked manually.\n",
    "# M=changeRxnBounds(M,'aceA',0,'b');\n",
    "model.reactions.get_by_id(\"aceA\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"aceA\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'aceB',0,'b');\n",
    "model.reactions.get_by_id(\"aceB\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"aceB\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'NH3_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"NH3_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"NH3_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'UREA_d',0,'b');\n",
    "model.reactions.get_by_id(\"UREA_d\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"UREA_d\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'UREA_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"UREA_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"UREA_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'SUC_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"SUC_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"SUC_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'FUM_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"FUM_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"FUM_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'MAL_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"MAL_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"MAL_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'NA_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"NA_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"NA_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'LAC_L_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"LAC_L_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"LAC_L_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'LYS_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"LYS_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"LYS_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'AC_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"AC_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"AC_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'NO3_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"NO3_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"NO3_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'GLU_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"GLU_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"GLU_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'THR_t_H',0,'b');\n",
    "model.reactions.get_by_id(\"THR_t_H\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"THR_t_H\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'nagB',0,'l');\n",
    "model.reactions.get_by_id(\"nagB\").lower_bound = lb\n",
    "\n",
    "# M=changeRxnBounds(M,'PPI_d',0,'b');\n",
    "model.reactions.get_by_id(\"PPI_d\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"PPI_d\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'tkt_1',0,'l');\n",
    "model.reactions.get_by_id(\"tkt_1\").lower_bound = lb\n",
    "\n",
    "# M=changeRxnBounds(M,'tkt_2',0,'l');\n",
    "model.reactions.get_by_id(\"tkt_2\").lower_bound = lb\n",
    "\n",
    "# M=changeRxnBounds(M,'tal',0,'l');\n",
    "model.reactions.get_by_id(\"tal\").lower_bound = lb\n",
    "\n",
    "# M=changeRxnBounds(M,'glgC',0,'b');\n",
    "model.reactions.get_by_id(\"glgC\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"glgC\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'CO2_d',0,'l');\n",
    "model.reactions.get_by_id(\"CO2_d\").lower_bound = lb\n",
    "\n",
    "# M=changeRxnBounds(M,'aspA',0,'l');\n",
    "model.reactions.get_by_id(\"aspA\").lower_bound = lb\n",
    "\n",
    "# M=changeRxnBounds(M,'aspB',0,'l');\n",
    "model.reactions.get_by_id(\"aspB\").lower_bound = lb\n",
    "\n",
    "# M=changeRxnBounds(M,'leakage',-50,'l');\n",
    "model.reactions.get_by_id(\"leakage\").lower_bound = -50\n",
    "\n",
    "# M=changeRxnBounds(M,'leakage',50,'u');\n",
    "model.reactions.get_by_id(\"leakage\").upper_bound = 50\n",
    "\n",
    "# M=changeRxnBounds(M,'folD2',-1,'l');\n",
    "model.reactions.get_by_id(\"folD2\").lower_bound = -1\n",
    "\n",
    "# M=changeRxnBounds(M,'metF',-1,'l');\n",
    "model.reactions.get_by_id(\"metF\").lower_bound = -1\n",
    "\n",
    "# M=changeRxnBounds(M,'folD2',1,'u');\n",
    "model.reactions.get_by_id(\"folD2\").upper_bound = 1\n",
    "\n",
    "# M=changeRxnBounds(M,'metF',1,'u');\n",
    "model.reactions.get_by_id(\"metF\").upper_bound = 1\n",
    "\n",
    "# M=changeRxnBounds(M,'pps',0,'b');\n",
    "model.reactions.get_by_id(\"pps\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"pps\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'glpD',0,'b');\n",
    "model.reactions.get_by_id(\"glpD\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"glpD\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'putA',0,'b');\n",
    "model.reactions.get_by_id(\"putA\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"putA\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'tpiA',-100,'l');\n",
    "model.reactions.get_by_id(\"tpiA\").lower_bound = -100\n",
    "\n",
    "# M=changeRxnBounds(M,'aceA',-100,'l');\n",
    "model.reactions.get_by_id(\"aceA\").lower_bound = -100\n",
    "\n",
    "# M=changeRxnBounds(M,'aceA',100,'u');\n",
    "model.reactions.get_by_id(\"aceA\").upper_bound = 100\n",
    "\n",
    "# M=changeRxnBounds(M,'aceB',100,'u');\n",
    "model.reactions.get_by_id(\"aceB\").upper_bound = 100\n",
    "\n",
    "# M=changeRxnBounds(M,'quiC',0,'b');\n",
    "model.reactions.get_by_id(\"quiC\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"quiC\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'PROTEIN_b',0,'b');\n",
    "model.reactions.get_by_id(\"PROTEIN_b\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"PROTEIN_b\").upper_bound = ub\n",
    "\n",
    "# M=changeRxnBounds(M,'DNA_a',0,'b');\n",
    "model.reactions.get_by_id(\"DNA_a\").lower_bound = lb\n",
    "model.reactions.get_by_id(\"DNA_a\").upper_bound = ub\n",
    "\n",
    "\n",
    "\n",
    "biomass_reaction = model.reactions.get_by_id('biomass_a')\n",
    "# Adjust stoichiometric coefficients of specific metabolites in the biomass reaction\n",
    "print('pre biomass_reaction')\n",
    "print(biomass_reaction)\n",
    "for metabolite in biomass_reaction.metabolites:\n",
    "    if metabolite.id == 'atp_c':\n",
    "        biomass_reaction.add_metabolites({metabolite: -(29.2 + 6.4)}, combine=False) # combine=False to replace old stoichiometric coefficients\n",
    "    elif metabolite.id == 'adp_c':\n",
    "        biomass_reaction.add_metabolites({metabolite: 29.2 + 6.4}, combine=False) # combine=False to replace old stoichiometric coefficients\n",
    "    elif metabolite.id == 'pi_c':\n",
    "        biomass_reaction.add_metabolites({metabolite: 29.2 + 6.4}, combine=False) # combine=False to replace old stoichiometric coefficients\n",
    "print('post biomass_reaction')\n",
    "print(biomass_reaction)\n",
    "\n",
    "# M=changeRxnBounds(M,'mt',0,'b'); % [1.08,1.8] nomineller Wert 1.4\n",
    "# [1.08, 1.8] nomineller wert 1.4\n",
    "# why is maintenance set to 0 in original cQuellen2024.m?\n",
    "model.reactions.get_by_id('mt').lower_bound = 0\n",
    "model.reactions.get_by_id('mt').upper_bound = 0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8e58730d-348d-46c5-a3ac-6b8442a0ca2c",
   "metadata": {},
   "source": [
    "# test PCA configuration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "db4d535e-ec8f-42b6-9bc4-8fce19cae849",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# Set the objective to glucose uptake and allow glucose uptake\n",
    "model_PCA = model.copy()\n",
    "model_PCA.solver = 'glpk' \n",
    "\n",
    "model_PCA.objective = 'EX_pca'\n",
    "model_PCA.objective.direction = \"max\"\n",
    "print('objective direction', model_PCA.objective.direction)\n",
    "print('objective expr', model_PCA.objective.expression)\n",
    "model_PCA.reactions.get_by_id('EX_glc_e').upper_bound = 0\n",
    "model_PCA.reactions.get_by_id('EX_glc_e').lower_bound = 0 \n",
    "model_PCA.reactions.get_by_id('EX_pca').lower_bound = -10 \n",
    "\n",
    "# Set the growth rate bounds on glucose + PCA as carbon source\n",
    "model_PCA.reactions.get_by_id('biomass_a').lower_bound = 0.1\n",
    "model_PCA.reactions.get_by_id('biomass_a').upper_bound = 0.1\n",
    "\n",
    "# Perform Flux Balance Analysis (FBA)\n",
    "print(model_PCA.reactions.biomass_a)\n",
    "# solution = cobra.flux_analysis.parsimonious.pfba(model_PCA)\n",
    "solution = model_PCA.optimize()\n",
    "print('For', model_PCA.objective)\n",
    "print('cobrapy found:', solution.objective_value, f'(~={-1.1007})') # -1.1007 is quickSolveFBA solution from matlab\n",
    "# Not storing this model, it was only a sanity check"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ec175a77-5448-4023-9dd4-28d45c7a0df3",
   "metadata": {},
   "source": [
    "# Read growth rate data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "35172211-fa41-46a2-90d6-3c60fa00496d",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "PCA-Gluc mu: 0.1557936152166388 +- 0.012774444510135584\n",
      "glucose-MOPS mu: 0.5829104732740061 +- 0.022196212314551926\n",
      "citrat-MOPS mu: 0.7229719008169772 +- 0.04890741496672533\n"
     ]
    }
   ],
   "source": [
    "all_mu = pd.read_csv('data/extracted_growth_rates_with_media.csv', index_col=0)\n",
    "method = \"area\"\n",
    "all_mu = all_mu[all_mu['method'].str.contains(method)]\n",
    "pca_gluc_mu = all_mu[all_mu['medium'] == \"PCA-Gluc\"].reset_index()\n",
    "gluc_mu = all_mu[all_mu['medium'] == \"Glucose-MOPS\"].reset_index()\n",
    "citr_mu = all_mu[all_mu['medium'] == \"Citrat-MOPS\"].reset_index()\n",
    "\n",
    "mean_pca_gluc_mu = float(pca_gluc_mu['mu'].mean())\n",
    "std_pca_gluc_mu = float(pca_gluc_mu['mu'].std())\n",
    "print('PCA-Gluc mu:', mean_pca_gluc_mu, '+-', std_pca_gluc_mu)\n",
    "\n",
    "mean_gluc_mu = float(gluc_mu['mu'].mean())\n",
    "std_gluc_mu = float(gluc_mu['mu'].std())\n",
    "print('glucose-MOPS mu:', mean_gluc_mu, '+-', std_gluc_mu)\n",
    "\n",
    "mean_citr_mu = float(citr_mu['mu'].mean())\n",
    "std_citr_mu = float(citr_mu['mu'].std())\n",
    "print('citrat-MOPS mu:', mean_citr_mu, '+-', std_citr_mu)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "cdde5a14-9eb1-4a4c-8862-d6a8265f598a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<Figure size 640x480 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from matplotlib import pyplot as plt\n",
    "pca_gluc_mu['mu'].hist(label='PCA-Gluc', density=True)\n",
    "gluc_mu['mu'].hist(label='glucose-MOPS', density=True)\n",
    "citr_mu['mu'].hist(label='citrat-MOPS', density=True)\n",
    "plt.legend()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "77008e3f-fe1d-4bba-923d-a59fbde39b47",
   "metadata": {
    "tags": []
   },
   "source": [
    "# create PCA-Gluc configuration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "00be610d-43bc-476e-ad2d-5bb30fa2b92e",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "objective direction max\n",
      "objective expr 1.0*EX_pca - 1.0*EX_pca_reverse_a20af\n",
      "For Maximize\n",
      "1.0*EX_pca - 1.0*EX_pca_reverse_a20af\n",
      "cobrapy found: -1.7148188304066478\n",
      "summary\n",
      "Objective\n",
      "=========\n",
      "1.0 EX_pca = -1.714818830406656\n",
      "\n",
      "Uptake\n",
      "------\n",
      "Metabolite Reaction   Flux  C-Number C-Flux\n",
      "     nh3_e EX_nh3_e  1.197         0  0.00%\n",
      "      o2_e  EX_o2_e  5.463         0  0.00%\n",
      "     pca_e   EX_pca  1.715         0  0.00%\n",
      "      pi_e  EX_pi_e 0.1277         0  0.00%\n",
      "     so3_e EX_so3_e 0.0187         0  0.00%\n",
      "       h_c  leakage    8.9         0  0.00%\n",
      "\n",
      "Secretion\n",
      "---------\n",
      "Metabolite Reaction   Flux  C-Number C-Flux\n",
      "     co2_e EX_co2_e -6.606         0  0.00%\n",
      "     h2o_e EX_h2o_e -10.67         0  0.00%\n"
     ]
    }
   ],
   "source": [
    "model_PCA_gluc = model.copy()\n",
    "model_PCA_gluc.solver = 'glpk' \n",
    "\n",
    "model_PCA_gluc.objective = 'EX_pca'\n",
    "model_PCA_gluc.objective.direction = \"max\"\n",
    "print('objective direction', model_PCA_gluc.objective.direction)\n",
    "print('objective expr', model_PCA_gluc.objective.expression)\n",
    "model_PCA_gluc.reactions.get_by_id('EX_glc_e').upper_bound = 0\n",
    "model_PCA_gluc.reactions.get_by_id('EX_glc_e').lower_bound = 0 \n",
    "\n",
    "# Guesstimate: with just PCA the cells take up  1.1 of PCA \n",
    "model_PCA_gluc.reactions.get_by_id('EX_pca').lower_bound = -30\n",
    "model_PCA_gluc.reactions.get_by_id('EX_pca').upper_bound = 0\n",
    "\n",
    "model_PCA_gluc.reactions.get_by_id('biomass_a').upper_bound = mean_pca_gluc_mu\n",
    "model_PCA_gluc.reactions.get_by_id('biomass_a').lower_bound = mean_pca_gluc_mu\n",
    "\n",
    "solution = model_PCA_gluc.optimize()\n",
    "print('For', model_PCA_gluc.objective)\n",
    "print('cobrapy found:', solution.objective_value)\n",
    "print(\"summary\")\n",
    "print(model_PCA_gluc.summary())\n",
    "model_PCA_gluc.reactions.get_by_id('biomass_a').upper_bound = 100\n",
    "model_PCA_gluc.reactions.get_by_id('biomass_a').lower_bound = 0\n",
    "cobra.io.write_sbml_model(model_PCA_gluc, \"models/iEZ481_PCA_Gluc.xml\")\n",
    "\n",
    "pca_uptake = solution.objective_value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "32694726-030f-45cf-bbab-01eb4a8ebfe2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-1.7148188304066478\n"
     ]
    }
   ],
   "source": [
    "print(solution.objective_value)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "abe1c1e9-6399-4ad8-9f7f-0ebd7a9ebe98",
   "metadata": {},
   "source": [
    "# create Glucose-MOPS configuration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "5b0a04f5-ae5a-4ca9-b595-c5f957e3ad0d",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "objective direction max\n",
      "objective expr 1.0*EX_glc_e - 1.0*EX_glc_e_reverse_6226d\n",
      "biomass_a: 0.095 ARABINOGALACTAN_c + 0.01 DNA_c + 0.102 MYCOLICACID_c + 0.095 PEPTIDOGLYCAN_c + 0.028 PHOSPHOLIPID_c + PROTEIN_c + 0.05 RNA_c + 35.6 atp_c --> 35.6 adp_c + 35.6 pi_c\n",
      "For Maximize\n",
      "1.0*EX_glc_e - 1.0*EX_glc_e_reverse_6226d\n",
      "cobrapy found: -3.796562996954184\n",
      "summary\n",
      "Objective\n",
      "=========\n",
      "1.0 EX_glc_e = -3.7965629969541745\n",
      "\n",
      "Uptake\n",
      "------\n",
      "Metabolite Reaction    Flux  C-Number C-Flux\n",
      "   glc_D_e EX_glc_e   3.797         0  0.00%\n",
      "     nh3_e EX_nh3_e   4.479         0  0.00%\n",
      "      o2_e  EX_o2_e   12.66         0  0.00%\n",
      "     pca_e   EX_pca   1.715         0  0.00%\n",
      "      pi_e  EX_pi_e  0.4778         0  0.00%\n",
      "     so3_e EX_so3_e 0.06995         0  0.00%\n",
      "       h_c  leakage   41.94         0  0.00%\n",
      "\n",
      "Secretion\n",
      "---------\n",
      "Metabolite Reaction   Flux  C-Number C-Flux\n",
      "     co2_e EX_co2_e -14.59         0  0.00%\n",
      "     h2o_e EX_h2o_e  -48.6         0  0.00%\n"
     ]
    }
   ],
   "source": [
    "# Guessed by FJ\n",
    "# Set the objective to glucose uptake and allow glucose uptake\n",
    "model_Glc = model.copy()\n",
    "model_Glc.solver = 'glpk' \n",
    "\n",
    "model_Glc.objective = 'EX_glc_e'\n",
    "model_Glc.objective.direction = \"max\"\n",
    "print('objective direction', model_Glc.objective.direction)\n",
    "print('objective expr', model_Glc.objective.expression)\n",
    "model_Glc.reactions.get_by_id('EX_glc_e').upper_bound = 0\n",
    "model_Glc.reactions.get_by_id('EX_glc_e').lower_bound = -30 \n",
    "# todo: check if we need pca\n",
    "model_Glc.reactions.get_by_id('EX_pca').lower_bound = pca_uptake \n",
    "model_Glc.reactions.get_by_id('EX_pca').upper_bound = pca_uptake \n",
    "\n",
    "# Wachstumsrate festsetzen auf mean\n",
    "model_Glc.reactions.get_by_id('biomass_a').lower_bound = mean_gluc_mu\n",
    "model_Glc.reactions.get_by_id('biomass_a').upper_bound = mean_gluc_mu\n",
    "\n",
    "# Perform Flux Balance Analysis (FBA)\n",
    "print(model_Glc.reactions.biomass_a)\n",
    "solution = model_Glc.optimize()\n",
    "print('For', model_Glc.objective)\n",
    "print('cobrapy found:', solution.objective_value)\n",
    "print(\"summary\")\n",
    "print(model_Glc.summary())\n",
    "model_Glc.reactions.get_by_id('biomass_a').lower_bound = 0\n",
    "model_Glc.reactions.get_by_id('biomass_a').upper_bound = 100\n",
    "cobra.io.write_sbml_model(model_Glc, \"models/iEZ481_Glucose-MOPS.xml\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "89830efc-83cf-41e1-9b66-20c0f2453fa1",
   "metadata": {},
   "source": [
    "# create Citrate-MOPS configuration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "da13edc5-24a9-4743-b487-a4c1108100b0",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "objective direction max\n",
      "objective expr 1.0*EX_cit_e - 1.0*EX_cit_e_reverse_0835e\n",
      "biomass_a: 0.095 ARABINOGALACTAN_c + 0.01 DNA_c + 0.102 MYCOLICACID_c + 0.095 PEPTIDOGLYCAN_c + 0.028 PHOSPHOLIPID_c + PROTEIN_c + 0.05 RNA_c + 35.6 atp_c --> 35.6 adp_c + 35.6 pi_c\n",
      "For Maximize\n",
      "1.0*EX_cit_e - 1.0*EX_cit_e_reverse_0835e\n",
      "cobrapy found: -7.447701141488194\n",
      "summary\n",
      "Objective\n",
      "=========\n",
      "1.0 EX_cit_e = -7.447701141488121\n",
      "\n",
      "Uptake\n",
      "------\n",
      "Metabolite Reaction    Flux  C-Number C-Flux\n",
      "     cit_e EX_cit_e   7.448         0  0.00%\n",
      "     nh3_e EX_nh3_e   5.556         0  0.00%\n",
      "      o2_e  EX_o2_e   18.29         0  0.00%\n",
      "     pca_e   EX_pca   1.715         0  0.00%\n",
      "      pi_e  EX_pi_e  0.5927         0  0.00%\n",
      "     so3_e EX_so3_e 0.08676         0  0.00%\n",
      "       h_c  leakage   46.12         0  0.00%\n",
      "\n",
      "Secretion\n",
      "---------\n",
      "Metabolite Reaction   Flux  C-Number C-Flux\n",
      "     co2_e EX_co2_e -31.64         0  0.00%\n",
      "     h2o_e EX_h2o_e -60.57         0  0.00%\n"
     ]
    }
   ],
   "source": [
    "# Guessed by FJ\n",
    "# Set the objective to glucose uptake and allow citrate uptake\n",
    "model_Citr = model.copy()\n",
    "model_Citr.solver = 'glpk' \n",
    "\n",
    "model_Citr.objective = 'EX_cit_e'\n",
    "model_Citr.objective.direction = \"max\"\n",
    "print('objective direction', model_Citr.objective.direction)\n",
    "print('objective expr', model_Citr.objective.expression)\n",
    "model_Citr.reactions.get_by_id('EX_glc_e').upper_bound = 0\n",
    "model_Citr.reactions.get_by_id('EX_glc_e').lower_bound = 0 \n",
    "model_Citr.reactions.get_by_id('EX_cit_e').upper_bound = 0\n",
    "model_Citr.reactions.get_by_id('EX_cit_e').lower_bound = -30 \n",
    "# todo: check if we need pca\n",
    "model_Citr.reactions.get_by_id('EX_pca').lower_bound = pca_uptake \n",
    "model_Citr.reactions.get_by_id('EX_pca').upper_bound = pca_uptake \n",
    "\n",
    "# Wachstumsrate festsetzen auf mean\n",
    "model_Citr.reactions.get_by_id('biomass_a').lower_bound = mean_citr_mu\n",
    "model_Citr.reactions.get_by_id('biomass_a').upper_bound = mean_citr_mu\n",
    "\n",
    "# Perform Flux Balance Analysis (FBA)\n",
    "print(model_Citr.reactions.biomass_a)\n",
    "solution = model_Citr.optimize()\n",
    "print('For', model_Citr.objective)\n",
    "print('cobrapy found:', solution.objective_value)\n",
    "print(\"summary\")\n",
    "print(model_Citr.summary())\n",
    "model_Citr.reactions.get_by_id('biomass_a').lower_bound = 0\n",
    "model_Citr.reactions.get_by_id('biomass_a').upper_bound = 100\n",
    "cobra.io.write_sbml_model(model_Citr, \"models/iEZ481_Citrat-MOPS.xml\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "addad39b-e53e-47ed-86d4-accf4bc89062",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f6164257-d969-45be-b255-3913f564b93e",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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