{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import cobra\n", "model = cobra.io.read_sbml_model('e_coli_core.xml')" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Namee_coli_core
Memory address0x021b1196a888
Number of metabolites72
Number of reactions95
Number of groups0
Objective expression1.0*BIOMASS_Ecoli_core_w_GAM - 1.0*BIOMASS_Ecoli_core_w_GAM_reverse_712e5
Compartmentsextracellular space, cytosol
" ], "text/plain": [ "" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "95\n", "72\n", "137\n" ] } ], "source": [ "print(len(model.reactions))\n", "print(len(model.metabolites))\n", "print(len(model.genes))" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Reaction identifierATPS4r
NameATP synthase (four protons for one ATP)
Memory address0x021b17ad6dc8
Stoichiometry\n", "

adp_c + 4.0 h_e + pi_c <=> atp_c + h2o_c + 3.0 h_c

\n", "

ADP C10H12N5O10P2 + 4.0 H+ + Phosphate <=> ATP C10H12N5O13P3 + H2O H2O + 3.0 H+

\n", "
GPR( ( b3736 and b3737 and b3738 ) and ( b3731 and b3732 and b3733 and b3734 and b3735 ) ) or ( ( b3...
Lower bound-1000.0
Upper bound1000.0
\n", " " ], "text/plain": [ "" ] }, "execution_count": 21, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model.reactions.ATPS4r" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Metabolites\n", " glc__D_e : C6H12O6\n", " gln__L_c : C5H10N2O3\n", " gln__L_e : C5H10N2O3\n", " glu__L_c : C5H8NO4\n", " glu__L_e : C5H8NO4\n", " glx_c : C2H1O3\n", " h2o_c : H2O\n", " h2o_e : H2O\n", " h_c : H\n", " h_e : H\n", " icit_c : C6H5O7\n", " lac__D_c : C3H5O3\n", " lac__D_e : C3H5O3\n", " mal__L_c : C4H4O5\n", " mal__L_e : C4H4O5\n", " nad_c : C21H26N7O14P2\n", " nadh_c : C21H27N7O14P2\n", " nadp_c : C21H25N7O17P3\n", " nadph_c : C21H26N7O17P3\n", " nh4_c : H4N\n", " 13dpg_c : C3H4O10P2\n", " nh4_e : H4N\n", " o2_c : O2\n", " 2pg_c : C3H4O7P\n", " o2_e : O2\n", " 3pg_c : C3H4O7P\n", " oaa_c : C4H2O5\n", " pep_c : C3H2O6P\n", " 6pgc_c : C6H10O10P\n", " pi_c : HO4P\n", " 6pgl_c : C6H9O9P\n", " pi_e : HO4P\n", " ac_c : C2H3O2\n", " pyr_c : C3H3O3\n", " pyr_e : C3H3O3\n", " q8_c : C49H74O4\n", " q8h2_c : C49H76O4\n", " r5p_c : C5H9O8P\n", "ru5p__D_c : C5H9O8P\n", " ac_e : C2H3O2\n", " acald_c : C2H4O\n", " s7p_c : C7H13O10P\n", " acald_e : C2H4O\n", " accoa_c : C23H34N7O17P3S\n", " succ_c : C4H4O4\n", " succ_e : C4H4O4\n", " succoa_c : C25H35N7O19P3S\n", " acon_C_c : C6H3O6\n", "xu5p__D_c : C5H9O8P\n", " actp_c : C2H3O5P\n", " adp_c : C10H12N5O10P2\n", " akg_c : C5H4O5\n", " akg_e : C5H4O5\n", " amp_c : C10H12N5O7P\n", " atp_c : C10H12N5O13P3\n", " cit_c : C6H5O7\n", " co2_c : CO2\n", " co2_e : CO2\n", " coa_c : C21H32N7O16P3S\n", " dhap_c : C3H5O6P\n", " e4p_c : C4H7O7P\n", " etoh_c : C2H6O\n", " etoh_e : C2H6O\n", " f6p_c : C6H11O9P\n", " fdp_c : C6H10O12P2\n", " for_c : CH1O2\n", " for_e : CH1O2\n", " fru_e : C6H12O6\n", " fum_c : C4H2O4\n", " fum_e : C4H2O4\n", " g3p_c : C3H5O6P\n", " g6p_c : C6H11O9P\n" ] } ], "source": [ "print(\"Metabolites\")\n", "for x in model.metabolites:\n", " print('%9s : %s' % (x.id, x.formula))" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Reactions\n", "PFK : atp_c + f6p_c --> adp_c + fdp_c + h_c\n", "PFL : coa_c + pyr_c --> accoa_c + for_c\n", "PGI : g6p_c <=> f6p_c\n", "PGK : 3pg_c + atp_c <=> 13dpg_c + adp_c\n", "PGL : 6pgl_c + h2o_c --> 6pgc_c + h_c\n", "ACALD : acald_c + coa_c + nad_c <=> accoa_c + h_c + nadh_c\n", "AKGt2r : akg_e + h_e <=> akg_c + h_c\n", "PGM : 2pg_c <=> 3pg_c\n", "PIt2r : h_e + pi_e <=> h_c + pi_c\n", "ALCD2x : etoh_c + nad_c <=> acald_c + h_c + nadh_c\n", "ACALDt : acald_e <=> acald_c\n", "ACKr : ac_c + atp_c <=> actp_c + adp_c\n", "PPC : co2_c + h2o_c + pep_c --> h_c + oaa_c + pi_c\n", "ACONTa : cit_c <=> acon_C_c + h2o_c\n", "ACONTb : acon_C_c + h2o_c <=> icit_c\n", "ATPM : atp_c + h2o_c --> adp_c + h_c + pi_c\n", "PPCK : atp_c + oaa_c --> adp_c + co2_c + pep_c\n", "ACt2r : ac_e + h_e <=> ac_c + h_c\n", "PPS : atp_c + h2o_c + pyr_c --> amp_c + 2.0 h_c + pep_c + pi_c\n", "ADK1 : amp_c + atp_c <=> 2.0 adp_c\n", "AKGDH : akg_c + coa_c + nad_c --> co2_c + nadh_c + succoa_c\n", "ATPS4r : adp_c + 4.0 h_e + pi_c <=> atp_c + h2o_c + 3.0 h_c\n", "PTAr : accoa_c + pi_c <=> actp_c + coa_c\n", "PYK : adp_c + h_c + pep_c --> atp_c + pyr_c\n", "BIOMASS_Ecoli_core_w_GAM : 1.496 3pg_c + 3.7478 accoa_c + 59.81 atp_c + 0.361 e4p_c + 0.0709 f6p_c + 0.129 g3p_c + 0.205 g6p_c + 0.2557 gln__L_c + 4.9414 glu__L_c + 59.81 h2o_c + 3.547 nad_c + 13.0279 nadph_c + 1.7867 oaa_c + 0.5191 pep_c + 2.8328 pyr_c + 0.8977 r5p_c --> 59.81 adp_c + 4.1182 akg_c + 3.7478 coa_c + 59.81 h_c + 3.547 nadh_c + 13.0279 nadp_c + 59.81 pi_c\n", "PYRt2 : h_e + pyr_e <=> h_c + pyr_c\n", "CO2t : co2_e <=> co2_c\n", "RPE : ru5p__D_c <=> xu5p__D_c\n", "CS : accoa_c + h2o_c + oaa_c --> cit_c + coa_c + h_c\n", "RPI : r5p_c <=> ru5p__D_c\n", "SUCCt2_2 : 2.0 h_e + succ_e --> 2.0 h_c + succ_c\n", "CYTBD : 2.0 h_c + 0.5 o2_c + q8h2_c --> h2o_c + 2.0 h_e + q8_c\n", "D_LACt2 : h_e + lac__D_e <=> h_c + lac__D_c\n", "ENO : 2pg_c <=> h2o_c + pep_c\n", "SUCCt3 : h_e + succ_c --> h_c + succ_e\n", "ETOHt2r : etoh_e + h_e <=> etoh_c + h_c\n", "SUCDi : q8_c + succ_c --> fum_c + q8h2_c\n", "SUCOAS : atp_c + coa_c + succ_c <=> adp_c + pi_c + succoa_c\n", "TALA : g3p_c + s7p_c <=> e4p_c + f6p_c\n", "THD2 : 2.0 h_e + nadh_c + nadp_c --> 2.0 h_c + nad_c + nadph_c\n", "TKT1 : r5p_c + xu5p__D_c <=> g3p_c + s7p_c\n", "TKT2 : e4p_c + xu5p__D_c <=> f6p_c + g3p_c\n", "TPI : dhap_c <=> g3p_c\n", "EX_ac_e : ac_e --> \n", "EX_acald_e : acald_e --> \n", "EX_akg_e : akg_e --> \n", "EX_co2_e : co2_e <=> \n", "EX_etoh_e : etoh_e --> \n", "EX_for_e : for_e --> \n", "EX_fru_e : fru_e --> \n", "EX_fum_e : fum_e --> \n", "EX_glc__D_e : glc__D_e <=> \n", "EX_gln__L_e : gln__L_e --> \n", "EX_glu__L_e : glu__L_e --> \n", "EX_h_e : h_e <=> \n", "EX_h2o_e : h2o_e <=> \n", "EX_lac__D_e : lac__D_e --> \n", "EX_mal__L_e : mal__L_e --> \n", "EX_nh4_e : nh4_e <=> \n", "EX_o2_e : o2_e <=> \n", "EX_pi_e : pi_e <=> \n", "EX_pyr_e : pyr_e --> \n", "EX_succ_e : succ_e --> \n", "FBA : fdp_c <=> dhap_c + g3p_c\n", "FBP : fdp_c + h2o_c --> f6p_c + pi_c\n", "FORt2 : for_e + h_e --> for_c + h_c\n", "FORt : for_e <-- for_c\n", "FRD7 : fum_c + q8h2_c --> q8_c + succ_c\n", "FRUpts2 : fru_e + pep_c --> f6p_c + pyr_c\n", "FUM : fum_c + h2o_c <=> mal__L_c\n", "FUMt2_2 : fum_e + 2.0 h_e --> fum_c + 2.0 h_c\n", "G6PDH2r : g6p_c + nadp_c <=> 6pgl_c + h_c + nadph_c\n", "GAPD : g3p_c + nad_c + pi_c <=> 13dpg_c + h_c + nadh_c\n", "GLCpts : glc__D_e + pep_c --> g6p_c + pyr_c\n", "GLNS : atp_c + glu__L_c + nh4_c --> adp_c + gln__L_c + h_c + pi_c\n", "GLNabc : atp_c + gln__L_e + h2o_c --> adp_c + gln__L_c + h_c + pi_c\n", "GLUDy : glu__L_c + h2o_c + nadp_c <=> akg_c + h_c + nadph_c + nh4_c\n", "GLUN : gln__L_c + h2o_c --> glu__L_c + nh4_c\n", "GLUSy : akg_c + gln__L_c + h_c + nadph_c --> 2.0 glu__L_c + nadp_c\n", "GLUt2r : glu__L_e + h_e <=> glu__L_c + h_c\n", "GND : 6pgc_c + nadp_c --> co2_c + nadph_c + ru5p__D_c\n", "H2Ot : h2o_e <=> h2o_c\n", "ICDHyr : icit_c + nadp_c <=> akg_c + co2_c + nadph_c\n", "ICL : icit_c --> glx_c + succ_c\n", "LDH_D : lac__D_c + nad_c <=> h_c + nadh_c + pyr_c\n", "MALS : accoa_c + glx_c + h2o_c --> coa_c + h_c + mal__L_c\n", "MALt2_2 : 2.0 h_e + mal__L_e --> 2.0 h_c + mal__L_c\n", "MDH : mal__L_c + nad_c <=> h_c + nadh_c + oaa_c\n", "ME1 : mal__L_c + nad_c --> co2_c + nadh_c + pyr_c\n", "ME2 : mal__L_c + nadp_c --> co2_c + nadph_c + pyr_c\n", "NADH16 : 4.0 h_c + nadh_c + q8_c --> 3.0 h_e + nad_c + q8h2_c\n", "NADTRHD : nad_c + nadph_c --> nadh_c + nadp_c\n", "NH4t : nh4_e <=> nh4_c\n", "O2t : o2_e <=> o2_c\n", "PDH : coa_c + nad_c + pyr_c --> accoa_c + co2_c + nadh_c\n" ] } ], "source": [ "print(\"Reactions\")\n", "for x in model.reactions:\n", " print(\"%s : %s\" % (x.id, x.reaction))" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "cobra.io.save_json_model(model, \"model.json\") #Para salvar o modelo em .json" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Metabolite identifierglx_c
NameGlyoxylate
Memory address0x021b179f8888
FormulaC2H1O3
Compartmentc
In 2 reaction(s)\n", " ICL, MALS
" ], "text/plain": [ "" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model.metabolites.glx_c" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/plain": [ "[,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ,\n", " ]" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model.metabolites" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "solution = model.optimize()\n", "print(solution)" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/html": [ "Optimal solution with objective value 0.507
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fluxesreduced_costs
PFK4.613985-1.387779e-17
PFL0.0000002.081668e-17
PGI3.2516890.000000e+00
PGK-9.7701036.938894e-18
PGL2.6443221.517883e-17
.........
NADH1624.2445570.000000e+00
NADTRHD0.000000-2.546243e-03
NH4t2.766001-1.387779e-17
O2t13.8267440.000000e+00
PDH5.857334-1.387779e-17
\n", "

95 rows × 2 columns

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" ], "text/plain": [ "" ] }, "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ "solution" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/plain": [ "PFK 7.477382\n", "PFL 0.000000\n", "PGI 4.860861\n", "PGK -16.023526\n", "PGL 4.959985\n", "ACALD 0.000000\n", "AKGt2r 0.000000\n", "PGM -14.716140\n", "PIt2r 3.214895\n", "ALCD2x 0.000000\n", "ACALDt 0.000000\n", "ACKr 0.000000\n", "PPC 2.504309\n", "ACONTa 6.007250\n", "ACONTb 6.007250\n", "ATPM 8.390000\n", "PPCK 0.000000\n", "ACt2r 0.000000\n", "PPS 0.000000\n", "ADK1 0.000000\n", "AKGDH 5.064376\n", "ATPS4r 45.514010\n", "PTAr 0.000000\n", "PYK 1.758177\n", "BIOMASS_Ecoli_core_w_GAM 0.873922\n", "PYRt2 0.000000\n", "CO2t -22.809833\n", "RPE 2.678482\n", "CS 6.007250\n", "RPI -2.281503\n", "SUCCt2_2 0.000000\n", "CYTBD 43.598985\n", "D_LACt2 0.000000\n", "ENO 14.716140\n", "SUCCt3 0.000000\n", "ETOHt2r 0.000000\n", "SUCDi 5.064376\n", "SUCOAS -5.064376\n", "TALA 1.496984\n", "THD2 0.000000\n", "TKT1 1.496984\n", "TKT2 1.181498\n", "TPI 7.477382\n", "EX_ac_e 0.000000\n", "EX_acald_e 0.000000\n", "EX_akg_e 0.000000\n", "EX_co2_e 22.809833\n", "EX_etoh_e 0.000000\n", "EX_for_e 0.000000\n", "EX_fru_e 0.000000\n", "EX_fum_e 0.000000\n", "EX_glc__D_e -10.000000\n", "EX_gln__L_e 0.000000\n", "EX_glu__L_e 0.000000\n", "EX_h_e 17.530865\n", "EX_h2o_e 29.175827\n", "EX_lac__D_e 0.000000\n", "EX_mal__L_e 0.000000\n", "EX_nh4_e -4.765319\n", "EX_o2_e -21.799493\n", "Name: fluxes, dtype: float64" ] }, "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], "source": [ "solution.fluxes[:60]" ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [], "source": [ "model.reactions.EX_o2_e.lower_bound = -20\n", "model.reactions.EX_glc__D_e.lower_bound = -6" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/plain": [ "PFK 4.613985\n", "PFL 0.000000\n", "PGI 3.251689\n", "PGK -9.770103\n", "PGL 2.644322\n", "ACALD 0.000000\n", "AKGt2r 0.000000\n", "PGM -9.011239\n", "PIt2r 1.866067\n", "ALCD2x 0.000000\n", "ACALDt 0.000000\n", "ACKr 0.000000\n", "PPC 1.453611\n", "ACONTa 3.956215\n", "ACONTb 3.956215\n", "ATPM 8.390000\n", "PPCK 0.000000\n", "ACt2r 0.000000\n", "PPS 0.000000\n", "ADK1 0.000000\n", "AKGDH 3.408930\n", "ATPS4r 28.999723\n", "PTAr 0.000000\n", "PYK 1.294307\n", "BIOMASS_Ecoli_core_w_GAM 0.507263\n", "PYRt2 0.000000\n", "CO2t -14.413190\n", "RPE 1.398261\n", "CS 3.956215\n", "RPI -1.246061\n", "SUCCt2_2 0.000000\n", "CYTBD 27.653487\n", "D_LACt2 0.000000\n", "ENO 9.011239\n", "SUCCt3 0.000000\n", "ETOHt2r 0.000000\n", "SUCDi 3.408930\n", "SUCOAS -3.408930\n", "TALA 0.790691\n", "THD2 0.000000\n", "TKT1 0.790691\n", "TKT2 0.607570\n", "TPI 4.613985\n", "EX_ac_e 0.000000\n", "EX_acald_e 0.000000\n", "EX_akg_e 0.000000\n", "EX_co2_e 14.413190\n", "EX_etoh_e 0.000000\n", "EX_for_e 0.000000\n", "EX_fru_e 0.000000\n", "EX_fum_e 0.000000\n", "EX_glc__D_e -6.000000\n", "EX_gln__L_e 0.000000\n", "EX_glu__L_e 0.000000\n", "EX_h_e 10.175686\n", "EX_h2o_e 18.108293\n", "EX_lac__D_e 0.000000\n", "EX_mal__L_e 0.000000\n", "EX_nh4_e -2.766001\n", "EX_o2_e -13.826744\n", "Name: fluxes, dtype: float64" ] }, "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [ "solution.fluxes[:60]" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [], "source": [ "model.objective = \"EX_ac_e\"" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "solution = model.optimize()\n", "print(solution)" ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/html": [ "
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IN_FLUXESOUT_FLUXESOBJECTIVES
IDFLUXIDFLUXIDFLUX
0o2_e6.0h_e24.0EX_ac_e12.0
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" ], "text/plain": [ "" ] }, "execution_count": 26, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model.summary()" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/plain": [ "PFK 6.000000e+00\n", "PFL 1.200000e+01\n", "PGI 6.000000e+00\n", "PGK -1.200000e+01\n", "PGL 0.000000e+00\n", "ACALD 0.000000e+00\n", "AKGt2r 0.000000e+00\n", "PGM -1.200000e+01\n", "PIt2r 1.508444e-15\n", "ALCD2x 0.000000e+00\n", "ACALDt 0.000000e+00\n", "ACKr -1.200000e+01\n", "PPC 0.000000e+00\n", "ACONTa 0.000000e+00\n", "ACONTb 2.355759e-15\n", "ATPM 8.390000e+00\n", "PPCK -8.427635e-15\n", "ACt2r -1.200000e+01\n", "PPS 0.000000e+00\n", "ADK1 0.000000e+00\n", "AKGDH 0.000000e+00\n", "ATPS4r 1.200000e+01\n", "PTAr 1.200000e+01\n", "PYK 6.000000e+00\n", "BIOMASS_Ecoli_core_w_GAM 0.000000e+00\n", "PYRt2 0.000000e+00\n", "CO2t -2.482468e-14\n", "RPE -2.957555e-16\n", "CS 0.000000e+00\n", "RPI -2.957555e-16\n", "SUCCt2_2 0.000000e+00\n", "CYTBD 1.200000e+01\n", "D_LACt2 0.000000e+00\n", "ENO 1.200000e+01\n", "SUCCt3 0.000000e+00\n", "ETOHt2r 0.000000e+00\n", "SUCDi 8.214922e-15\n", "SUCOAS 0.000000e+00\n", "TALA -8.717934e-17\n", "THD2 0.000000e+00\n", "TKT1 9.965175e-18\n", "TKT2 -2.200456e-16\n", "TPI 6.000000e+00\n", "EX_ac_e 1.200000e+01\n", "EX_acald_e 0.000000e+00\n", "EX_akg_e 0.000000e+00\n", "EX_co2_e 2.482468e-14\n", "EX_etoh_e 0.000000e+00\n", "EX_for_e 1.200000e+01\n", "EX_fru_e 0.000000e+00\n", "EX_fum_e 0.000000e+00\n", "EX_glc__D_e -6.000000e+00\n", "EX_gln__L_e 0.000000e+00\n", "EX_glu__L_e 0.000000e+00\n", "EX_h_e 2.400000e+01\n", "EX_h2o_e 1.074297e-13\n", "EX_lac__D_e 0.000000e+00\n", "EX_mal__L_e 0.000000e+00\n", "EX_nh4_e -2.495692e-15\n", "EX_o2_e -6.000000e+00\n", "Name: fluxes, dtype: float64" ] }, "execution_count": 27, "metadata": {}, "output_type": "execute_result" } ], "source": [ "solution.fluxes[:60]" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "model.add_reaction()\n", "model.add_metabolites()" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.4" } }, "nbformat": 4, "nbformat_minor": 4 }