view test-data/e_coli_core.xml @ 9:6a2871e89352 draft default tip

planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 537d7fefe58984b8f7ca66010153a2fdc35ddf4b
author tduigou
date Wed, 14 Feb 2024 15:25:38 +0000
parents 9b5947d48192
children
line wrap: on
line source

<?xml version='1.0' encoding='UTF-8'?>
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  <model fbc:strict="true" id="e_coli_core">
    <listOfUnitDefinitions>
      <unitDefinition id="mmol_per_gDW_per_hr">
        <listOfUnits>
          <unit kind="mole" scale="-3" multiplier="1" exponent="1"/>
          <unit kind="gram" scale="0" multiplier="1" exponent="-1"/>
          <unit kind="second" scale="0" multiplier="3600" exponent="-1"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
    <fbc:listOfObjectives fbc:activeObjective="obj">
      <fbc:objective fbc:id="obj" fbc:type="maximize">
        <fbc:listOfFluxObjectives>
          <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ecoli_core_w_GAM" fbc:coefficient="1"/>
        </fbc:listOfFluxObjectives>
      </fbc:objective>
    </fbc:listOfObjectives>
    <listOfParameters>
      <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
      <parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
      <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
      <parameter id="R_ATPM_lower_bound" value="8.39" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>
      <parameter id="R_EX_glc__D_e_lower_bound" value="-10" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>
    </listOfParameters>
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        </sbml:annotation>
        <listOfReactants>
          <speciesReference species="M_h_c" stoichiometry="4" constant="true"/>
          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="M_h_e" stoichiometry="3" constant="true"/>
          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <fbc:geneProductAssociation>
          <fbc:and>
            <fbc:geneProductRef fbc:geneProduct="G_b2276"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2277"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2278"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2279"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2280"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2281"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2282"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2283"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2284"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2285"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2286"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2287"/>
            <fbc:geneProductRef fbc:geneProduct="G_b2288"/>
          </fbc:and>
        </fbc:geneProductAssociation>
      </reaction>
      <reaction id="R_NADTRHD" fast="false" reversible="false" name="NAD transhydrogenase" metaid="R_NADTRHD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
            <rdf:Description rdf:about="#R_NADTRHD">
              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADTRHD"/>
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRNUTRANSHYDROGEN-RXN"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.3"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.2"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.1"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00112"/>
                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101898"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/11692"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/11695"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/11694"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/11693"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00083"/>
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              </bqbiol:is>
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          </rdf:RDF>
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        <listOfReactants>
          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <fbc:geneProductAssociation>
          <fbc:or>
            <fbc:geneProductRef fbc:geneProduct="G_b3962"/>
            <fbc:and>
              <fbc:geneProductRef fbc:geneProduct="G_b1602"/>
              <fbc:geneProductRef fbc:geneProduct="G_b1603"/>
            </fbc:and>
          </fbc:or>
        </fbc:geneProductAssociation>
      </reaction>
      <reaction id="R_NH4t" fast="false" reversible="true" name="Ammonia reversible transport" metaid="R_NH4t" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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            <rdf:Description rdf:about="#R_NH4t">
              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NH4t"/>
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-206"/>
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9615"/>
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-544"/>
                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101950"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-444416"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/28749"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/28748"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/28750"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/28747"/>
                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11683"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13364"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09835"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05466"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08987"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08986"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09736"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </sbml:annotation>
        <listOfReactants>
          <speciesReference species="M_nh4_e" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <fbc:geneProductAssociation>
          <fbc:or>
            <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
            <fbc:geneProductRef fbc:geneProduct="G_b0451"/>
          </fbc:or>
        </fbc:geneProductAssociation>
      </reaction>
      <reaction id="R_O2t" fast="false" reversible="true" name="O2 transport  diffusion " metaid="R_O2t" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
            <rdf:Description rdf:about="#R_O2t">
              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O2t"/>
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-474"/>
                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102090"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </sbml:annotation>
        <listOfReactants>
          <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <fbc:geneProductAssociation>
          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
        </fbc:geneProductAssociation>
      </reaction>
      <reaction id="R_PDH" fast="false" reversible="false" name="Pyruvate dehydrogenase" metaid="R_PDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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            <rdf:Description rdf:about="#R_PDH">
              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PDH"/>
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRUVDEH-RXN"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.4"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.51"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.4.1"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.12"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00209"/>
                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102425"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373177"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71397"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/28043"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/28045"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/28044"/>
                  <rdf:li rdf:resource="http://identifiers.org/rhea/28042"/>
                  <rdf:li rdf:resource="http://identifiers.org/sabiork/523"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00154"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </sbml:annotation>
        <listOfReactants>
          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <fbc:geneProductAssociation>
          <fbc:and>
            <fbc:geneProductRef fbc:geneProduct="G_b0114"/>
            <fbc:geneProductRef fbc:geneProduct="G_b0115"/>
            <fbc:geneProductRef fbc:geneProduct="G_b0116"/>
          </fbc:and>
        </fbc:geneProductAssociation>
      </reaction>
    </listOfReactions>
  </model>
</sbml>