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ToyCon.xml
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ToyCon.xml
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<?xml version='1.0' encoding='UTF-8'?>
<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" sboTerm="SBO:0000624" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false">
<model fbc:strict="true" id="ToyCon">
<listOfUnitDefinitions>
<unitDefinition id="mmol_per_gDW_per_hr">
<listOfUnits>
<unit exponent="1" kind="mole" multiplier="1" scale="-3"/>
<unit exponent="-1" kind="gram" multiplier="1" scale="0"/>
<unit exponent="-1" kind="second" multiplier="3600" scale="0"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<fbc:listOfObjectives fbc:activeObjective="obj">
<fbc:objective fbc:id="obj" fbc:type="maximize">
<fbc:listOfFluxObjectives>
<fbc:fluxObjective fbc:reaction="R_R4" fbc:coefficient="1"/>
</fbc:listOfFluxObjectives>
</fbc:objective>
</fbc:listOfObjectives>
<listOfParameters>
<parameter constant="true" id="cobra_default_lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-1000"/>
<parameter constant="true" id="cobra_default_ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="1000"/>
<parameter constant="true" id="cobra_0_bound" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="0"/>
<parameter constant="true" id="R_E1_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="-1"/>
</listOfParameters>
<listOfCompartments/>
<listOfSpecies>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m04c" name="glucose" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m07c" name="lactate" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m08c" name="02" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m06c" name="H20" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m03c" name="CO2" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m01c" name="ADP" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m09c" name="Pi" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m02c" name="ATP" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m05c" name="H" compartment="c"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_m05m" name="H" compartment="m"/>
</listOfSpecies>
<fbc:listOfGeneProducts>
<fbc:geneProduct fbc:id="G_HK" fbc:label="HK" fbc:name="HK"/>
<fbc:geneProduct fbc:id="G_LDH" fbc:label="LDH" fbc:name="LDH"/>
<fbc:geneProduct fbc:id="G_ETC" fbc:label="ETC" fbc:name="ETC"/>
<fbc:geneProduct fbc:id="G_AQP" fbc:label="AQP" fbc:name="AQP"/>
<fbc:geneProduct fbc:id="G_CO2" fbc:label="CO2" fbc:name="CO2"/>
<fbc:geneProduct fbc:id="G_PFK" fbc:label="PFK" fbc:name="PFK"/>
<fbc:geneProduct fbc:id="G_PDH" fbc:label="PDH" fbc:name="PDH"/>
<fbc:geneProduct fbc:id="G_ATPV" fbc:label="ATPV" fbc:name="ATPV"/>
<fbc:geneProduct fbc:id="G_MYH2" fbc:label="MYH2" fbc:name="MYH2"/>
</fbc:listOfGeneProducts>
<listOfReactions>
<reaction fast="false" id="R_E1" reversible="true" name="glucose exchange" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="R_E1_lower_bound">
<listOfReactants>
<speciesReference constant="true" species="M_m04c" stoichiometry="1"/>
</listOfReactants>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_HK"/>
</fbc:geneProductAssociation>
</reaction>
<reaction fast="false" id="R_E2" reversible="false" name="lactate exchange" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_m07c" stoichiometry="1"/>
</listOfReactants>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_LDH"/>
</fbc:geneProductAssociation>
</reaction>
<reaction fast="false" id="R_E3" reversible="true" name="O2 exchange" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_m08c" stoichiometry="1"/>
</listOfReactants>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_ETC"/>
</fbc:geneProductAssociation>
</reaction>
<reaction fast="false" id="R_E4" reversible="true" name="H20 exchange" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_m06c" stoichiometry="1"/>
</listOfReactants>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_AQP"/>
</fbc:geneProductAssociation>
</reaction>
<reaction fast="false" id="R_E5" reversible="true" name="CO2 exchange" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
<listOfReactants>
<speciesReference constant="true" species="M_m03c" stoichiometry="1"/>
</listOfReactants>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_CO2"/>
</fbc:geneProductAssociation>
</reaction>
<reaction fast="false" id="R_R1" reversible="false" name="glycolysis" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_m01c" stoichiometry="2"/>
<speciesReference constant="true" species="M_m04c" stoichiometry="1"/>
<speciesReference constant="true" species="M_m09c" stoichiometry="2"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_m02c" stoichiometry="2"/>
<speciesReference constant="true" species="M_m06c" stoichiometry="2"/>
<speciesReference constant="true" species="M_m07c" stoichiometry="2"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_PFK"/>
</fbc:geneProductAssociation>
</reaction>
<reaction fast="false" id="R_R2" reversible="false" name="respiration" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_m01c" stoichiometry="1"/>
<speciesReference constant="true" species="M_m05m" stoichiometry="56"/>
<speciesReference constant="true" species="M_m07c" stoichiometry="1"/>
<speciesReference constant="true" species="M_m08c" stoichiometry="3"/>
<speciesReference constant="true" species="M_m09c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_m02c" stoichiometry="1"/>
<speciesReference constant="true" species="M_m03c" stoichiometry="3"/>
<speciesReference constant="true" species="M_m05c" stoichiometry="56"/>
<speciesReference constant="true" species="M_m06c" stoichiometry="4"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_PDH"/>
</fbc:geneProductAssociation>
</reaction>
<reaction fast="false" id="R_R3" reversible="false" name="ATP synthase" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_m01c" stoichiometry="1"/>
<speciesReference constant="true" species="M_m05c" stoichiometry="4"/>
<speciesReference constant="true" species="M_m09c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_m02c" stoichiometry="1"/>
<speciesReference constant="true" species="M_m05m" stoichiometry="4"/>
<speciesReference constant="true" species="M_m06c" stoichiometry="1"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_ATPV"/>
</fbc:geneProductAssociation>
</reaction>
<reaction fast="false" id="R_R4" reversible="false" name="ATP demand" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
<listOfReactants>
<speciesReference constant="true" species="M_m02c" stoichiometry="1"/>
<speciesReference constant="true" species="M_m06c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_m01c" stoichiometry="1"/>
<speciesReference constant="true" species="M_m09c" stoichiometry="1"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_MYH2"/>
</fbc:geneProductAssociation>
</reaction>
</listOfReactions>
</model>
</sbml>