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Cho_Shin_LungCancer_GRN_UninformedParameterRanges_InformedInitialConditions.cps
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Cho_Shin_LungCancer_GRN_UninformedParameterRanges_InformedInitialConditions.cps
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<?xml version="1.0" encoding="UTF-8"?>
<!-- generated with COPASI 4.44 (Build 295) (http://www.copasi.org) at 2024-08-07T18:28:42Z -->
<?oxygen RNGSchema="http://www.copasi.org/static/schema/CopasiML.rng" type="xml"?>
<COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="44" versionDevel="295" copasiSourcesModified="0">
<ListOfFunctions>
<Function key="Function_13" name="Mass action (irreversible)" type="MassAction" reversible="false">
<MiriamAnnotation>
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Function_13">
<CopasiMT:is rdf:resource="urn:miriam:obo.sbo:SBO:0000163" />
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
<body xmlns="http://www.w3.org/1999/xhtml">
<b>Mass action rate law for irreversible reactions</b>
<p>
Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant.
</p>
</body>
</Comment>
<Expression>
k1*PRODUCT<substrate_i>
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_80" name="k1" order="0" role="constant"/>
<ParameterDescription key="FunctionParameter_81" name="substrate" order="1" role="substrate"/>
</ListOfParameterDescriptions>
</Function>
<Function key="Function_41" name="Cho_Shin_Creation_HillFunction_OneSpecies" type="UserDefined" reversible="unspecified">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Function_41">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
(G/FC)*(FC+((1-FC)/(1+(y/TH)^N)))
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_275" name="G" order="0" role="constant"/>
<ParameterDescription key="FunctionParameter_274" name="FC" order="1" role="constant"/>
<ParameterDescription key="FunctionParameter_273" name="y" order="2" role="modifier"/>
<ParameterDescription key="FunctionParameter_272" name="TH" order="3" role="constant"/>
<ParameterDescription key="FunctionParameter_266" name="N" order="4" role="constant"/>
</ListOfParameterDescriptions>
</Function>
<Function key="Function_42" name="Cho_Shin_Creation_HillFunction_ThreeSpecies" type="UserDefined" reversible="unspecified">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Function_42">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
(G/FC1)*(FC1+((1-FC1)/(1+(y1/TH1)^N1)))*(1/FC2)*(FC2+((1-FC2)/(1+(y2/TH2)^N2)))*(1/FC3)*(FC3+((1-FC3)/(1+(y3/TH3)^N3)))
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_280" name="G" order="0" role="constant"/>
<ParameterDescription key="FunctionParameter_279" name="FC1" order="1" role="constant"/>
<ParameterDescription key="FunctionParameter_278" name="y1" order="2" role="modifier"/>
<ParameterDescription key="FunctionParameter_277" name="TH1" order="3" role="constant"/>
<ParameterDescription key="FunctionParameter_276" name="N1" order="4" role="constant"/>
<ParameterDescription key="FunctionParameter_281" name="FC2" order="5" role="constant"/>
<ParameterDescription key="FunctionParameter_282" name="y2" order="6" role="modifier"/>
<ParameterDescription key="FunctionParameter_283" name="TH2" order="7" role="constant"/>
<ParameterDescription key="FunctionParameter_284" name="N2" order="8" role="constant"/>
<ParameterDescription key="FunctionParameter_285" name="FC3" order="9" role="constant"/>
<ParameterDescription key="FunctionParameter_286" name="y3" order="10" role="modifier"/>
<ParameterDescription key="FunctionParameter_287" name="TH3" order="11" role="constant"/>
<ParameterDescription key="FunctionParameter_288" name="N3" order="12" role="constant"/>
</ListOfParameterDescriptions>
</Function>
</ListOfFunctions>
<Model key="Model_1" name="Cho_Shin_LungCancer_GRN" simulationType="time" timeUnit="s" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mol" type="deterministic" avogadroConstant="6.0221407599999999e+23">
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xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Model_1">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2024-07-16T17:42:23Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
ODE model of lung cancer cells at the critical transition point, taken from Cho and Shin's manuscript "Critical transition and reversion of tumorigenesis". Sampled 200 random parameter sets. Ranges for parameter sampling were NOT informed by Cho and Shin's published parameter set, and were instead set assuming that we did not know what the appropriate range was. Ranges for initial network conditions likewise ranged from 0 to a maximum as determined by examining the original lung cancer dataset, NOT sampled logarithmically. Sampled 200 random initial states per parameter set.
</Comment>
<ListOfCompartments>
<Compartment key="Compartment_0" name="compartment" simulationType="fixed" dimensionality="3" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Compartment_0">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Compartment>
</ListOfCompartments>
<ListOfMetabolites>
<Metabolite key="Metabolite_0" name="Y1" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<Metabolite key="Metabolite_1" name="Y2" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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<rdf:Description rdf:about="#Metabolite_1">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_2" name="Y3" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_2">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_3" name="Y4" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_3">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_4" name="Y5" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_4">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_5" name="Y6" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_6" name="Y7" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_6">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_7" name="Y8" simulationType="reactions" compartment="Compartment_0" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_7">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
</ListOfMetabolites>
<ListOfReactions>
<Reaction key="Reaction_0" name="Y1 destruction" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_0">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_0" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_5506" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_5506"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_0"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_1" name="Y1 creation" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_1">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_0" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_5509" name="G" value="0.1"/>
<Constant key="Parameter_4675" name="FC" value="0.1"/>
<Constant key="Parameter_4676" name="TH" value="0.1"/>
<Constant key="Parameter_4679" name="N" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_275">
<SourceParameter reference="Parameter_5509"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_274">
<SourceParameter reference="Parameter_4675"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_272">
<SourceParameter reference="Parameter_4676"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_266">
<SourceParameter reference="Parameter_4679"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_2" name="Y2 destruction" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
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<rdf:Description rdf:about="#Reaction_2">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_4674" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_4674"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_3" name="Y2 creation" reversible="false" fast="false" addNoise="false">
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<rdf:Description rdf:about="#Reaction_3">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_0" stoichiometry="1"/>
<Modifier metabolite="Metabolite_2" stoichiometry="1"/>
<Modifier metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_4678" name="G" value="0.1"/>
<Constant key="Parameter_4677" name="FC1" value="0.1"/>
<Constant key="Parameter_6923" name="TH1" value="0.1"/>
<Constant key="Parameter_6924" name="N1" value="0.1"/>
<Constant key="Parameter_6927" name="FC2" value="0.1"/>
<Constant key="Parameter_6922" name="TH2" value="0.1"/>
<Constant key="Parameter_6926" name="N2" value="0.1"/>
<Constant key="Parameter_6925" name="FC3" value="0.1"/>
<Constant key="Parameter_4647" name="TH3" value="0.1"/>
<Constant key="Parameter_4648" name="N3" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_42" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_280">
<SourceParameter reference="Parameter_4678"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_279">
<SourceParameter reference="Parameter_4677"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_278">
<SourceParameter reference="Metabolite_0"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_277">
<SourceParameter reference="Parameter_6923"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_276">
<SourceParameter reference="Parameter_6924"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_281">
<SourceParameter reference="Parameter_6927"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_282">
<SourceParameter reference="Metabolite_2"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_283">
<SourceParameter reference="Parameter_6922"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_284">
<SourceParameter reference="Parameter_6926"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_285">
<SourceParameter reference="Parameter_6925"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_286">
<SourceParameter reference="Metabolite_6"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_287">
<SourceParameter reference="Parameter_4647"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_288">
<SourceParameter reference="Parameter_4648"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_4" name="Y3 destruction" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_4">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_2" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_4654" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_4654"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_2"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_5" name="Y3 creation" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_5">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_2" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_4646" name="G" value="0.1"/>
<Constant key="Parameter_4650" name="FC" value="0.1"/>
<Constant key="Parameter_4652" name="TH" value="0.1"/>
<Constant key="Parameter_4653" name="N" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_275">
<SourceParameter reference="Parameter_4646"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_274">
<SourceParameter reference="Parameter_4650"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_272">
<SourceParameter reference="Parameter_4652"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_266">
<SourceParameter reference="Parameter_4653"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_6" name="Y4 destruction" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_6">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_4651" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_4651"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_7" name="Y4 creation" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_7">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_2" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_4649" name="G" value="0.1"/>
<Constant key="Parameter_7507" name="FC" value="0.1"/>
<Constant key="Parameter_7508" name="TH" value="0.1"/>
<Constant key="Parameter_7511" name="N" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_275">
<SourceParameter reference="Parameter_4649"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_274">
<SourceParameter reference="Parameter_7507"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_2"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_272">
<SourceParameter reference="Parameter_7508"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_266">
<SourceParameter reference="Parameter_7511"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_8" name="Y5 destruction" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_8">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_4" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_7506" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_7506"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_4"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_9" name="Y5 creation" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_9">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_4" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_2" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_7510" name="G" value="0.1"/>
<Constant key="Parameter_7509" name="FC" value="0.1"/>
<Constant key="Parameter_6026" name="TH" value="0.1"/>
<Constant key="Parameter_6027" name="N" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_275">
<SourceParameter reference="Parameter_7510"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_274">
<SourceParameter reference="Parameter_7509"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_2"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_272">
<SourceParameter reference="Parameter_6026"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_266">
<SourceParameter reference="Parameter_6027"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_10" name="Y6 destruction" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_10">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_6029" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_6029"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_5"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_11" name="Y6 creation" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_11">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_4" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_6025" name="G" value="0.1"/>
<Constant key="Parameter_6028" name="FC" value="0.1"/>
<Constant key="Parameter_6510" name="TH" value="0.1"/>
<Constant key="Parameter_6511" name="N" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_275">
<SourceParameter reference="Parameter_6025"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_274">
<SourceParameter reference="Parameter_6028"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_4"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_272">
<SourceParameter reference="Parameter_6510"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_266">
<SourceParameter reference="Parameter_6511"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_12" name="Y7 destruction" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_12">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_6513" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_6513"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_6"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_13" name="Y7 creation" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_13">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_6" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_6509" name="G" value="0.1"/>
<Constant key="Parameter_6512" name="FC" value="0.1"/>
<Constant key="Parameter_7345" name="TH" value="0.1"/>
<Constant key="Parameter_7346" name="N" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_275">
<SourceParameter reference="Parameter_6509"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_274">
<SourceParameter reference="Parameter_6512"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_273">
<SourceParameter reference="Metabolite_5"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_272">
<SourceParameter reference="Parameter_7345"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_266">
<SourceParameter reference="Parameter_7346"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_14" name="Y8 destruction" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_14">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_7348" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="Parameter_7348"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_7"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_15" name="Y8 creation" reversible="false" fast="false" addNoise="false">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_15">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_0" stoichiometry="1"/>
<Modifier metabolite="Metabolite_1" stoichiometry="1"/>
<Modifier metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_7344" name="G" value="0.1"/>
<Constant key="Parameter_7347" name="FC1" value="0.1"/>
<Constant key="Parameter_4926" name="TH1" value="0.1"/>
<Constant key="Parameter_4927" name="N1" value="0.1"/>
<Constant key="Parameter_4929" name="FC2" value="0.1"/>
<Constant key="Parameter_4925" name="TH2" value="0.1"/>
<Constant key="Parameter_4928" name="N2" value="0.1"/>
<Constant key="Parameter_6777" name="FC3" value="0.1"/>
<Constant key="Parameter_6778" name="TH3" value="0.1"/>
<Constant key="Parameter_6780" name="N3" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_42" unitType="Default" scalingCompartment="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_280">
<SourceParameter reference="Parameter_7344"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_279">
<SourceParameter reference="Parameter_7347"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_278">
<SourceParameter reference="Metabolite_0"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_277">
<SourceParameter reference="Parameter_4926"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_276">
<SourceParameter reference="Parameter_4927"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_281">
<SourceParameter reference="Parameter_4929"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_282">
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_283">
<SourceParameter reference="Parameter_4925"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_284">
<SourceParameter reference="Parameter_4928"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_285">
<SourceParameter reference="Parameter_6777"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_286">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_287">
<SourceParameter reference="Parameter_6778"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_288">
<SourceParameter reference="Parameter_6780"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
</ListOfReactions>
<ListOfModelParameterSets activeSet="ModelParameterSet_1">
<ModelParameterSet key="ModelParameterSet_1" name="Initial State">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#ModelParameterSet_1">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ModelParameterGroup cn="String=Initial Time" type="Group">
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN" value="0" type="Model" simulationType="time"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment]" value="1" type="Compartment" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Species Values" type="Group">
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment],Vector=Metabolites[Y1]" value="6.0221407599999636e+23" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment],Vector=Metabolites[Y2]" value="6.022140759999967e+23" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment],Vector=Metabolites[Y3]" value="6.0221407599999717e+23" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment],Vector=Metabolites[Y4]" value="6.0221407599999744e+23" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment],Vector=Metabolites[Y5]" value="6.0221407599999771e+23" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment],Vector=Metabolites[Y6]" value="6.0221407599999804e+23" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment],Vector=Metabolites[Y7]" value="6.0221407599999831e+23" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Compartments[compartment],Vector=Metabolites[Y8]" value="6.0221407599999864e+23" type="Species" simulationType="reactions"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
</ModelParameterGroup>
<ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
<ModelParameterGroup cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y1 destruction]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y1 destruction],ParameterGroup=Parameters,Parameter=k1" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y1 creation]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y1 creation],ParameterGroup=Parameters,Parameter=G" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y1 creation],ParameterGroup=Parameters,Parameter=FC" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y1 creation],ParameterGroup=Parameters,Parameter=TH" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y1 creation],ParameterGroup=Parameters,Parameter=N" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y2 destruction]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y2 destruction],ParameterGroup=Parameters,Parameter=k1" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y2 creation]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y2 creation],ParameterGroup=Parameters,Parameter=G" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y2 creation],ParameterGroup=Parameters,Parameter=FC1" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y2 creation],ParameterGroup=Parameters,Parameter=TH1" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Cho_Shin_LungCancer_GRN,Vector=Reactions[Y2 creation],ParameterGroup=Parameters,Parameter=N1" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
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