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model_Raia_CancerResearch2011.xml
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model_Raia_CancerResearch2011.xml
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="Raia_CancerResearch2011" name="Raia_CancerResearch2011">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PEtab implementation of the model from Raia et al. (2011), Cancer Res February 1 2011 (71) (3) 693-704</pre>
</body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#arFramework3">
<dc:creator>
<rdf:Bag>
<rdf:li rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Raia</vCard:Family>
<vCard:Given>Valentina</vCard:Given>
</vCard:N>
</rdf:li>
</rdf:Bag>
</dc:creator>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2019-11-29T09:41:48Z</dcterms:W3CDTF>
</dcterms:created>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2019-11-29T09:41:48Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/doi/10.1158/0008-5472.CAN-10-2987"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfUnitDefinitions>
<unitDefinition id="time" name="time">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="60"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="cyt" spatialDimensions="3" size="100" constant="true"/>
<compartment id="nuc" spatialDimensions="3" size="10" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="Rec" name="Rec" compartment="cyt" initialConcentration="1.3" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="Rec_i" name="Rec_i" compartment="cyt" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="IL13_Rec" name="IL13_Rec" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="p_IL13_Rec" name="p_IL13_Rec" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="p_IL13_Rec_i" name="p_IL13_Rec_i" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="JAK2" name="JAK2" compartment="cyt" initialConcentration="2.8" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="pJAK2" name="pJAK2" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="STAT5" name="STAT5" compartment="cyt" initialConcentration="165" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="pSTAT5" name="pSTAT5" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="SOCS3mRNA" name="SOCS3mRNA" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="DecoyR" name="DecoyR" compartment="cyt" initialConcentration="0.34" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="IL13_DecoyR" name="IL13_DecoyR" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="SOCS3" name="SOCS3" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="CD274mRNA" name="CD274mRNA" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="CD274mRNA_production" value="0.0212147662359417" constant="true"/>
<parameter id="DecoyR_binding" value="0.00385131628576674" constant="true"/>
<parameter id="JAK2_p_inhibition" value="0.0781525077338162" constant="true"/>
<parameter id="JAK2_phosphorylation" value="1.01746467089712" constant="true"/>
<parameter id="Kon_IL13Rec" value="0.00227786060666076" constant="true"/>
<parameter id="Rec_intern" value="0.34406435794877" constant="true"/>
<parameter id="Rec_phosphorylation" value="999.999392430661" constant="true"/>
<parameter id="Rec_recycle" value="0.00209816322890055" constant="true"/>
<parameter id="SOCS3_accumulation" value="451.596818983405" constant="true"/>
<parameter id="SOCS3_degradation" value="0.0433887549297662" constant="true"/>
<parameter id="SOCS3_translation" value="15.7244261244746" constant="true"/>
<parameter id="SOCS3mRNA_production" value="0.14327812349295" constant="true"/>
<parameter id="STAT5_phosphorylation" value="0.0194768335754619" constant="true"/>
<parameter id="init_Rec_i" value="234.959456370893" constant="true"/>
<parameter id="pJAK2_dephosphorylation" value="0.000175821249579369" constant="true"/>
<parameter id="pRec_degradation" value="0.209532118970476" constant="true"/>
<parameter id="pRec_intern" value="0.585096263629737" constant="true"/>
<parameter id="pSTAT5_dephosphorylation" value="0.000274790322592677" constant="true"/>
<parameter id="il13_level" value="0" constant="false"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="Rec_i">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_Rec_i </ci>
</math>
</initialAssignment>
</listOfInitialAssignments>
<listOfReactions>
<reaction id="v1_v_0" name="v_0" reversible="false">
<listOfReactants>
<speciesReference species="Rec" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="IL13_Rec" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<cn> 2.265 </cn>
<ci> il13_level </ci>
<ci> Kon_IL13Rec </ci>
<ci> Rec </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v2_v_1" name="v_1" reversible="false">
<listOfReactants>
<speciesReference species="Rec" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Rec_i" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> Rec </ci>
<ci> Rec_intern </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v3_v_2" name="v_2" reversible="false">
<listOfReactants>
<speciesReference species="Rec_i" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Rec" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> Rec_i </ci>
<ci> Rec_recycle </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v4_v_3" name="v_3" reversible="false">
<listOfReactants>
<speciesReference species="IL13_Rec" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="p_IL13_Rec" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="pJAK2"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IL13_Rec </ci>
<ci> Rec_phosphorylation </ci>
<ci> pJAK2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v5_v_4" name="v_4" reversible="false">
<listOfReactants>
<speciesReference species="JAK2" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pJAK2" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="IL13_Rec"/>
<modifierSpeciesReference species="SOCS3"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> IL13_Rec </ci>
<ci> JAK2 </ci>
<ci> JAK2_phosphorylation </ci>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> JAK2_p_inhibition </ci>
<ci> SOCS3 </ci>
</apply>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v6_v_5" name="v_5" reversible="false">
<listOfReactants>
<speciesReference species="JAK2" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pJAK2" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="SOCS3"/>
<modifierSpeciesReference species="p_IL13_Rec"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> JAK2 </ci>
<ci> JAK2_phosphorylation </ci>
<ci> p_IL13_Rec </ci>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> JAK2_p_inhibition </ci>
<ci> SOCS3 </ci>
</apply>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v7_v_6" name="v_6" reversible="false">
<listOfReactants>
<speciesReference species="p_IL13_Rec" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="p_IL13_Rec_i" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> pRec_intern </ci>
<ci> p_IL13_Rec </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v8_v_7" name="v_7" reversible="false">
<listOfReactants>
<speciesReference species="p_IL13_Rec_i" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> pRec_degradation </ci>
<ci> p_IL13_Rec_i </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v9_v_8" name="v_8" reversible="false">
<listOfReactants>
<speciesReference species="pJAK2" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="JAK2" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<cn type="integer"> 91 </cn>
<ci> pJAK2 </ci>
<ci> pJAK2_dephosphorylation </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v10_v_9" name="v_9" reversible="false">
<listOfReactants>
<speciesReference species="STAT5" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pSTAT5" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="pJAK2"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> STAT5 </ci>
<ci> STAT5_phosphorylation </ci>
<ci> pJAK2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v11_v_10" name="v_10" reversible="false">
<listOfReactants>
<speciesReference species="pSTAT5" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="STAT5" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<cn type="integer"> 91 </cn>
<ci> pSTAT5 </ci>
<ci> pSTAT5_dephosphorylation </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v12_v_11" name="v_11" reversible="false">
<listOfReactants>
<speciesReference species="DecoyR" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="IL13_DecoyR" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<cn> 2.265 </cn>
<ci> il13_level </ci>
<ci> DecoyR </ci>
<ci> DecoyR_binding </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v13_v_12" name="v_12" reversible="false">
<listOfProducts>
<speciesReference species="SOCS3mRNA" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="pSTAT5"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> nuc </ci>
<ci> SOCS3mRNA_production </ci>
<ci> pSTAT5 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v14_v_13" name="v_13" reversible="false">
<listOfProducts>
<speciesReference species="SOCS3" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="SOCS3mRNA"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> SOCS3mRNA </ci>
<ci> SOCS3_translation </ci>
</apply>
<apply>
<plus/>
<ci> SOCS3mRNA </ci>
<ci> SOCS3_accumulation </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v15_v_14" name="v_14" reversible="false">
<listOfReactants>
<speciesReference species="SOCS3" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> SOCS3 </ci>
<ci> SOCS3_degradation </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v16_v_15" name="v_15" reversible="false">
<listOfProducts>
<speciesReference species="CD274mRNA" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="pSTAT5"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> nuc </ci>
<ci> CD274mRNA_production </ci>
<ci> pSTAT5 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>