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model_Lucarelli_CellSystems2018.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="Lucarelli_CellSystems2018" name="Lucarelli_CellSystems2018">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PEtab implementation of the model from Lucarelli et al. (2018), Cell Syst. 2018 Jan 24;6(1):75-89.e11</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>Lucarelli</vCard:Family>
<vCard:Given>Philippe</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/10.1016/j.cels.2017.11.010"/>
</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="cell" spatialDimensions="3" size="13.17" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="TGFb" name="TGFb" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="Rec" name="Rec" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="TGFb_pRec" name="TGFb_pRec" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S2" name="S2" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S3" name="S3" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S4" name="S4" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S2_S4_S4" name="S2_S4_S4" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS2_ppS2_ppS2" name="ppS2_ppS2_ppS2" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS3_ppS3_ppS3" name="ppS3_ppS3_ppS3" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S4_S4_S4" name="S4_S4_S4" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="pS2" name="pS2" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="pS3" name="pS3" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS2" name="ppS2" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS3" name="ppS3" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS2_ppS2_S4" name="ppS2_ppS2_S4" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS2_ppS2_ppS3" name="ppS2_ppS2_ppS3" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS2_ppS3_ppS3" name="ppS2_ppS3_ppS3" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS3_ppS3_S4" name="ppS3_ppS3_S4" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS2_ppS3_S4" name="ppS2_ppS3_S4" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS3_S4_S4" name="ppS3_S4_S4" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ppS2_S4_S4" name="ppS2_S4_S4" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneA" name="geneA" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneB" name="geneB" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneC" name="geneC" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneD" name="geneD" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneE" name="geneE" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneF" name="geneF" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneG" name="geneG" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneH" name="geneH" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneI" name="geneI" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneJ" name="geneJ" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneK" name="geneK" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="geneL" name="geneL" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="Rec_act" value="0.00598343088790046" constant="true"/>
<parameter id="init_TGFb" value="0" constant="true"/>
<parameter id="init_S2" value="0" constant="true"/>
<parameter id="init_S3" value="0" constant="true"/>
<parameter id="init_S4" value="0" constant="true"/>
<parameter id="S_dephos" value="0.286397320264704" constant="true"/>
<parameter id="S_dephosphos" value="0.0489949146416608" constant="true"/>
<parameter id="S_phos" value="0.379720142751521" constant="true"/>
<parameter id="geneA_act1" value="0.0141389661164018" constant="true"/>
<parameter id="geneA_act2" value="0.000797280887701997" constant="true"/>
<parameter id="geneA_act3" value="0" constant="true"/>
<parameter id="geneA_inh1" value="0" constant="true"/>
<parameter id="geneA_inh2" value="0.0462523981984203" constant="true"/>
<parameter id="geneA_inh3" value="0.026381058989095" constant="true"/>
<parameter id="geneA_turn" value="0.00455788978022206" constant="true"/>
<parameter id="geneB_act1" value="0.461699170803527" constant="true"/>
<parameter id="geneB_act2" value="0.073852775177442" constant="true"/>
<parameter id="geneB_act3" value="0.0304255473876269" constant="true"/>
<parameter id="geneB_inh1" value="0" constant="true"/>
<parameter id="geneB_inh2" value="0.747200749545747" constant="true"/>
<parameter id="geneB_inh3" value="0.407329851468312" constant="true"/>
<parameter id="geneB_turn" value="0.0112459404708192" constant="true"/>
<parameter id="geneC_act1" value="0.00714636599139809" constant="true"/>
<parameter id="geneC_act2" value="0" constant="true"/>
<parameter id="geneC_act3" value="0" constant="true"/>
<parameter id="geneC_inh1" value="0" constant="true"/>
<parameter id="geneC_inh2" value="0.018441582221635" constant="true"/>
<parameter id="geneC_inh3" value="0.035379693264711" constant="true"/>
<parameter id="geneC_turn" value="0.00378630404521753" constant="true"/>
<parameter id="geneD_act1" value="0.0111673720417551" constant="true"/>
<parameter id="geneD_act2" value="0.000268942132758932" constant="true"/>
<parameter id="geneD_act3" value="0" constant="true"/>
<parameter id="geneD_inh1" value="0" constant="true"/>
<parameter id="geneD_inh2" value="0.0868803385899104" constant="true"/>
<parameter id="geneD_inh3" value="0.101419105775767" constant="true"/>
<parameter id="geneD_turn" value="0.000802160834341515" constant="true"/>
<parameter id="geneE_act1" value="0" constant="true"/>
<parameter id="geneE_act2" value="1.03661055568903" constant="true"/>
<parameter id="geneE_act3" value="6.10224669858575" constant="true"/>
<parameter id="geneE_inh1" value="8.20035989079744" constant="true"/>
<parameter id="geneE_inh2" value="1.4392548717489" constant="true"/>
<parameter id="geneE_inh3" value="9.67035015330535" constant="true"/>
<parameter id="geneE_turn" value="0.124380538819967" constant="true"/>
<parameter id="geneF_act1" value="998.299919973209" constant="true"/>
<parameter id="geneF_act2" value="0.135655043663672" constant="true"/>
<parameter id="geneF_act3" value="20.6442242166861" constant="true"/>
<parameter id="geneF_inh1" value="3.63157061548523" constant="true"/>
<parameter id="geneF_inh2" value="0" constant="true"/>
<parameter id="geneF_inh3" value="0" constant="true"/>
<parameter id="geneF_turn" value="36.6724104315148" constant="true"/>
<parameter id="geneG_act1" value="626.768522107231" constant="true"/>
<parameter id="geneG_act2" value="55.9534537604082" constant="true"/>
<parameter id="geneG_act3" value="0" constant="true"/>
<parameter id="geneG_inh1" value="0" constant="true"/>
<parameter id="geneG_inh2" value="0.0175854489108708" constant="true"/>
<parameter id="geneG_inh3" value="0.000815621975867545" constant="true"/>
<parameter id="geneG_turn" value="295.971427530835" constant="true"/>
<parameter id="geneH_act1" value="0" constant="true"/>
<parameter id="geneH_act2" value="89.9866382703511" constant="true"/>
<parameter id="geneH_act3" value="999.921986303898" constant="true"/>
<parameter id="geneH_inh1" value="999.998960700206" constant="true"/>
<parameter id="geneH_inh2" value="19.0317907364409" constant="true"/>
<parameter id="geneH_inh3" value="218.356690800299" constant="true"/>
<parameter id="geneH_turn" value="0.992827361229694" constant="true"/>
<parameter id="geneI_act1" value="9.30152789301652" constant="true"/>
<parameter id="geneI_act2" value="0" constant="true"/>
<parameter id="geneI_act3" value="0" constant="true"/>
<parameter id="geneI_inh1" value="0" constant="true"/>
<parameter id="geneI_inh2" value="320.763519415643" constant="true"/>
<parameter id="geneI_inh3" value="999.981624754706" constant="true"/>
<parameter id="geneI_turn" value="0.00328197841814657" constant="true"/>
<parameter id="geneJ_act1" value="0" constant="true"/>
<parameter id="geneJ_act2" value="0" constant="true"/>
<parameter id="geneJ_act3" value="0" constant="true"/>
<parameter id="geneJ_inh1" value="0.47739150796461" constant="true"/>
<parameter id="geneJ_inh2" value="0.00985305306597475" constant="true"/>
<parameter id="geneJ_inh3" value="0.00851371884219428" constant="true"/>
<parameter id="geneJ_turn" value="0.0140190729281921" constant="true"/>
<parameter id="geneK_act1" value="0.0125133830064198" constant="true"/>
<parameter id="geneK_act2" value="0.000284224503418874" constant="true"/>
<parameter id="geneK_act3" value="0" constant="true"/>
<parameter id="geneK_inh1" value="0" constant="true"/>
<parameter id="geneK_inh2" value="1.36603583936842" constant="true"/>
<parameter id="geneK_inh3" value="2.43594567888689" constant="true"/>
<parameter id="geneK_turn" value="0.00359915570352007" constant="true"/>
<parameter id="geneL_act1" value="0" constant="true"/>
<parameter id="geneL_act2" value="0.000474849473374749" constant="true"/>
<parameter id="geneL_act3" value="0" constant="true"/>
<parameter id="geneL_inh1" value="1.29976503414042" constant="true"/>
<parameter id="geneL_inh2" value="0.062323573525662" constant="true"/>
<parameter id="geneL_inh3" value="0.13414856027346" constant="true"/>
<parameter id="geneL_turn" value="0.0149504509077553" constant="true"/>
<parameter id="init_Rec" value="1.83614829885072" constant="true"/>
<parameter id="k_223" value="0" constant="true"/>
<parameter id="k_224" value="0" constant="true"/>
<parameter id="k_233" value="0.148655616115831" constant="true"/>
<parameter id="k_234" value="0.000403100938582095" constant="true"/>
<parameter id="k_244" value="8.56307475687022e-06" constant="true"/>
<parameter id="k_334" value="0" constant="true"/>
<parameter id="k_344" value="0" constant="true"/>
<parameter id="k_on_u" value="0" constant="true"/>
<parameter id="kdiss_SS" value="0" constant="true"/>
<parameter id="khomo2" value="0" constant="true"/>
<parameter id="khomo3" value="0" constant="true"/>
<parameter id="khomo4" value="0" constant="true"/>
<parameter id="pRec_degind" value="0.0404498417896043" constant="true"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="Rec">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_Rec </ci>
</math>
</initialAssignment>
<initialAssignment symbol="TGFb">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_TGFb </ci>
</math>
</initialAssignment>
<initialAssignment symbol="S2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_S2 </ci>
</math>
</initialAssignment>
<initialAssignment symbol="S3">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_S3 </ci>
</math>
</initialAssignment>
<initialAssignment symbol="S4">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_S4 </ci>
</math>
</initialAssignment>
</listOfInitialAssignments>
<listOfReactions>
<reaction id="v1_v_0" name="v_0" reversible="false">
<listOfReactants>
<speciesReference species="TGFb" stoichiometry="1"/>
<speciesReference species="Rec" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="TGFb_pRec" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> Rec </ci>
<ci> Rec_act </ci>
<ci> TGFb </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v2_v_1" name="v_1" reversible="false">
<listOfReactants>
<speciesReference species="TGFb_pRec" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> TGFb_pRec </ci>
<ci> pRec_degind </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v3_v_2" name="v_2" reversible="false">
<listOfReactants>
<speciesReference species="S2" stoichiometry="1"/>
<speciesReference species="S4" stoichiometry="2"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S2_S4_S4" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S2 </ci>
<apply>
<power/>
<ci> S4 </ci>
<cn type="integer"> 2 </cn>
</apply>
<ci> k_on_u </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v4_v_3" name="v_3" reversible="false">
<listOfReactants>
<speciesReference species="S2_S4_S4" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S2" stoichiometry="1"/>
<speciesReference species="S4" stoichiometry="2"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S2_S4_S4 </ci>
<ci> kdiss_SS </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v5_v_4" name="v_4" reversible="false">
<listOfReactants>
<speciesReference species="ppS2" stoichiometry="3"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS2_ppS2_ppS2" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> khomo2 </ci>
<apply>
<power/>
<ci> ppS2 </ci>
<cn type="integer"> 3 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v6_v_5" name="v_5" reversible="false">
<listOfReactants>
<speciesReference species="ppS2_ppS2_ppS2" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pS2" stoichiometry="1"/>
<speciesReference species="ppS2" stoichiometry="2"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<cn type="integer"> 3 </cn>
<ci> S_dephosphos </ci>
<ci> ppS2_ppS2_ppS2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v7_v_6" name="v_6" reversible="false">
<listOfReactants>
<speciesReference species="ppS3" stoichiometry="3"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS3_ppS3_ppS3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> khomo3 </ci>
<apply>
<power/>
<ci> ppS3 </ci>
<cn type="integer"> 3 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v8_v_7" name="v_7" reversible="false">
<listOfReactants>
<speciesReference species="ppS3_ppS3_ppS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pS3" stoichiometry="1"/>
<speciesReference species="ppS3" stoichiometry="2"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<cn type="integer"> 3 </cn>
<ci> S_dephosphos </ci>
<ci> ppS3_ppS3_ppS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v9_v_8" name="v_8" reversible="false">
<listOfReactants>
<speciesReference species="S4" stoichiometry="3"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S4_S4_S4" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<apply>
<power/>
<ci> S4 </ci>
<cn type="integer"> 3 </cn>
</apply>
<ci> khomo4 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v10_v_9" name="v_9" reversible="false">
<listOfReactants>
<speciesReference species="S4_S4_S4" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S4" stoichiometry="3"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S4_S4_S4 </ci>
<ci> kdiss_SS </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v11_v_10" name="v_10" reversible="false">
<listOfReactants>
<speciesReference species="S2" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS2" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="TGFb_pRec"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S2 </ci>
<ci> S_phos </ci>
<ci> TGFb_pRec </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v12_v_11" name="v_11" reversible="false">
<listOfReactants>
<speciesReference species="ppS2" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pS2" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephosphos </ci>
<ci> ppS2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v13_v_12" name="v_12" reversible="false">
<listOfReactants>
<speciesReference species="pS2" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S2" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephos </ci>
<ci> pS2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v14_v_13" name="v_13" reversible="false">
<listOfReactants>
<speciesReference species="S3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS3" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="TGFb_pRec"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S3 </ci>
<ci> S_phos </ci>
<ci> TGFb_pRec </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v15_v_14" name="v_14" reversible="false">
<listOfReactants>
<speciesReference species="ppS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pS3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephosphos </ci>
<ci> ppS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v16_v_15" name="v_15" reversible="false">
<listOfReactants>
<speciesReference species="pS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephos </ci>
<ci> pS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v17_v_16" name="v_16" reversible="false">
<listOfReactants>
<speciesReference species="ppS2" stoichiometry="2"/>
<speciesReference species="ppS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS2_ppS2_ppS3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> k_223 </ci>
<apply>
<power/>
<ci> ppS2 </ci>
<cn type="integer"> 2 </cn>
</apply>
<ci> ppS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v18_v_17" name="v_17" reversible="false">
<listOfReactants>
<speciesReference species="ppS2_ppS2_ppS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pS2" stoichiometry="1"/>
<speciesReference species="ppS2" stoichiometry="1"/>
<speciesReference species="ppS3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<cn type="integer"> 2 </cn>
<ci> S_dephosphos </ci>
<ci> ppS2_ppS2_ppS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v19_v_18" name="v_18" reversible="false">
<listOfReactants>
<speciesReference species="ppS2_ppS2_ppS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pS3" stoichiometry="1"/>
<speciesReference species="ppS2" stoichiometry="2"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephosphos </ci>
<ci> ppS2_ppS2_ppS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v20_v_19" name="v_19" reversible="false">
<listOfReactants>
<speciesReference species="S4" stoichiometry="1"/>
<speciesReference species="ppS2" stoichiometry="2"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS2_ppS2_S4" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S4 </ci>
<ci> k_224 </ci>
<apply>
<power/>
<ci> ppS2 </ci>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v21_v_20" name="v_20" reversible="false">
<listOfReactants>
<speciesReference species="ppS2_ppS2_S4" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S4" stoichiometry="1"/>
<speciesReference species="pS2" stoichiometry="1"/>
<speciesReference species="ppS2" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<cn type="integer"> 2 </cn>
<ci> S_dephosphos </ci>
<ci> ppS2_ppS2_S4 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v22_v_21" name="v_21" reversible="false">
<listOfReactants>
<speciesReference species="ppS2" stoichiometry="1"/>
<speciesReference species="ppS3" stoichiometry="2"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS2_ppS3_ppS3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> k_233 </ci>
<ci> ppS2 </ci>
<apply>
<power/>
<ci> ppS3 </ci>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v23_v_22" name="v_22" reversible="false">
<listOfReactants>
<speciesReference species="ppS2_ppS3_ppS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pS2" stoichiometry="1"/>
<speciesReference species="ppS3" stoichiometry="2"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephosphos </ci>
<ci> ppS2_ppS3_ppS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v24_v_23" name="v_23" reversible="false">
<listOfReactants>
<speciesReference species="ppS2_ppS3_ppS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pS3" stoichiometry="1"/>
<speciesReference species="ppS2" stoichiometry="1"/>
<speciesReference species="ppS3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<cn type="integer"> 2 </cn>
<ci> S_dephosphos </ci>
<ci> ppS2_ppS3_ppS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v25_v_24" name="v_24" reversible="false">
<listOfReactants>
<speciesReference species="S4" stoichiometry="1"/>
<speciesReference species="ppS3" stoichiometry="2"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS3_ppS3_S4" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S4 </ci>
<ci> k_334 </ci>
<apply>
<power/>
<ci> ppS3 </ci>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v26_v_25" name="v_25" reversible="false">
<listOfReactants>
<speciesReference species="ppS3_ppS3_S4" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S4" stoichiometry="1"/>
<speciesReference species="pS3" stoichiometry="1"/>
<speciesReference species="ppS3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<cn type="integer"> 2 </cn>
<ci> S_dephosphos </ci>
<ci> ppS3_ppS3_S4 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v27_v_26" name="v_26" reversible="false">
<listOfReactants>
<speciesReference species="S4" stoichiometry="2"/>
<speciesReference species="ppS2" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS2_S4_S4" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<apply>
<power/>
<ci> S4 </ci>
<cn type="integer"> 2 </cn>
</apply>
<ci> k_244 </ci>
<ci> ppS2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v28_v_27" name="v_27" reversible="false">
<listOfReactants>
<speciesReference species="ppS2_S4_S4" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S4" stoichiometry="2"/>
<speciesReference species="pS2" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephosphos </ci>
<ci> ppS2_S4_S4 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v29_v_28" name="v_28" reversible="false">
<listOfReactants>
<speciesReference species="S4" stoichiometry="2"/>
<speciesReference species="ppS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS3_S4_S4" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<apply>
<power/>
<ci> S4 </ci>
<cn type="integer"> 2 </cn>
</apply>
<ci> k_344 </ci>
<ci> ppS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v30_v_29" name="v_29" reversible="false">
<listOfReactants>
<speciesReference species="ppS3_S4_S4" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S4" stoichiometry="2"/>
<speciesReference species="pS3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephosphos </ci>
<ci> ppS3_S4_S4 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v31_v_30" name="v_30" reversible="false">
<listOfReactants>
<speciesReference species="S4" stoichiometry="1"/>
<speciesReference species="ppS2" stoichiometry="1"/>
<speciesReference species="ppS3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ppS2_ppS3_S4" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S4 </ci>
<ci> k_234 </ci>
<ci> ppS2 </ci>
<ci> ppS3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v32_v_31" name="v_31" reversible="false">
<listOfReactants>
<speciesReference species="ppS2_ppS3_S4" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S4" stoichiometry="1"/>
<speciesReference species="pS2" stoichiometry="1"/>
<speciesReference species="ppS3" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephosphos </ci>
<ci> ppS2_ppS3_S4 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v33_v_32" name="v_32" reversible="false">
<listOfReactants>
<speciesReference species="ppS2_ppS3_S4" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S4" stoichiometry="1"/>
<speciesReference species="pS3" stoichiometry="1"/>
<speciesReference species="ppS2" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> S_dephosphos </ci>
<ci> ppS2_ppS3_S4 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v34_v_33" name="v_33" reversible="false">
<listOfProducts>
<speciesReference species="geneA" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="ppS2_S4_S4"/>
<modifierSpeciesReference species="ppS2_ppS3_S4"/>
<modifierSpeciesReference species="ppS2_ppS3_ppS3"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<apply>
<divide/>
<apply>
<plus/>
<ci> geneA_turn </ci>
<apply>
<times/>
<ci> geneA_act2 </ci>
<ci> ppS2_S4_S4 </ci>
</apply>
<apply>
<times/>
<ci> geneA_act1 </ci>
<ci> ppS2_ppS3_S4 </ci>
</apply>
<apply>
<times/>
<ci> geneA_act3 </ci>
<ci> ppS2_ppS3_ppS3 </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> geneA_inh2 </ci>
<ci> ppS2_S4_S4 </ci>
</apply>
<apply>
<times/>
<ci> geneA_inh1 </ci>
<ci> ppS2_ppS3_S4 </ci>
</apply>
<apply>
<times/>
<ci> geneA_inh3 </ci>
<ci> ppS2_ppS3_ppS3 </ci>
</apply>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v35_v_34" name="v_34" reversible="false">
<listOfReactants>
<speciesReference species="geneA" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> geneA </ci>
<ci> geneA_turn </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v36_v_35" name="v_35" reversible="false">
<listOfProducts>
<speciesReference species="geneB" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="ppS2_S4_S4"/>
<modifierSpeciesReference species="ppS2_ppS3_S4"/>
<modifierSpeciesReference species="ppS2_ppS3_ppS3"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<apply>
<divide/>
<apply>
<plus/>
<ci> geneB_turn </ci>
<apply>
<times/>
<ci> geneB_act2 </ci>
<ci> ppS2_S4_S4 </ci>
</apply>
<apply>
<times/>