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model_Borghans_BiophysChem1997.xml
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model_Borghans_BiophysChem1997.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="Borghans_BiophysChem1997" name="Borghans_BiophysChem1997">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PEtab implementation of the model from Borghans et al. (1997), Biophysical Chemistry 66(1) 25-41</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>Borghans</vCard:Family>
<vCard:Given>José</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/s0301-4622(97)00010-0"/>
</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="extracellular" spatialDimensions="3" size="1" constant="true"/>
<compartment id="cytosol" spatialDimensions="3" size="1" constant="true"/>
<compartment id="intravesicular" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="Z_state" name="Ca^{2+} in cytosol" compartment="cytosol" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="Y_state" name="Ca^{2+} in Ca^{2+}-sensitive pool" compartment="intravesicular" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="A_state" name="IP_3 concentration" compartment="cytosol" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="K2" value="0.0999485580156493" constant="true"/>
<parameter id="K_par" value="11.4120804594265" constant="true"/>
<parameter id="Ka" value="0.197593940310187" constant="true"/>
<parameter id="Kd" value="0.392497512107474" constant="true"/>
<parameter id="Kf" value="1.13794968361236" constant="true"/>
<parameter id="Kp" value="0.996567464196473" constant="true"/>
<parameter id="Ky" value="0.200364133028272" constant="true"/>
<parameter id="Kz" value="0.303353547057472" constant="true"/>
<parameter id="Vd" value="92.8739300577965" constant="true"/>
<parameter id="Vm2" value="7.45712445492225" constant="true"/>
<parameter id="Vm3" value="22.7025248825351" constant="true"/>
<parameter id="Vp" value="2.75685784345759" constant="true"/>
<parameter id="beta_par" value="1.12395230256787" constant="true"/>
<parameter id="epsilon_par" value="0.163232195306189" constant="true"/>
<parameter id="init_A_state" value="0.99999999999996" constant="true"/>
<parameter id="init_Y_state" value="0.999348084438687" constant="true"/>
<parameter id="init_Z_state" value="0.0879205244255038" constant="true"/>
<parameter id="n_par" value="4.1025144127497" constant="true"/>
<parameter id="v0" value="2.31778715779187" constant="true"/>
<parameter id="v1" value="1.00488755696677" constant="true"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="Z_state">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_Z_state </ci>
</math>
</initialAssignment>
<initialAssignment symbol="Y_state">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_Y_state </ci>
</math>
</initialAssignment>
<initialAssignment symbol="A_state">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_A_state </ci>
</math>
</initialAssignment>
</listOfInitialAssignments>
<listOfReactions>
<reaction id="v1_v_0" name="v_0" reversible="false">
<listOfProducts>
<speciesReference species="Z_state" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cytosol </ci>
<apply>
<plus/>
<ci> v0 </ci>
<apply>
<times/>
<ci> beta_par </ci>
<ci> v1 </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v2_v_1" name="v_1" reversible="false">
<listOfReactants>
<speciesReference species="Z_state" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Y_state" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cytosol </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> Vm2 </ci>
<apply>
<power/>
<ci> Z_state </ci>
<cn type="integer"> 2 </cn>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> K2 </ci>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<power/>
<ci> Z_state </ci>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v3_v_2" name="v_2" reversible="false">
<listOfReactants>
<speciesReference species="Y_state" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Z_state" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="A_state"/>
<modifierSpeciesReference species="Z_state"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> intravesicular </ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<power/>
<ci> A_state </ci>
<cn type="integer"> 4 </cn>
</apply>
<ci> Vm3 </ci>
<apply>
<power/>
<ci> Y_state </ci>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<power/>
<ci> Z_state </ci>
<cn type="integer"> 4 </cn>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<apply>
<power/>
<ci> A_state </ci>
<cn type="integer"> 4 </cn>
</apply>
<apply>
<power/>
<ci> Ka </ci>
<cn type="integer"> 4 </cn>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> Ky </ci>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<power/>
<ci> Y_state </ci>
<cn type="integer"> 2 </cn>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> Kz </ci>
<cn type="integer"> 4 </cn>
</apply>
<apply>
<power/>
<ci> Z_state </ci>
<cn type="integer"> 4 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v4_v_3" name="v_3" reversible="false">
<listOfReactants>
<speciesReference species="Y_state" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Z_state" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> intravesicular </ci>
<ci> Kf </ci>
<ci> Y_state </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v5_v_4" name="v_4" reversible="false">
<listOfReactants>
<speciesReference species="Z_state" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cytosol </ci>
<ci> K_par </ci>
<ci> Z_state </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v6_v_5" name="v_5" reversible="false">
<listOfProducts>
<speciesReference species="A_state" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cytosol </ci>
<ci> Vp </ci>
<ci> beta_par </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v7_v_6" name="v_6" reversible="false">
<listOfReactants>
<speciesReference species="A_state" stoichiometry="1"/>
</listOfReactants>
<listOfModifiers>
<modifierSpeciesReference species="Z_state"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cytosol </ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<power/>
<ci> A_state </ci>
<cn type="integer"> 2 </cn>
</apply>
<ci> Vd </ci>
<apply>
<power/>
<ci> Z_state </ci>
<ci> n_par </ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<apply>
<power/>
<ci> Kd </ci>
<ci> n_par </ci>
</apply>
<apply>
<power/>
<ci> Z_state </ci>
<ci> n_par </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> A_state </ci>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<power/>
<ci> Kp </ci>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v8_v_7" name="v_7" reversible="false">
<listOfReactants>
<speciesReference species="A_state" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cytosol </ci>
<ci> A_state </ci>
<ci> epsilon_par </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>