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model_Bruno_JExpBot2016.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="Bruno_JExpBot2016" name="Bruno_JExpBot2016">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PEtab implementation of the model from Bruno et al. (2016), J Exp Bot.; 67(21): 5993–6005</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>Bruno</vCard:Family>
<vCard:Given>Mark</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/10.1093/jxb/erw356"/>
</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="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="bcar" name="beta-carotin" compartment="cyt" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="bcry" name="cry" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="b10" name="beta-10" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="bio" name="beta-io" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ohb10" name="OH-beta-10" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="ohbio" name="OH-beta-io" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="zea" name="zea" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="init_b10" value="3.25673310603827" constant="true"/>
<parameter id="init_bcar" value="3.25673310603827" constant="true"/>
<parameter id="init_bcry" value="3.25673310603827" constant="true"/>
<parameter id="init_ohb10" value="3.25673310603827" constant="true"/>
<parameter id="init_zea" value="3.25673310603827" constant="true"/>
<parameter id="k5" value="0.00305007086506138" constant="true"/>
<parameter id="kb1" value="0.0164169857330715" constant="true"/>
<parameter id="kb2" value="0.00537146249584483" constant="true"/>
<parameter id="kc1" value="0.00162720870139293" constant="true"/>
<parameter id="kc2" value="0.00673060855967958" constant="true"/>
<parameter id="kc4" value="0.00617966905040397" constant="true"/>
<parameter id="k5_multiplier" value="0.521817105884857" constant="true"/>
<parameter id="kb1_multiplier" value="0.521817105884857" constant="true"/>
<parameter id="kb2_multiplier" value="0.521817105884857" constant="true"/>
<parameter id="kc1_multiplier" value="0.521817105884857" constant="true"/>
<parameter id="kc2_multiplier" value="0.521817105884857" constant="true"/>
<parameter id="kc4_multiplier" value="0.521817105884857" constant="true"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="bcar">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_bcar </ci>
</math>
</initialAssignment>
<initialAssignment symbol="b10">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_b10 </ci>
</math>
</initialAssignment>
<initialAssignment symbol="bcry">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_bcry </ci>
</math>
</initialAssignment>
<initialAssignment symbol="ohb10">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_ohb10 </ci>
</math>
</initialAssignment>
<initialAssignment symbol="zea">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> init_zea </ci>
</math>
</initialAssignment>
</listOfInitialAssignments>
<listOfReactions>
<reaction id="v1_ReactionName" name="ReactionName" reversible="false">
<listOfReactants>
<speciesReference species="bcar" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="b10" stoichiometry="1"/>
<speciesReference species="bio" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> bcar </ci>
<ci> kb1 </ci>
<ci> kb1_multiplier </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v2_ReactionName" name="ReactionName" reversible="false">
<listOfReactants>
<speciesReference species="b10" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="bio" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> b10 </ci>
<ci> kb2 </ci>
<ci> kb2_multiplier </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v3_ReactionName" name="ReactionName" reversible="false">
<listOfReactants>
<speciesReference species="bcry" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="b10" stoichiometry="1"/>
<speciesReference species="ohbio" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> bcry </ci>
<ci> kc1 </ci>
<ci> kc1_multiplier </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v4_ReactionName" name="ReactionName" reversible="false">
<listOfReactants>
<speciesReference species="bcry" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="bio" stoichiometry="1"/>
<speciesReference species="ohb10" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> bcry </ci>
<ci> kc2 </ci>
<ci> kc2_multiplier </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v5_ReactionName" name="ReactionName" reversible="false">
<listOfReactants>
<speciesReference species="ohb10" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ohbio" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> kc4 </ci>
<ci> kc4_multiplier </ci>
<ci> ohb10 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="v6_ReactionName" name="ReactionName" reversible="false">
<listOfReactants>
<speciesReference species="zea" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ohb10" stoichiometry="1"/>
<speciesReference species="ohbio" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> k5 </ci>
<ci> k5_multiplier </ci>
<ci> zea </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>