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model_Brannmark_JBC2010.xml
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model_Brannmark_JBC2010.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 metaid="arFramework3" id="Brannmark_JBC2010" name="Brannmark_JBC2010">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PEtab implementation of the model from Brannmark et al. (2010), THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 285, NO. 26, pp. 20171–20179, </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>Brannmark</vCard:Family>
<vCard:Given>Cecilia</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/10.1074/jbc.M110.106849"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfUnitDefinitions>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00038" kind="second" multiplier="60"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="substance" id="substance" name="substance">
<listOfUnits>
<unit metaid="CDMT00039" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00040" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00041" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00042" kind="metre"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
<compartment metaid="cyt" id="cyt" name="cyt" size="1" units="volume" outside="default"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="IR" id="IR" name="IR" compartment="cyt" initialConcentration="9.94957642787569"/>
<species metaid="IRins" id="IRins" name="IRins" compartment="cyt" initialConcentration="0.0173972221725393"/>
<species metaid="IRp" id="IRp" name="IRp" compartment="cyt" initialConcentration="1.7629010620181e-09"/>
<species metaid="IRiP" id="IRiP" name="IRiP" compartment="cyt" initialConcentration="1.11590026152296e-05"/>
<species metaid="IRi" id="IRi" name="IRi" compartment="cyt" initialConcentration="0.0330151891862681"/>
<species metaid="IRS" id="IRS" name="IRS" compartment="cyt" initialConcentration="9.86699348701367"/>
<species metaid="IRSiP" id="IRSiP" name="IRSiP" compartment="cyt" initialConcentration="0.133006512986336"/>
<species metaid="X" id="X" name="X" compartment="cyt" initialConcentration="9.99984199487351"/>
<species metaid="Xp" id="Xp" name="Xp" compartment="cyt" initialConcentration="0.000158005126497888"/>
</listOfSpecies>
<listOfParameters>
<parameter metaid="k1a" id="k1a" value="0.177252330941141"/>
<parameter metaid="k1aBasic" id="k1aBasic" value="0.000394105679186913"/>
<parameter metaid="k1b" id="k1b" value="0.174529566448397"/>
<parameter metaid="k1c" id="k1c" value="0.050861851404055"/>
<parameter metaid="k1d" id="k1d" value="499999.999999974"/>
<parameter metaid="k1e" id="k1e" value="1.00000000000005e-06"/>
<parameter metaid="k1f" id="k1f" value="499999.990737798"/>
<parameter metaid="k1g" id="k1g" value="1931.1338834437"/>
<parameter metaid="k1r" id="k1r" value="0.0266983879216281"/>
<parameter metaid="k21" id="k21" value="2.13019897196189"/>
<parameter metaid="k22" id="k22" value="658.762927786248"/>
<parameter metaid="k3" id="k3" value="4.94369803061052e-05"/>
<parameter metaid="k_IRSiP_DosR" id="k_IRSiP_DosR" value="37.9636812744313"/>
<parameter metaid="km2" id="km2" value="1.16168060611079"/>
<parameter metaid="km3" id="km3" value="0.416147033419453"/>
<parameter metaid="insulin" id="insulin" value="0.3" constant="false"/>
<parameter metaid="insulin_time_1" id="insulin_time_1" value="0" units="time"/>
<parameter metaid="insulin_time_2" id="insulin_time_2" value="1000" units="time"/>
<parameter metaid="insulin_dose_1" id="insulin_dose_1" value="0.3" units="substance"/>
<parameter metaid="insulin_dose_2" id="insulin_dose_2" value="0" units="substance"/>
</listOfParameters>
<listOfRules>
<assignmentRule metaid="CDMT00043" variable="insulin">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<times/>
<ci> insulin_dose_1 </ci>
<piecewise>
<piece>
<cn type="integer"> 0 </cn>
<apply>
<lt/>
<apply>
<minus/>
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
<ci> insulin_time_1 </ci>
</apply>
<cn type="integer"> 0 </cn>
</apply>
</piece>
<otherwise>
<cn type="integer"> 1 </cn>
</otherwise>
</piecewise>
</apply>
<apply>
<times/>
<ci> insulin_dose_2 </ci>
<piecewise>
<piece>
<cn type="integer"> 0 </cn>
<apply>
<lt/>
<apply>
<minus/>
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
<ci> insulin_time_2 </ci>
</apply>
<cn type="integer"> 0 </cn>
</apply>
</piece>
<otherwise>
<cn type="integer"> 1 </cn>
</otherwise>
</piecewise>
</apply>
</apply>
</math>
</assignmentRule>
</listOfRules>
<listOfReactions>
<reaction metaid="v1_v_0" id="v1_v_0" name="v_0" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00001" species="IR"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00002" species="IRins"/>
</listOfProducts>
<kineticLaw metaid="CDMT00003">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<apply>
<plus/>
<apply>
<times/>
<ci> IR </ci>
<ci> k1aBasic </ci>
</apply>
<apply>
<times/>
<ci> IR </ci>
<ci> insulin </ci>
<ci> k1a </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v2_v_1" id="v2_v_1" name="v_1" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00004" species="IRins"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00005" species="IR"/>
</listOfProducts>
<kineticLaw metaid="CDMT00006">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IRins </ci>
<ci> k1b </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v3_v_2" id="v3_v_2" name="v_2" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00007" species="IRins"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00008" species="IRp"/>
</listOfProducts>
<kineticLaw metaid="CDMT00009">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IRins </ci>
<ci> k1c </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v4_v_3" id="v4_v_3" name="v_3" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00010" species="IRp"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00011" species="IRiP"/>
</listOfProducts>
<kineticLaw metaid="CDMT00012">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IRp </ci>
<ci> k1d </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v5_v_4" id="v5_v_4" name="v_4" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00013" species="IRiP"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00014" species="IRi"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00015" species="Xp"/>
</listOfModifiers>
<kineticLaw metaid="CDMT00016">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IRiP </ci>
<apply>
<plus/>
<ci> k1e </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> Xp </ci>
<ci> k1f </ci>
</apply>
<apply>
<plus/>
<ci> Xp </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v6_v_5" id="v6_v_5" name="v_5" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00017" species="IRp"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00018" species="IR"/>
</listOfProducts>
<kineticLaw metaid="CDMT00019">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IRp </ci>
<ci> k1g </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v7_v_6" id="v7_v_6" name="v_6" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00020" species="IRi"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00021" species="IR"/>
</listOfProducts>
<kineticLaw metaid="CDMT00022">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IRi </ci>
<ci> k1r </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v8_v_7" id="v8_v_7" name="v_7" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00023" species="IRS"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00024" species="IRSiP"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00025" species="IRiP"/>
<modifierSpeciesReference metaid="CDMT00026" species="IRp"/>
</listOfModifiers>
<kineticLaw metaid="CDMT00027">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IRS </ci>
<ci> k21 </ci>
<apply>
<plus/>
<ci> IRp </ci>
<apply>
<times/>
<ci> IRiP </ci>
<ci> k22 </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v9_v_8" id="v9_v_8" name="v_8" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00028" species="IRSiP"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00029" species="IRS"/>
</listOfProducts>
<kineticLaw metaid="CDMT00030">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IRSiP </ci>
<ci> km2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v10_v_9" id="v10_v_9" name="v_9" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00031" species="X"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00032" species="Xp"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00033" species="IRSiP"/>
</listOfModifiers>
<kineticLaw metaid="CDMT00034">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> IRSiP </ci>
<ci> X </ci>
<ci> k3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="v11_v_10" id="v11_v_10" name="v_10" reversible="false">
<listOfReactants>
<speciesReference metaid="CDMT00035" species="Xp"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00036" species="X"/>
</listOfProducts>
<kineticLaw metaid="CDMT00037">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cyt </ci>
<ci> Xp </ci>
<ci> km3 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>