466 lines
19 KiB
XML
466 lines
19 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" layout:required="false" comp:required="true">
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<model metaid="iBioSim1" id="Population">
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<listOfFunctionDefinitions>
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<functionDefinition id="get2DArrayElement" name="get2DArrayElement">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<lambda>
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<bvar>
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<ci> a </ci>
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</bvar>
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<bvar>
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<ci> b </ci>
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</bvar>
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<bvar>
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<ci> c </ci>
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</bvar>
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<ci> a </ci>
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</lambda>
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</math>
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</functionDefinition>
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</listOfFunctionDefinitions>
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<listOfUnitDefinitions>
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<unitDefinition id="u_1_second_n1">
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<listOfUnits>
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<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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</listOfUnitDefinitions>
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<listOfCompartments>
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<compartment id="Grid" spatialDimensions="3" size="1" constant="true">
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<annotation>
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<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
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</annotation>
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</compartment>
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</listOfCompartments>
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<listOfSpecies>
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<species metaid="iBioSim26" id="CII" compartment="Grid" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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<annotation>
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<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
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</annotation>
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</species>
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</listOfSpecies>
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<listOfParameters>
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<parameter metaid="iBioSim2" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
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<parameter metaid="iBioSim3" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim4" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
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<parameter metaid="iBioSim5" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim6" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
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<parameter metaid="iBioSim7" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim8" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim9" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim10" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
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<parameter metaid="iBioSim11" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
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<parameter metaid="iBioSim12" id="kmdiff_f" name="Forward membrane diffusion rate" value="1" constant="true"/>
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<parameter metaid="iBioSim13" id="kmdiff_r" name="Reverse membrane diffusion rate" value="0.01" constant="true"/>
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<parameter metaid="iBioSim14" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
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<parameter metaid="iBioSim15" id="kecd" name="Extracellular degradation rate" value="0.005" constant="true"/>
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<parameter metaid="iBioSim16" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
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<parameter metaid="iBioSim17" id="nr" name="Initial RNAP count" value="30" constant="true"/>
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<parameter metaid="iBioSim18" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
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<parameter metaid="iBioSim19" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
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<parameter metaid="iBioSim20" id="ng" name="Initial promoter count" value="2" constant="true"/>
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<parameter metaid="iBioSim21" id="np" name="Stoichiometry of production" value="10" constant="true"/>
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<parameter metaid="iBioSim22" id="ka" name="Activated production rate" value="0.25" constant="true"/>
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<parameter metaid="iBioSim23" id="kecdiff" name="Extracellular diffusion rate" value="1" constant="true"/>
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<parameter metaid="iBioSim24" id="lambda__locations" value="0" constant="false">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:C1="(0,0)"/>
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</annotation>
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</parameter>
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<parameter id="Divide__locations" value="0" constant="false">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:C2="(0,1)"/>
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</annotation>
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</parameter>
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</listOfParameters>
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<listOfReactions>
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<reaction metaid="Degradation_CII" sboTerm="SBO:0000179" id="Degradation_CII" reversible="false" fast="false" compartment="Grid">
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<annotation>
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<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
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</annotation>
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<listOfReactants>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfReactants>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> kecd </ci>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<ci> i </ci>
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<ci> j </ci>
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</apply>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="i">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
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</annotation>
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</localParameter>
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<localParameter id="j">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
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</annotation>
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</localParameter>
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<localParameter id="kecd" value="0.005" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="Diffusion_CII_Above" id="Diffusion_CII_Above" reversible="true" fast="false" compartment="Grid">
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<annotation>
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<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
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</annotation>
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<listOfReactants>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<times/>
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<ci> kecdiff </ci>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<ci> i </ci>
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<ci> j </ci>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci> kecdiff </ci>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<apply>
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<minus/>
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<ci> i </ci>
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<cn type="integer"> 1 </cn>
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</apply>
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<apply>
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<plus/>
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<ci> j </ci>
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<cn type="integer"> 0 </cn>
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</apply>
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</apply>
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</apply>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="i">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
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</annotation>
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</localParameter>
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<localParameter id="j">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
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</annotation>
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</localParameter>
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<localParameter id="kecdiff" value="1" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="Diffusion_CII_Below" id="Diffusion_CII_Below" reversible="true" fast="false" compartment="Grid">
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<annotation>
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<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
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</annotation>
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<listOfReactants>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<times/>
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<ci> kecdiff </ci>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<ci> i </ci>
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<ci> j </ci>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci> kecdiff </ci>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<apply>
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<plus/>
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<ci> i </ci>
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<cn type="integer"> 1 </cn>
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</apply>
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<apply>
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<plus/>
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<ci> j </ci>
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<cn type="integer"> 0 </cn>
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</apply>
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</apply>
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</apply>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="i">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
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</annotation>
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</localParameter>
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<localParameter id="j">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
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</annotation>
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</localParameter>
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<localParameter id="kecdiff" value="1" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="Diffusion_CII_Left" id="Diffusion_CII_Left" reversible="true" fast="false" compartment="Grid">
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<annotation>
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<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
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</annotation>
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<listOfReactants>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<times/>
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<ci> kecdiff </ci>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<ci> i </ci>
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<ci> j </ci>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci> kecdiff </ci>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<apply>
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<plus/>
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<ci> i </ci>
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<cn type="integer"> 0 </cn>
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</apply>
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<apply>
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<minus/>
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<ci> j </ci>
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<cn type="integer"> 1 </cn>
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</apply>
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</apply>
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</apply>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="i">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
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</annotation>
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</localParameter>
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<localParameter id="j">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
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</annotation>
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</localParameter>
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<localParameter id="kecdiff" value="1" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="Diffusion_CII_Right" id="Diffusion_CII_Right" reversible="true" fast="false" compartment="Grid">
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<annotation>
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<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
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</annotation>
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<listOfReactants>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<times/>
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<ci> kecdiff </ci>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<ci> i </ci>
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<ci> j </ci>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci> kecdiff </ci>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<apply>
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<plus/>
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<ci> i </ci>
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<cn type="integer"> 0 </cn>
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</apply>
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<apply>
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<plus/>
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<ci> j </ci>
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<cn type="integer"> 1 </cn>
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</apply>
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</apply>
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</apply>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="i">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
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</annotation>
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</localParameter>
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<localParameter id="j">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
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</annotation>
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</localParameter>
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<localParameter id="kecdiff" value="1" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="MembraneDiffusion_CII" id="MembraneDiffusion_CII" reversible="true" fast="false" compartment="Grid">
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<annotation>
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<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:type="grid"/>
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</annotation>
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<listOfReactants>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="CII" stoichiometry="1" constant="false"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<times/>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> kmdiff_f </ci>
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<ci> i </ci>
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<ci> j </ci>
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</apply>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<ci> i </ci>
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<ci> j </ci>
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</apply>
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</apply>
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<apply>
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<times/>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> kmdiff_r </ci>
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<ci> i </ci>
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<ci> j </ci>
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</apply>
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<apply>
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<ci> get2DArrayElement </ci>
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<ci> CII </ci>
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<ci> i </ci>
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<ci> j </ci>
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</apply>
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</apply>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="i">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
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</annotation>
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</localParameter>
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<localParameter id="j">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
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</annotation>
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</localParameter>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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</listOfReactions>
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<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
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<layout:layout layout:id="iBioSim">
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<layout:dimensions layout:width="0" layout:height="0"/>
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<layout:listOfTextGlyphs>
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<layout:textGlyph layout:id="TextGlyph__C1" layout:text="C1" layout:graphicalObject="Glyph__C1">
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<layout:boundingBox>
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<layout:position layout:x="30" layout:y="30"/>
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<layout:dimensions layout:width="80" layout:height="40"/>
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</layout:boundingBox>
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</layout:textGlyph>
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<layout:textGlyph layout:id="TextGlyph__C2" layout:text="C2" layout:graphicalObject="Glyph__C2">
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<layout:boundingBox>
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<layout:position layout:x="140" layout:y="30"/>
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<layout:dimensions layout:width="80" layout:height="40"/>
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</layout:boundingBox>
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</layout:textGlyph>
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</layout:listOfTextGlyphs>
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<layout:listOfAdditionalGraphicalObjects>
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<layout:generalGlyph layout:id="Glyph__C1" layout:reference="C1">
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<layout:boundingBox>
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<layout:position layout:x="30" layout:y="30"/>
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<layout:dimensions layout:width="80" layout:height="40"/>
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</layout:boundingBox>
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</layout:generalGlyph>
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<layout:generalGlyph layout:id="Glyph__C2" layout:reference="C2">
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<layout:boundingBox>
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<layout:position layout:x="140" layout:y="30"/>
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<layout:dimensions layout:width="80" layout:height="40"/>
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</layout:boundingBox>
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</layout:generalGlyph>
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</layout:listOfAdditionalGraphicalObjects>
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</layout:layout>
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</layout:listOfLayouts>
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<comp:listOfSubmodels>
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<comp:submodel metaid="iBioSim25" comp:id="GRID__lambda" comp:modelRef="lambda">
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<annotation>
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<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
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</annotation>
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<comp:listOfDeletions>
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<comp:deletion comp:portRef="rule__Total"/>
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<comp:deletion comp:portRef="constraint__CI20"/>
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<comp:deletion comp:portRef="constraint__CII50"/>
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<comp:deletion comp:portRef="event__CellDivision"/>
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</comp:listOfDeletions>
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</comp:submodel>
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<comp:submodel comp:id="GRID__Divide" comp:modelRef="Divide">
|
|
<annotation>
|
|
<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
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|
</annotation>
|
|
</comp:submodel>
|
|
</comp:listOfSubmodels>
|
|
</model>
|
|
<comp:listOfExternalModelDefinitions>
|
|
<comp:externalModelDefinition comp:id="lambda" comp:source="file:lambda.xml" comp:md5="9fb1f105f55254ab934bf32ed25a0708"/>
|
|
<comp:externalModelDefinition comp:id="Divide" comp:source="file:Divide.xml" comp:md5="0a417cb64224a4ab9c9b82acab9082d4"/>
|
|
</comp:listOfExternalModelDefinitions>
|
|
</sbml>
|