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<?xml version="1.0" encoding="UTF-8"?> |
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<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true"> |
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<model id="optoPlexin_PRG_rule_based_1_Dimensional" name="optoPlexin-PRG rule-based_1-Dimensional"> |
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<annotation> |
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<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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<vcell:VCMLSpecific> |
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<vcell:BioModel Name="optoPlexin_PRG_rule_based" KeyValue="115460581"/> |
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<vcell:SimulationSpec Name="_one__Dimensional" KeyValue="115460562"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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<listOfUnitDefinitions> |
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<unitDefinition id="substance"> |
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<listOfUnits> |
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<unit kind="item" exponent="1" scale="0" multiplier="1"/> |
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</listOfUnits> |
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</unitDefinition> |
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<unitDefinition id="volume"> |
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<listOfUnits> |
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<unit kind="metre" exponent="3" scale="-18" multiplier="1"/> |
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</listOfUnits> |
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</unitDefinition> |
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<unitDefinition id="area"> |
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<listOfUnits> |
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<unit kind="metre" exponent="2" scale="-12" multiplier="1"/> |
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</listOfUnits> |
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</unitDefinition> |
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<unitDefinition id="length"> |
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<listOfUnits> |
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<unit kind="metre" exponent="1" scale="-6" multiplier="1"/> |
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</listOfUnits> |
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</unitDefinition> |
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<unitDefinition id="time"> |
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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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<unitDefinition id="molecules"> |
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<listOfUnits> |
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<unit kind="item" exponent="1" scale="0" multiplier="1"/> |
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</listOfUnits> |
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</unitDefinition> |
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<unitDefinition id="s_1"> |
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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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<unitDefinition id="molecules_um_2"> |
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<listOfUnits> |
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<unit kind="dimensionless" exponent="1" scale="12" multiplier="1"/> |
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<unit kind="item" exponent="1" scale="0" multiplier="1"/> |
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<unit kind="metre" exponent="-2" scale="0" multiplier="1"/> |
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</listOfUnits> |
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</unitDefinition> |
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<unitDefinition id="uM"> |
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<listOfUnits> |
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<unit kind="dimensionless" exponent="1" scale="-3" multiplier="1"/> |
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<unit kind="mole" exponent="1" scale="0" multiplier="1"/> |
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<unit kind="metre" exponent="3" 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="Cyt" name="Cyt" spatialDimensions="3" size="50000" units="um3" constant="true"> |
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<spatial:compartmentMapping spatial:id="CytCyt" spatial:domainType="Cyt" spatial:unitSize="1"/> |
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</compartment> |
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<compartment id="EC" name="EC" spatialDimensions="3" size="50000" units="um3" constant="true"> |
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<spatial:compartmentMapping spatial:id="ECEC" spatial:domainType="EC" spatial:unitSize="1"/> |
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</compartment> |
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<compartment id="PM" name="PM" spatialDimensions="2" size="6563" constant="true"> |
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<spatial:compartmentMapping spatial:id="Cyt_EC_membranePM" spatial:domainType="Cyt_EC_membrane" spatial:unitSize="1"/> |
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</compartment> |
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</listOfCompartments> |
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<listOfSpecies> |
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<species id="opN" compartment="Cyt" initialConcentration="0.585" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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<annotation> |
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<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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<vcell:VCMLSpecific> |
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<vcell:Compound Name="s0"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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</species> |
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<species id="PRG" compartment="Cyt" initialConcentration="0.756" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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<annotation> |
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<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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<vcell:VCMLSpecific> |
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<vcell:Compound Name="s1"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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</species> |
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<species id="CIB1" compartment="PM" initialConcentration="564" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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<annotation> |
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<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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<vcell:VCMLSpecific> |
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<vcell:Compound Name="s2"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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</species> |
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<species id="opN_PRG" compartment="Cyt" initialConcentration="0.221" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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<annotation> |
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<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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<vcell:VCMLSpecific> |
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<vcell:Compound Name="s3"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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</species> |
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<species id="opN_CIB1" compartment="PM" initialConcentration="82" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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<annotation> |
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<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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<vcell:VCMLSpecific> |
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<vcell:Compound Name="s4"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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</species> |
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<species id="opA" compartment="Cyt" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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<annotation> |
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<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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<vcell:VCMLSpecific> |
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<vcell:Compound Name="s5"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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</species> |
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<species id="opA_PRG" compartment="Cyt" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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<annotation> |
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<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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|
<vcell:VCMLSpecific> |
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<vcell:Compound Name="s6"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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</species> |
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<species id="opA_CIB1" compartment="PM" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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|
<annotation> |
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|
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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<vcell:VCMLSpecific> |
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<vcell:Compound Name="s7"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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</species> |
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<species id="opN_PRG_CIB1" compartment="PM" initialConcentration="31.2" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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<annotation> |
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|
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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<vcell:VCMLSpecific> |
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<vcell:Compound Name="s8"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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</annotation> |
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</species> |
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<species id="opA_PRG_CIB1" compartment="PM" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> |
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|
<annotation> |
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|
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell"> |
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|
<vcell:VCMLSpecific> |
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<vcell:Compound Name="s9"/> |
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</vcell:VCMLSpecific> |
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</vcell:VCellInfo> |
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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 id="x" value="0" constant="true"> |
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<spatial:spatialSymbolReference spatial:spatialRef="x"/> |
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</parameter> |
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<parameter id="opN_diff" value="5" constant="true"> |
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<spatial:diffusionCoefficient spatial:variable="opN" spatial:type="isotropic"/> |
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</parameter> |
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<parameter id="opN_BC_Xm" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="opN" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/> |
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</parameter> |
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<parameter id="opN_BC_Xp" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="opN" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/> |
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</parameter> |
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<parameter id="PRG_diff" value="5" constant="true"> |
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<spatial:diffusionCoefficient spatial:variable="PRG" spatial:type="isotropic"/> |
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</parameter> |
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<parameter id="PRG_BC_Xm" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="PRG" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/> |
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</parameter> |
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<parameter id="PRG_BC_Xp" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="PRG" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/> |
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</parameter> |
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<parameter id="opN_PRG_diff" value="3" constant="true"> |
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<spatial:diffusionCoefficient spatial:variable="opN_PRG" spatial:type="isotropic"/> |
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</parameter> |
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<parameter id="opN_PRG_BC_Xm" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="opN_PRG" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/> |
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</parameter> |
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<parameter id="opN_PRG_BC_Xp" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="opN_PRG" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/> |
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</parameter> |
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<parameter id="opA_diff" value="5" constant="true"> |
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<spatial:diffusionCoefficient spatial:variable="opA" spatial:type="isotropic"/> |
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</parameter> |
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<parameter id="opA_BC_Xm" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="opA" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/> |
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</parameter> |
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<parameter id="opA_BC_Xp" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="opA" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/> |
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</parameter> |
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<parameter id="opA_PRG_diff" value="3" constant="true"> |
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<spatial:diffusionCoefficient spatial:variable="opA_PRG" spatial:type="isotropic"/> |
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</parameter> |
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<parameter id="opA_PRG_BC_Xm" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="opA_PRG" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/> |
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</parameter> |
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<parameter id="opA_PRG_BC_Xp" value="0" constant="true"> |
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<spatial:boundaryCondition spatial:variable="opA_PRG" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/> |
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</parameter> |
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<parameter id="Laser" units="s_1" constant="false"/> |
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<parameter id="op_PM_tot" units="molecules_um_2" constant="false"/> |
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<parameter id="PRG_PM_tot" units="molecules_um_2" constant="false"/> |
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<parameter id="op_Cyt_tot" units="uM" constant="false"/> |
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<parameter id="PRG_Cyt_tot" units="uM" constant="false"/> |
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<parameter id="Kdeff_opA_CIB1" value="1" units="uM" constant="true"/> |
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<parameter id="Kd_opN_CIB1" value="4" units="uM" constant="true"/> |
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<parameter id="Kd_op_PRG" value="2" units="uM" constant="true"/> |
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</listOfParameters> |
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<listOfRules> |
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<assignmentRule variable="Laser"> |
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|
<math xmlns="http://www.w3.org/1998/Math/MathML"> |
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|
<piecewise> |
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|
<piece> |
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|
<cn> 0.14 </cn> |
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<apply> |
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<gt/> |
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<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol> |
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<cn> 96 </cn> |
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</apply> |
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</piece> |
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<otherwise> |
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<cn> 0 </cn> |
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</otherwise> |
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</piecewise> |
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</math> |
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</assignmentRule> |
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<assignmentRule variable="op_PM_tot"> |
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<math xmlns="http://www.w3.org/1998/Math/MathML"> |
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<apply> |
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<plus/> |
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<ci> opA_CIB1 </ci> |
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<ci> opN_CIB1 </ci> |
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<ci> opA_PRG_CIB1 </ci> |
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<ci> opN_PRG_CIB1 </ci> |
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</apply> |
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</math> |
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</assignmentRule> |
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<assignmentRule variable="PRG_PM_tot"> |
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<math xmlns="http://www.w3.org/1998/Math/MathML"> |
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<apply> |
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|
<plus/> |
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<ci> opA_PRG_CIB1 </ci> |
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<ci> opN_PRG_CIB1 </ci> |
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</apply> |
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|
</math> |
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</assignmentRule> |
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|
<assignmentRule variable="op_Cyt_tot"> |
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|
<math xmlns="http://www.w3.org/1998/Math/MathML"> |
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|
<apply> |
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|
<plus/> |
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<ci> opA </ci> |
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<ci> opN </ci> |
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<ci> opA_PRG </ci> |
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<ci> opN_PRG </ci> |
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</apply> |
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|
</math> |
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|
</assignmentRule> |
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|
<assignmentRule variable="PRG_Cyt_tot"> |
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|
<math xmlns="http://www.w3.org/1998/Math/MathML"> |
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<apply> |
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|
<plus/> |
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<ci> PRG </ci> |
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<ci> opA_PRG </ci> |
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<ci> opN_PRG </ci> |
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</apply> |
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</math> |
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</assignmentRule> |
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</listOfRules> |
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|
<spatial:geometry spatial:id="vcell" spatial:coordinateSystem="cartesian"> |
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|
<spatial:listOfCoordinateComponents> |
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|
<spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX" spatial:unit="length"> |
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|
<spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/> |
|
|
<spatial:boundaryMax spatial:id="Xmax" spatial:value="1"/> |
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|
</spatial:coordinateComponent> |
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|
</spatial:listOfCoordinateComponents> |
|
|
<spatial:listOfDomainTypes> |
|
|
<spatial:domainType spatial:id="EC" spatial:spatialDimensions="3"/> |
|
|
<spatial:domainType spatial:id="Cyt" spatial:spatialDimensions="3"/> |
|
|
<spatial:domainType spatial:id="Cyt_EC_membrane" spatial:spatialDimensions="2"/> |
|
|
</spatial:listOfDomainTypes> |
|
|
<spatial:listOfDomains> |
|
|
<spatial:domain spatial:id="EC0" spatial:domainType="EC"> |
|
|
<spatial:listOfInteriorPoints> |
|
|
<spatial:interiorPoint spatial:coord1="0" spatial:coord2="5" spatial:coord3="5"/> |
|
|
</spatial:listOfInteriorPoints> |
|
|
</spatial:domain> |
|
|
<spatial:domain spatial:id="Cyt1" spatial:domainType="Cyt"> |
|
|
<spatial:listOfInteriorPoints> |
|
|
<spatial:interiorPoint spatial:coord1="0.0204081632653061" spatial:coord2="5" spatial:coord3="5"/> |
|
|
</spatial:listOfInteriorPoints> |
|
|
</spatial:domain> |
|
|
<spatial:domain spatial:id="membrane_EC0_Cyt1" spatial:domainType="Cyt_EC_membrane"/> |
|
|
</spatial:listOfDomains> |
|
|
<spatial:listOfAdjacentDomains> |
|
|
<spatial:adjacentDomains spatial:id="membrane_EC0_Cyt1_Cyt1" spatial:domain1="membrane_EC0_Cyt1" spatial:domain2="Cyt1"/> |
|
|
<spatial:adjacentDomains spatial:id="membrane_EC0_Cyt1_EC0" spatial:domain1="membrane_EC0_Cyt1" spatial:domain2="EC0"/> |
|
|
</spatial:listOfAdjacentDomains> |
|
|
<spatial:listOfGeometryDefinitions> |
|
|
<spatial:analyticGeometry spatial:id="Analytic_Geometry10" spatial:isActive="true"> |
|
|
<spatial:listOfAnalyticVolumes> |
|
|
<spatial:analyticVolume spatial:id="EC" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="EC"> |
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML"> |
|
|
<piecewise> |
|
|
<piece> |
|
|
<cn> 1 </cn> |
|
|
<apply> |
|
|
<lt/> |
|
|
<ci> x </ci> |
|
|
<cn> 0.01 </cn> |
|
|
</apply> |
|
|
</piece> |
|
|
<otherwise> |
|
|
<cn> 0 </cn> |
|
|
</otherwise> |
|
|
</piecewise> |
|
|
</math> |
|
|
</spatial:analyticVolume> |
|
|
<spatial:analyticVolume spatial:id="Cyt" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="Cyt"> |
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML"> |
|
|
<cn> 1 </cn> |
|
|
</math> |
|
|
</spatial:analyticVolume> |
|
|
</spatial:listOfAnalyticVolumes> |
|
|
</spatial:analyticGeometry> |
|
|
</spatial:listOfGeometryDefinitions> |
|
|
</spatial:geometry> |
|
|
</model> |
|
|
</sbml> |
|
|
|
