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BioModel.xml
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BioModel.xml
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<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" spatial:required="true" version="1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
<model id="optoPlexin_PRG_rule_based_1_Dimensional" name="optoPlexin-PRG rule-based_1-Dimensional">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:BioModel Name="optoPlexin_PRG_rule_based" KeyValue="115460581"/>
<vcell:SimulationSpec Name="_one__Dimensional" KeyValue="115460562"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
<spatial:geometry xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" id="vcell" spatial:coordinateSystem="cartesian" spatial:id="vcell">
<spatial:listOfAdjacentDomains>
<spatial:adjacentDomains id="membrane_EC0_Cyt1_Cyt1" spatial:domain1="membrane_EC0_Cyt1" spatial:domain2="Cyt1" spatial:id="membrane_EC0_Cyt1_Cyt1"/>
<spatial:adjacentDomains id="membrane_EC0_Cyt1_EC0" spatial:domain1="membrane_EC0_Cyt1" spatial:domain2="EC0" spatial:id="membrane_EC0_Cyt1_EC0"/>
</spatial:listOfAdjacentDomains>
<spatial:listOfCoordinateComponents>
<spatial:coordinateComponent id="x" spatial:id="x" spatial:type="cartesianX" spatial:unit="length">
<spatial:boundaryMin id="Xmin" spatial:id="Xmin" spatial:value="0.0"/>
<spatial:boundaryMax id="Xmax" spatial:id="Xmax" spatial:value="1.0"/>
</spatial:coordinateComponent>
</spatial:listOfCoordinateComponents>
<spatial:listOfDomains>
<spatial:domain id="EC0" spatial:domainType="EC" spatial:id="EC0">
<spatial:listOfInteriorPoints>
<spatial:interiorPoint spatial:coord1="0.0" spatial:coord2="5.0" spatial:coord3="5.0"/>
</spatial:listOfInteriorPoints>
</spatial:domain>
<spatial:domain id="Cyt1" spatial:domainType="Cyt" spatial:id="Cyt1">
<spatial:listOfInteriorPoints>
<spatial:interiorPoint spatial:coord1="0.0204081632653061" spatial:coord2="5.0" spatial:coord3="5.0"/>
</spatial:listOfInteriorPoints>
</spatial:domain>
<spatial:domain id="membrane_EC0_Cyt1" spatial:domainType="Cyt_EC_membrane" spatial:id="membrane_EC0_Cyt1"/>
</spatial:listOfDomains>
<spatial:listOfDomainTypes>
<spatial:domainType id="EC" spatial:id="EC" spatial:spatialDimensions="3"/>
<spatial:domainType id="Cyt" spatial:id="Cyt" spatial:spatialDimensions="3"/>
<spatial:domainType id="Cyt_EC_membrane" spatial:id="Cyt_EC_membrane" spatial:spatialDimensions="2"/>
</spatial:listOfDomainTypes>
<spatial:listOfGeometryDefinitions>
<spatial:analyticGeometry id="Analytic_Geometry10" spatial:id="Analytic_Geometry10" spatial:isActive="true">
<spatial:listOfAnalyticVolumes>
<spatial:analyticVolume spatial:domainType="EC" spatial:functionType="layered" spatial:ordinal="1">
<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:domainType="Cyt" spatial:functionType="layered" spatial:ordinal="0">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn> 1 </cn>
</math>
</spatial:analyticVolume>
</spatial:listOfAnalyticVolumes>
</spatial:analyticGeometry>
</spatial:listOfGeometryDefinitions>
</spatial:geometry>
<listOfUnitDefinitions>
<unitDefinition id="substance">
<listOfUnits>
<unit exponent="1" kind="item" multiplier="1" scale="0"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="volume">
<listOfUnits>
<unit exponent="3" kind="metre" multiplier="1" scale="-18"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="area">
<listOfUnits>
<unit exponent="2" kind="metre" multiplier="1" scale="-12"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="length">
<listOfUnits>
<unit exponent="1" kind="metre" multiplier="1" scale="-6"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="time">
<listOfUnits>
<unit exponent="1" kind="second" multiplier="1" scale="0"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="molecules">
<listOfUnits>
<unit exponent="1" kind="item" multiplier="1" scale="0"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="s_1">
<listOfUnits>
<unit exponent="-1" kind="second" multiplier="1" scale="0"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="molecules_um_2">
<listOfUnits>
<unit exponent="1" kind="dimensionless" multiplier="1" scale="12"/>
<unit exponent="1" kind="item" multiplier="1" scale="0"/>
<unit exponent="-2" kind="metre" multiplier="1" scale="0"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="uM">
<listOfUnits>
<unit exponent="1" kind="dimensionless" multiplier="1" scale="-3"/>
<unit exponent="1" kind="mole" multiplier="1" scale="0"/>
<unit exponent="3" kind="metre" multiplier="1" scale="0"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment constant="true" id="Cyt" name="Cyt" size="50000" spatialDimensions="3" units="um3">
<spatial:compartmentMapping xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" id="CytCyt" spatial:domainType="Cyt" spatial:id="CytCyt" spatial:unitSize="1.0"/>
</compartment>
<compartment constant="true" id="EC" name="EC" size="50000" spatialDimensions="3" units="um3">
<spatial:compartmentMapping xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" id="ECEC" spatial:domainType="EC" spatial:id="ECEC" spatial:unitSize="1.0"/>
</compartment>
<compartment constant="true" id="PM" name="PM" size="6563" spatialDimensions="2">
<spatial:compartmentMapping xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" id="Cyt_EC_membranePM" spatial:domainType="Cyt_EC_membrane" spatial:id="Cyt_EC_membranePM" spatial:unitSize="1.0"/>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="Cyt" constant="false" hasOnlySubstanceUnits="false" id="opN" initialConcentration="0.585" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s0"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
<species boundaryCondition="false" compartment="Cyt" constant="false" hasOnlySubstanceUnits="false" id="PRG" initialConcentration="0.756" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s1"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
<species boundaryCondition="false" compartment="PM" constant="false" hasOnlySubstanceUnits="false" id="CIB1" initialConcentration="564" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s2"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
<species boundaryCondition="false" compartment="Cyt" constant="false" hasOnlySubstanceUnits="false" id="opN_PRG" initialConcentration="0.221" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s3"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
<species boundaryCondition="false" compartment="PM" constant="false" hasOnlySubstanceUnits="false" id="opN_CIB1" initialConcentration="82" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s4"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
<species boundaryCondition="false" compartment="Cyt" constant="false" hasOnlySubstanceUnits="false" id="opA" initialConcentration="0" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s5"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
<species boundaryCondition="false" compartment="Cyt" constant="false" hasOnlySubstanceUnits="false" id="opA_PRG" initialConcentration="0" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s6"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
<species boundaryCondition="false" compartment="PM" constant="false" hasOnlySubstanceUnits="false" id="opA_CIB1" initialConcentration="0" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s7"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
<species boundaryCondition="false" compartment="PM" constant="false" hasOnlySubstanceUnits="false" id="opN_PRG_CIB1" initialConcentration="31.2" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s8"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
<species boundaryCondition="false" compartment="PM" constant="false" hasOnlySubstanceUnits="false" id="opA_PRG_CIB1" initialConcentration="0" substanceUnits="molecules">
<annotation>
<vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
<vcell:VCMLSpecific>
<vcell:Compound Name="s9"/>
</vcell:VCMLSpecific>
</vcell:VCellInfo>
</annotation>
</species>
</listOfSpecies>
<listOfParameters>
<parameter constant="true" id="x" value="0">
<spatial:spatialSymbolReference xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:spatialRef="x"/>
</parameter>
<parameter constant="true" id="opN_diff" value="5">
<spatial:diffusionCoefficient xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:type="isotropic" spatial:variable="opN"/>
</parameter>
<parameter constant="true" id="opN_BC_Xm" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmin" spatial:type="Neumann" spatial:variable="opN"/>
</parameter>
<parameter constant="true" id="opN_BC_Xp" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmax" spatial:type="Neumann" spatial:variable="opN"/>
</parameter>
<parameter constant="true" id="PRG_diff" value="5">
<spatial:diffusionCoefficient xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:type="isotropic" spatial:variable="PRG"/>
</parameter>
<parameter constant="true" id="PRG_BC_Xm" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmin" spatial:type="Neumann" spatial:variable="PRG"/>
</parameter>
<parameter constant="true" id="PRG_BC_Xp" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmax" spatial:type="Neumann" spatial:variable="PRG"/>
</parameter>
<parameter constant="true" id="opN_PRG_diff" value="3">
<spatial:diffusionCoefficient xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:type="isotropic" spatial:variable="opN_PRG"/>
</parameter>
<parameter constant="true" id="opN_PRG_BC_Xm" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmin" spatial:type="Neumann" spatial:variable="opN_PRG"/>
</parameter>
<parameter constant="true" id="opN_PRG_BC_Xp" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmax" spatial:type="Neumann" spatial:variable="opN_PRG"/>
</parameter>
<parameter constant="true" id="opA_diff" value="5">
<spatial:diffusionCoefficient xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:type="isotropic" spatial:variable="opA"/>
</parameter>
<parameter constant="true" id="opA_BC_Xm" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmin" spatial:type="Neumann" spatial:variable="opA"/>
</parameter>
<parameter constant="true" id="opA_BC_Xp" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmax" spatial:type="Neumann" spatial:variable="opA"/>
</parameter>
<parameter constant="true" id="opA_PRG_diff" value="3">
<spatial:diffusionCoefficient xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:type="isotropic" spatial:variable="opA_PRG"/>
</parameter>
<parameter constant="true" id="opA_PRG_BC_Xm" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmin" spatial:type="Neumann" spatial:variable="opA_PRG"/>
</parameter>
<parameter constant="true" id="opA_PRG_BC_Xp" value="0">
<spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Xmax" spatial:type="Neumann" spatial:variable="opA_PRG"/>
</parameter>
<parameter constant="false" id="Laser" units="s_1"/>
</listOfParameters>
<listOfRules>
<assignmentRule variable="Laser">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<piecewise>
<piece>
<cn> 0.14 </cn>
<apply>
<gt/>
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
<cn> 96 </cn>
</apply>
</piece>
<otherwise>
<cn> 0 </cn>
</otherwise>
</piecewise>
</math>
</assignmentRule>
</listOfRules>
</model>
</sbml>