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- corrected examples
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@fbergmann
fbergmann committed Dec 4, 2013
1 parent 1b7b206 commit e52ccdf
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Showing 9 changed files with 610 additions and 663 deletions.
43 changes: 21 additions & 22 deletions examples/The_Brusselator.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
<model id="The_Brusselator_Application0" name="The Brusselator_Application0">
<listOfUnitDefinitions>
<unitDefinition id="substance">
Expand Down Expand Up @@ -120,10 +120,10 @@
</species>
</listOfSpecies>
<listOfParameters>
<parameter id="x" value="0" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
<parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
<spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
</parameter>
<parameter id="y" value="0" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
<parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
<spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
</parameter>
<parameter id="X_diff" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
Expand Down Expand Up @@ -182,7 +182,7 @@
</vcell:VCellInfo>
</annotation>
<listOfProducts>
<speciesReference species="X" stoichiometry="1"/>
<speciesReference species="X" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
Expand All @@ -204,10 +204,10 @@
</vcell:VCellInfo>
</annotation>
<listOfReactants>
<speciesReference species="Y" stoichiometry="1"/>
<speciesReference species="Y" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="X" stoichiometry="1"/>
<speciesReference species="X" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
Expand All @@ -231,10 +231,10 @@
</vcell:VCellInfo>
</annotation>
<listOfReactants>
<speciesReference species="X" stoichiometry="1"/>
<speciesReference species="X" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Y" stoichiometry="1"/>
<speciesReference species="Y" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
Expand All @@ -257,7 +257,7 @@
</vcell:VCellInfo>
</annotation>
<listOfReactants>
<speciesReference species="X" stoichiometry="1"/>
<speciesReference species="X" stoichiometry="1" constant="true"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
Expand Down Expand Up @@ -287,17 +287,17 @@
<spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
</spatial:listOfDomainTypes>
<spatial:listOfDomains>
<spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain1" spatial:implicit="false">
<spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain1">
<spatial:listOfInteriorPoints>
<spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
</spatial:listOfInteriorPoints>
</spatial:domain>
<spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain0" spatial:implicit="false">
<spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain0">
<spatial:listOfInteriorPoints>
<spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
</spatial:listOfInteriorPoints>
</spatial:domain>
<spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane" spatial:implicit="true"/>
<spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
</spatial:listOfDomains>
<spatial:listOfAdjacentDomains>
<spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
Expand All @@ -306,45 +306,44 @@
<spatial:listOfGeometryDefinitions>
<spatial:analyticGeometry spatial:spatialId="Geometry3">
<spatial:listOfAnalyticVolumes>

<spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="0">
<spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<piecewise>
<piece>
<cn> 1 </cn>
<cn type="integer"> 1 </cn>
<apply>
<and/>
<apply>
<geq/>
<ci> x </ci>
<cn> 2 </cn>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<leq/>
<ci> x </ci>
<cn> 98 </cn>
<cn type="integer"> 98 </cn>
</apply>
<apply>
<geq/>
<ci> y </ci>
<cn> 2 </cn>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<leq/>
<ci> y </ci>
<cn> 98 </cn>
<cn type="integer"> 98 </cn>
</apply>
</apply>
</piece>
<otherwise>
<cn> 0 </cn>
<cn type="integer"> 0 </cn>
</otherwise>
</piecewise>
</math>
</spatial:analyticVolume>
<spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="1">
<spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn> 1 </cn>
<cn type="integer"> 1 </cn>
</math>
</spatial:analyticVolume>
</spatial:listOfAnalyticVolumes>
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43 changes: 21 additions & 22 deletions examples/The_Brusselator_300x300.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
<model id="The_Brusselator_Application0" name="The Brusselator_Application0">
<listOfUnitDefinitions>
<unitDefinition id="substance">
Expand Down Expand Up @@ -120,10 +120,10 @@
</species>
</listOfSpecies>
<listOfParameters>
<parameter id="x" value="0" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
<parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
<spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
</parameter>
<parameter id="y" value="0" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
<parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
<spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
</parameter>
<parameter id="X_diff" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
Expand Down Expand Up @@ -182,7 +182,7 @@
</vcell:VCellInfo>
</annotation>
<listOfProducts>
<speciesReference species="X" stoichiometry="1"/>
<speciesReference species="X" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
Expand All @@ -204,10 +204,10 @@
</vcell:VCellInfo>
</annotation>
<listOfReactants>
<speciesReference species="Y" stoichiometry="1"/>
<speciesReference species="Y" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="X" stoichiometry="1"/>
<speciesReference species="X" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
Expand All @@ -231,10 +231,10 @@
</vcell:VCellInfo>
</annotation>
<listOfReactants>
<speciesReference species="X" stoichiometry="1"/>
<speciesReference species="X" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Y" stoichiometry="1"/>
<speciesReference species="Y" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
Expand All @@ -257,7 +257,7 @@
</vcell:VCellInfo>
</annotation>
<listOfReactants>
<speciesReference species="X" stoichiometry="1"/>
<speciesReference species="X" stoichiometry="1" constant="true"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
Expand Down Expand Up @@ -287,17 +287,17 @@
<spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
</spatial:listOfDomainTypes>
<spatial:listOfDomains>
<spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain1" spatial:implicit="false">
<spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain1">
<spatial:listOfInteriorPoints>
<spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
</spatial:listOfInteriorPoints>
</spatial:domain>
<spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain0" spatial:implicit="false">
<spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain0">
<spatial:listOfInteriorPoints>
<spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
</spatial:listOfInteriorPoints>
</spatial:domain>
<spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane" spatial:implicit="true"/>
<spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
</spatial:listOfDomains>
<spatial:listOfAdjacentDomains>
<spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
Expand All @@ -306,45 +306,44 @@
<spatial:listOfGeometryDefinitions>
<spatial:analyticGeometry spatial:spatialId="Geometry3">
<spatial:listOfAnalyticVolumes>

<spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="0">
<spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<piecewise>
<piece>
<cn> 1 </cn>
<cn type="integer"> 1 </cn>
<apply>
<and/>
<apply>
<geq/>
<ci> x </ci>
<cn> 2 </cn>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<leq/>
<ci> x </ci>
<cn> 298 </cn>
<cn type="integer"> 298 </cn>
</apply>
<apply>
<geq/>
<ci> y </ci>
<cn> 2 </cn>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<leq/>
<ci> y </ci>
<cn> 298 </cn>
<cn type="integer"> 298 </cn>
</apply>
</apply>
</piece>
<otherwise>
<cn> 0 </cn>
<cn type="integer"> 0 </cn>
</otherwise>
</piecewise>
</math>
</spatial:analyticVolume>
<spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="1">
<spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn> 1 </cn>
<cn type="integer"> 1 </cn>
</math>
</spatial:analyticVolume>
</spatial:listOfAnalyticVolumes>
Expand Down
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