data/vcell-rest/src/test/resources/TestVCML.vcml

<?xml version="1.0" encoding="UTF-8"?>
<!--This biomodel was generated in VCML Version JimDev_Version_7.5.0_build_1234-->
<vcml xmlns="http://sourceforge.net/projects/vcell/vcml" Version="JimDev_Version_7.5.0_build_1234">
  <BioModel Name="TestBioModel">
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cloned from 'Solver Suite test_with_estimation' owned by user frm
cloned from 'Solver Suite beta' owned by user anu
cloned from 'Solver Suite' owned by user schaff
cloned from 'Site visit ' owned by user les</Annotation>
    <Model Name="unnamed">
      <Annotation>cloned from 'unnamed' owned by user schaff
cloned from 'unnamed' owned by user frm
cloned from 'unnamed' owned by user anu
cloned from 'unnamed' owned by user schaff
cloned from 'unnamed' owned by user les</Annotation>
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      <Compound Name="s1" />
      <Compound Name="s4" />
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      <Feature Name="nuc" KeyValue="91347990" />
      <Feature Name="EC" KeyValue="91347984" />
      <Membrane InsideFeature="nuc" OutsideFeature="cyt" PositiveFeature="nuc" NegativeFeature="cyt" MembraneVoltage="Voltage_nm" Name="nm" KeyValue="91347989" />
      <Membrane InsideFeature="cyt" OutsideFeature="EC" PositiveFeature="cyt" NegativeFeature="EC" MembraneVoltage="Voltage_pm" Name="pm" KeyValue="91347986" />
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      <LocalizedCompound Name="Ran_cyt" CompoundRef="s1" Structure="cyt" OverrideName="true" KeyValue="91347997" />
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        <Reactant LocalizedCompoundRef="RanC_cyt" Stoichiometry="1" KeyValue="91347999" />
        <Product LocalizedCompoundRef="C_cyt" Stoichiometry="1" KeyValue="91348000" />
        <Product LocalizedCompoundRef="Ran_cyt" Stoichiometry="1" KeyValue="91348001" />
        <Kinetics KineticsType="MassAction">
          <Parameter Name="J" Role="reaction rate" Unit="uM.s-1">((Kf * RanC_cyt) - ((Kr * C_cyt) * Ran_cyt))</Parameter>
          <Parameter Name="Kf" Role="forward rate constant" Unit="s-1">1.0</Parameter>
          <Parameter Name="Kr" Role="reverse rate constant" Unit="s-1.uM-1">1000.0</Parameter>
        </Kinetics>
      </SimpleReaction>
      <FluxStep Name="flux0" Structure="nm" Reversible="true" FluxOption="MolecularOnly" KeyValue="91348002">
        <Reactant LocalizedCompoundRef="RanC_cyt" Stoichiometry="1" />
        <Product LocalizedCompoundRef="RanC_nuc" Stoichiometry="1" />
        <Kinetics KineticsType="GeneralKinetics">
          <Parameter Name="J" Role="reaction rate" Unit="uM.um.s-1">(kfl * (RanC_cyt - RanC_nuc))</Parameter>
          <Parameter Name="I" Role="inward current density" Unit="pA.um-2">0.0</Parameter>
          <Parameter Name="netValence" Role="net charge valence" Unit="1">1.0</Parameter>
          <Parameter Name="kfl" Role="user defined" Unit="um.s-1">2.0</Parameter>
        </Kinetics>
      </FluxStep>
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cloned from 'non-spatial ODE' owned by user anu
cloned from 'non-spatial ODE' owned by user schaff
cloned from 'non-spatial ODE' owned by user les
(copied from non-spatial stochastic) (copied from 3D pde)</Annotation>
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        </FeatureMapping>
        <FeatureMapping Feature="nuc" GeometryClass="Compartment" SubVolume="Compartment" Size="3697.013658772733">
          <BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
        </FeatureMapping>
        <FeatureMapping Feature="EC" GeometryClass="Compartment" SubVolume="Compartment" Size="124712.10435961554">
          <BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
        </FeatureMapping>
        <MembraneMapping Membrane="nm" Size="1406.7733692487282" CalculateVoltage="false" SpecificCapacitance="1.0" InitialVoltage="0.0" GeometryClass="Compartment">
          <BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
        </MembraneMapping>
        <MembraneMapping Membrane="pm" Size="4738.640600365477" CalculateVoltage="false" SpecificCapacitance="1.0" InitialVoltage="0.0" GeometryClass="Compartment">
          <BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
        </MembraneMapping>
      </GeometryContext>
      <ReactionContext>
        <LocalizedCompoundSpec LocalizedCompoundRef="RanC_cyt" ForceConstant="false" WellMixed="false" ForceContinuous="false">
          <InitialConcentration>0.0</InitialConcentration>
          <Diffusion>10.0</Diffusion>
        </LocalizedCompoundSpec>
        <LocalizedCompoundSpec LocalizedCompoundRef="Ran_cyt" ForceConstant="false" WellMixed="false" ForceContinuous="false">
          <InitialConcentration>0.0</InitialConcentration>
          <Diffusion>10.0</Diffusion>
        </LocalizedCompoundSpec>
        <LocalizedCompoundSpec LocalizedCompoundRef="C_cyt" ForceConstant="false" WellMixed="false" ForceContinuous="false">
          <InitialConcentration>0.0</InitialConcentration>
          <Diffusion>10.0</Diffusion>
        </LocalizedCompoundSpec>
        <LocalizedCompoundSpec LocalizedCompoundRef="RanC_nuc" ForceConstant="false" WellMixed="false" ForceContinuous="false">
          <InitialConcentration>4.493165893949507E-4</InitialConcentration>
          <Diffusion>10.0</Diffusion>
        </LocalizedCompoundSpec>
        <ReactionSpec ReactionStepRef="r0" ReactionMapping="included" />
        <ReactionSpec ReactionStepRef="flux0" ReactionMapping="included" />
      </ReactionContext>
      <MathDescription Name="non-spatial ODE_generated">
        <Annotation>cloned from 'non-spatial ODE_generated' owned by user schaff
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        <Constant Name="_F_">96480.0</Constant>
        <Constant Name="_F_nmol_">9.648E-5</Constant>
        <Constant Name="_K_GHK_">1.0E-9</Constant>
        <Constant Name="_N_pmol_">6.02E11</Constant>
        <Constant Name="_PI_">3.141592653589793</Constant>
        <Constant Name="_R_">8314.0</Constant>
        <Constant Name="_T_">300.0</Constant>
        <Constant Name="C_cyt_init_uM">0.0</Constant>
        <Constant Name="K_millivolts_per_volt">1000.0</Constant>
        <Constant Name="Kf">1.0</Constant>
        <Constant Name="kfl">2.0</Constant>
        <Constant Name="KMOLE">(1.0 / 602.0)</Constant>
        <Constant Name="Kr">1000.0</Constant>
        <Constant Name="netValence">1.0</Constant>
        <Constant Name="Ran_cyt_init_uM">0.0</Constant>
        <Constant Name="RanC_cyt_init_uM">0.0</Constant>
        <Constant Name="RanC_nuc_init_uM">4.493165893949507E-4</Constant>
        <Constant Name="Size_cyt">14891.899581611733</Constant>
        <Constant Name="Size_EC">124712.10435961554</Constant>
        <Constant Name="Size_nm">1406.7733692487282</Constant>
        <Constant Name="Size_nuc">3697.013658772733</Constant>
        <Constant Name="Size_pm">4738.640600365477</Constant>
        <Constant Name="Voltage_nm">0.0</Constant>
        <Constant Name="Voltage_pm">0.0</Constant>
        <VolumeVariable Name="C_cyt" Domain="Compartment" />
        <VolumeVariable Name="RanC_nuc" Domain="Compartment" />
        <Function Name="J_flux0" Domain="Compartment">(kfl * (RanC_cyt - RanC_nuc))</Function>
        <Function Name="J_r0" Domain="Compartment">((Kf * RanC_cyt) - ((Kr * C_cyt) * Ran_cyt))</Function>
        <Function Name="K_Ran_cyt_total" Domain="Compartment">((Size_cyt * Ran_cyt_init_uM) - (Size_cyt * C_cyt_init_uM))</Function>
        <Function Name="K_RanC_cyt_total" Domain="Compartment">((Size_cyt * RanC_cyt_init_uM) + (Size_cyt * C_cyt_init_uM) + (Size_nuc * RanC_nuc_init_uM))</Function>
        <Function Name="KFlux_nm_cyt" Domain="Compartment">(Size_nm / Size_cyt)</Function>
        <Function Name="KFlux_nm_nuc" Domain="Compartment">(Size_nm / Size_nuc)</Function>
        <Function Name="Ran_cyt" Domain="Compartment">((K_Ran_cyt_total + (Size_cyt * C_cyt)) / Size_cyt)</Function>
        <Function Name="RanC_cyt" Domain="Compartment">((K_RanC_cyt_total - (Size_cyt * C_cyt) - (Size_nuc * RanC_nuc)) / Size_cyt)</Function>
        <CompartmentSubDomain Name="Compartment">
          <BoundaryType Boundary="Xm" Type="Value" />
          <BoundaryType Boundary="Xp" Type="Value" />
          <BoundaryType Boundary="Ym" Type="Value" />
          <BoundaryType Boundary="Yp" Type="Value" />
          <BoundaryType Boundary="Zm" Type="Value" />
          <BoundaryType Boundary="Zp" Type="Value" />
          <OdeEquation Name="C_cyt" SolutionType="Unknown">
            <Rate>J_r0</Rate>
            <Initial>C_cyt_init_uM</Initial>
          </OdeEquation>
          <OdeEquation Name="RanC_nuc" SolutionType="Unknown">
            <Rate>(KFlux_nm_nuc * J_flux0)</Rate>
            <Initial>RanC_nuc_init_uM</Initial>
          </OdeEquation>
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      </MathDescription>
      <Simulation Name="test">
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        <SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Combined Stiff Solver (IDA/CVODE)">
          <TimeBound StartTime="0.0" EndTime="10.0" />
          <TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
          <ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
          <OutputOptions OutputTimeStep="0.2" />
          <NumberProcessors>1</NumberProcessors>
        </SolverTaskDescription>
        <MathOverrides />
      </Simulation>
      <AnalysisTaskList>
        <ParameterEstimationTask Name="task1">
          <parameterMappingSpecList>
            <parameterMappingSpec parameterReferenceAttribute="unnamed.r0.Kf" lowLimit="0.1" highLimit="10.0" currentValue="1.0" selected="true" />
            <parameterMappingSpec parameterReferenceAttribute="unnamed.r0.Kr" lowLimit="100.0" highLimit="10000.0" currentValue="1000.0" selected="true" />
            <parameterMappingSpec parameterReferenceAttribute="unnamed.flux0.netValence" lowLimit="0.1" highLimit="10.0" currentValue="1.0" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="unnamed.flux0.kfl" lowLimit="0.2" highLimit="20.0" currentValue="2.0" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.RanC_cyt_scs.initConc" lowLimit="0.0" highLimit="0.0" currentValue="0.0" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.Ran_cyt_scs.initConc" lowLimit="0.0" highLimit="0.0" currentValue="0.0" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.C_cyt_scs.initConc" lowLimit="0.0" highLimit="0.0" currentValue="0.0" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.RanC_nuc_scs.initConc" lowLimit="4.493165893949507E-5" highLimit="0.004493165893949507" currentValue="4.493165893949507E-4" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.cyt_mapping.Size" lowLimit="1489.1899581611733" highLimit="148918.99581611733" currentValue="14891.899581611733" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.nuc_mapping.Size" lowLimit="369.7013658772733" highLimit="36970.13658772733" currentValue="3697.013658772733" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.EC_mapping.Size" lowLimit="12471.210435961555" highLimit="1247121.0435961555" currentValue="124712.10435961554" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.nm_mapping.Voltage_nm_init" lowLimit="0.0" highLimit="0.0" currentValue="0.0" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.nm_mapping.Size" lowLimit="140.67733692487283" highLimit="14067.733692487282" currentValue="1406.7733692487282" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.pm_mapping.Voltage_pm_init" lowLimit="0.0" highLimit="0.0" currentValue="0.0" selected="false" />
            <parameterMappingSpec parameterReferenceAttribute="non_spatial_ODE.pm_mapping.Size" lowLimit="473.86406003654776" highLimit="47386.406003654774" currentValue="4738.640600365477" selected="false" />
          </parameterMappingSpecList>
          <referenceData numRows="3" numColumns="3">
            <dataColumnList>
              <dataColumn Name="t" weight="1.0" />
              <dataColumn Name="data1" weight="1.0" />
              <dataColumn Name="data2" weight="1.0" />
            </dataColumnList>
            <dataRowList>
              <dataRow>0.0 0.1 0.21</dataRow>
              <dataRow>0.1 0.15 0.31</dataRow>
              <dataRow>0.2 0.16 0.44</dataRow>
            </dataRowList>
          </referenceData>
          <referenceDataMappingSpecList>
            <referenceDataMappingSpec referenceDataColumnName="t" referenceDataModelSymbol="t" />
            <referenceDataMappingSpec referenceDataColumnName="data1" referenceDataModelSymbol="RanC_cyt" />
            <referenceDataMappingSpec referenceDataColumnName="data2" referenceDataModelSymbol="RanC_nuc" />
          </referenceDataMappingSpecList>
          <optimizationSolverSpec optimizationSolverType="Evolutionary Programming" NumOfRuns="1">
            <ListOfParameters>
              <Parameter Name="Number of Generations" Value="200.0" />
              <Parameter Name="Population Size" Value="20.0" />
              <Parameter Name="Random Number Generator" Value="1.0" />
              <Parameter Name="Seed" Value="0.0" />
            </ListOfParameters>
          </optimizationSolverSpec>
          <OptimizationResultSet>
            <bestOptRunResultSet>
              <ListOfParameters>
                <Parameter Name="Kf" Value="0.1" />
                <Parameter Name="Kr" Value="10000.0" />
              </ListOfParameters>
              <objectiveFunction Value="0.116056" />
              <ObjectiveFunctionEvaluations Value="4004" />
            </bestOptRunResultSet>
          </OptimizationResultSet>
        </ParameterEstimationTask>
      </AnalysisTaskList>
      <MicroscopeMeasurement Name="fluor">
        <ConvolutionKernel Type="ProjectionZKernel" />
      </MicroscopeMeasurement>
    </SimulationSpec>
    <pathwayModel>
      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" version="3.0" />
    </pathwayModel>
    <relationshipModel>
      <RMNS version="3.0" />
    </relationshipModel>
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      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
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