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<?xml version="1.0" encoding="UTF-8"?>
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<vcml xmlns="http://sourceforge.net/projects/vcell/vcml" Version="Alpha_Version_7.4.0_build_85">
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<BioModel Name="BioModel2">
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<Model Name="model">
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<Compound Name="s0"/>
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<Compound Name="s1"/>
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<Feature Name="c0"/>
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<LocalizedCompound Name="s0" CompoundRef="s0" Structure="c0" OverrideName="true"/>
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<LocalizedCompound Name="s1" CompoundRef="s1" Structure="c0" OverrideName="true"/>
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<SimpleReaction Structure="c0" Name="r0" Reversible="true" FluxOption="MolecularOnly">
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<Reactant LocalizedCompoundRef="s0" Stoichiometry="1"/>
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<Product LocalizedCompoundRef="s1" Stoichiometry="1"/>
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<Kinetics KineticsType="MassAction">
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<Parameter Name="J" Role="reaction rate" Unit="uM.s-1">((Kf * s0) - (Kr * s1))</Parameter>
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<Parameter Name="Kf" Role="forward rate constant" Unit="s-1">1.0</Parameter>
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<Parameter Name="Kr" Role="reverse rate constant" Unit="s-1">2.0</Parameter>
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</Kinetics>
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</SimpleReaction>
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<Diagram Name="c0" Structure="c0">
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<SimpleReactionShape NodeReferenceModeAttrTag="molecule" SimpleReactionRef="r0" LocationX="252"
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LocationY="102"/>
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="s0" LocationX="144"
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LocationY="86"/>
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="s1" LocationX="361"
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LocationY="118"/>
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</Diagram>
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<ModelUnitSystem VolumeSubstanceUnit="uM.um3" MembraneSubstanceUnit="molecules"
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LumpedReactionSubstanceUnit="molecules" VolumeUnit="um3" AreaUnit="um2" LengthUnit="um"
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TimeUnit="s"/>
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</Model>
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<SimulationSpec Name="Application0" Stochastic="false" UseConcentration="true" RuleBased="false"
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MassConservationModelReduction="false" InsufficientIterations="false"
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InsufficientMaxMolecules="false">
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<NetworkConstraints RbmMaxIteration="1" RbmMaxMoleculesPerSpecies="10" RbmSpeciesLimit="800"
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RbmReactionsLimit="2500"/>
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<Annotation></Annotation>
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<Geometry Name="non-spatial" Dimension="0">
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<Extent X="10.0" Y="10.0" Z="10.0"/>
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<Origin X="0.0" Y="0.0" Z="0.0"/>
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<SubVolume Name="Compartment" Handle="0" Type="Compartmental"/>
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</Geometry>
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<GeometryContext>
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<FeatureMapping Feature="c0" GeometryClass="Compartment" SubVolume="Compartment" Size="50000.0">
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<BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux"/>
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</FeatureMapping>
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</GeometryContext>
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<ReactionContext>
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<LocalizedCompoundSpec LocalizedCompoundRef="s0" ForceConstant="false" WellMixed="false"
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ForceContinuous="false">
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<InitialConcentration>5.0</InitialConcentration>
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<Diffusion>0.0</Diffusion>
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</LocalizedCompoundSpec>
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<LocalizedCompoundSpec LocalizedCompoundRef="s1" ForceConstant="false" WellMixed="false"
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ForceContinuous="false">
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<InitialConcentration>4.0</InitialConcentration>
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<Diffusion>0.0</Diffusion>
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</LocalizedCompoundSpec>
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<ReactionSpec ReactionStepRef="r0" ReactionMapping="included"/>
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</ReactionContext>
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<MathDescription Name="Application0_generated">
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<Constant Name="_F_">96485.3321</Constant>
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<Constant Name="_F_nmol_">9.64853321E-5</Constant>
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<Constant Name="_K_GHK_">1.0E-9</Constant>
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<Constant Name="_N_pmol_">6.02214179E11</Constant>
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<Constant Name="_PI_">3.141592653589793</Constant>
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<Constant Name="_R_">8314.46261815</Constant>
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<Constant Name="_T_">300.0</Constant>
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<Constant Name="K_millivolts_per_volt">1000.0</Constant>
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<Constant Name="Kf">1.0</Constant>
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<Constant Name="KMOLE">0.001660538783162726</Constant>
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<Constant Name="Kr">2.0</Constant>
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<Constant Name="s0_init_uM">5.0</Constant>
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<Constant Name="s1_init_uM">4.0</Constant>
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<Constant Name="Size_c0">50000.0</Constant>
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<VolumeVariable Name="s0" Domain="Compartment"/>
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<VolumeVariable Name="s1" Domain="Compartment"/>
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<Function Name="J_r0" Domain="Compartment">((Kf * s0) - (Kr * s1))</Function>
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<CompartmentSubDomain Name="Compartment">
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<BoundaryType Boundary="Xm" Type="Value"/>
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<BoundaryType Boundary="Xp" Type="Value"/>
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<BoundaryType Boundary="Ym" Type="Value"/>
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<BoundaryType Boundary="Yp" Type="Value"/>
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<BoundaryType Boundary="Zm" Type="Value"/>
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<BoundaryType Boundary="Zp" Type="Value"/>
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<OdeEquation Name="s0" SolutionType="Unknown">
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<Rate>- J_r0</Rate>
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<Initial>s0_init_uM</Initial>
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</OdeEquation>
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<OdeEquation Name="s1" SolutionType="Unknown">
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<Rate>J_r0</Rate>
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<Initial>s1_init_uM</Initial>
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</OdeEquation>
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</CompartmentSubDomain>
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</MathDescription>
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<Simulation Name="Simulation0">
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<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false"
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Solver="Combined Stiff Solver (IDA/CVODE)">
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<TimeBound StartTime="0.0" EndTime="1.0"/>
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<TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0"/>
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<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9"/>
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<OutputOptions KeepEvery="1" KeepAtMost="1000"/>
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<NumberProcessors>1</NumberProcessors>
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</SolverTaskDescription>
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<MathOverrides/>
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<Version Name="temp simulation" KeyValue="487586140" BranchId="1" Archived="1"
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Date="30-Nov-2022 12:21:03" FromVersionable="false">
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<Owner Name="temp" Identifier="123"/>
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<GroupAccess Type="1"/>
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</Version>
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</Simulation>
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<AnalysisTaskList>
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<ParameterEstimationTask Name="DefaultTask">
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<parameterMappingSpecList>
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<parameterMappingSpec parameterReferenceAttribute="model.r0.Kf" lowLimit="0.1" highLimit="10.0"
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currentValue="0.2" selected="true"/>
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<parameterMappingSpec parameterReferenceAttribute="model.r0.Kr" lowLimit="0.2" highLimit="20.0"
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currentValue="0.3" selected="true"/>
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<parameterMappingSpec parameterReferenceAttribute="Application0.s0_scs.initConc" lowLimit="0.0"
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highLimit="20.0" currentValue="2.0" selected="true"/>
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<parameterMappingSpec parameterReferenceAttribute="Application0.s1_scs.initConc" lowLimit="0.0"
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highLimit="0.0" currentValue="0.0" selected="false"/>
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<parameterMappingSpec parameterReferenceAttribute="Application0.c0_mapping.Size"
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lowLimit="5000.0" highLimit="500000.0" currentValue="50000.0"
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selected="false"/>
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</parameterMappingSpecList>
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<referenceData numRows="22" numColumns="2">
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<dataColumnList>
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<dataColumn Name="t" weight="1.0"/>
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<dataColumn Name="s1" weight="1.0"/>
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</dataColumnList>
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<dataRowList>
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<dataRow>0.0 4.0</dataRow>
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<dataRow>1.295720285971286E-4 3.999611366663021</dataRow>
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<dataRow>4.924083761030788E-4 3.998523873442699</dataRow>
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<dataRow>0.003065662851935472 3.990845173277069</dataRow>
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<dataRow>0.0076815973758065205 3.9772186929899127</dataRow>
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<dataRow>0.014574181044930384 3.957219491908877</dataRow>
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<dataRow>0.02497272803898938 3.92781938129364</dataRow>
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<dataRow>0.040662945860187746 3.8851582405505694</dataRow>
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<dataRow>0.07469412103283095 3.799249276503241</dataRow>
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<dataRow>0.10735857823648513 3.724643285643995</dataRow>
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<dataRow>0.15042425159162362 3.636817112208214</dataRow>
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<dataRow>0.2109351969932674 3.531099655992511</dataRow>
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<dataRow>0.29257831007997415 3.4157235027261508</dataRow>
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<dataRow>0.37422142316668094 3.325411678114914</dataRow>
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<dataRow>0.45586453625338774 3.2547192053620813</dataRow>
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<dataRow>0.5375076493400945 3.1993839741215537</dataRow>
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<dataRow>0.6191507624268013 3.156069775277858</dataRow>
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<dataRow>0.7007938755135081 3.1221651582678236</dataRow>
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<dataRow>0.7824369886002149 3.0956259843893053</dataRow>
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<dataRow>0.8640801016869217 3.0748521838801746</dataRow>
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<dataRow>0.9457232147736285 3.058591286326842</dataRow>
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<dataRow>1.0 3.049787087039816</dataRow>
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</dataRowList>
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</referenceData>
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<referenceDataMappingSpecList>
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<referenceDataMappingSpec referenceDataColumnName="t" referenceDataModelSymbol="t"/>
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<referenceDataMappingSpec referenceDataColumnName="s1" referenceDataModelSymbol="s1"/>
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</referenceDataMappingSpecList>
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<optimizationSolverSpec optimizationSolverType="Evolutionary Programming" NumOfRuns="1">
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<ListOfParameters>
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<Parameter Name="Number of Generations" Value="200.0"/>
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<Parameter Name="Population Size" Value="20.0"/>
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<Parameter Name="Random Number Generator" Value="1.0"/>
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<Parameter Name="Seed" Value="0.0"/>
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</ListOfParameters>
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</optimizationSolverSpec>
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</ParameterEstimationTask>
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</AnalysisTaskList>
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<MicroscopeMeasurement Name="fluor">
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<ConvolutionKernel Type="ProjectionZKernel"/>
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</MicroscopeMeasurement>
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</SimulationSpec>
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<pathwayModel>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" version="3.0"/>
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</pathwayModel>
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<relationshipModel>
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<RMNS version="3.0"/>
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</relationshipModel>
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<vcmetadata>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
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<nonrdfAnnotationList/>
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<uriBindingList/>
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</vcmetadata>
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</BioModel>
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</vcml>
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