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<?xml version="1.0" encoding="UTF-8"?>
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<vcml xmlns="http://sourceforge.net/projects/vcell/vcml" Version="Rel_Version_7.4.0_build_34-1p">
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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="full" SimpleReactionRef="r0" LocationX="244" LocationY="128" />
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<LocalizedCompoundShape NodeReferenceModeAttrTag="full" LocalizedCompoundRef="s0" LocationX="470" LocationY="220" />
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<LocalizedCompoundShape NodeReferenceModeAttrTag="full" LocalizedCompoundRef="s1" LocationX="14" LocationY="34" />
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<SimpleReactionShape NodeReferenceModeAttrTag="molecule" SimpleReactionRef="r0" LocationX="252" LocationY="102" />
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="s0" LocationX="144" LocationY="86" />
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="s1" LocationX="361" LocationY="118" />
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</Diagram>
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<ModelUnitSystem VolumeSubstanceUnit="uM.um3" MembraneSubstanceUnit="molecules" LumpedReactionSubstanceUnit="molecules" VolumeUnit="um3" AreaUnit="um2" LengthUnit="um" TimeUnit="s" />
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</Model>
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<SimulationSpec Name="Application0" Stochastic="false" UseConcentration="true" RuleBased="false" MassConservationModelReduction="false" InsufficientIterations="false" InsufficientMaxMolecules="false">
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<NetworkConstraints RbmMaxIteration="1" RbmMaxMoleculesPerSpecies="10" RbmSpeciesLimit="800" 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" 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" 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="SimulationNominal">
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<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Combined Stiff Solver (IDA/CVODE)">
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<TimeBound StartTime="0.0" EndTime="2.0" />
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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" 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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<Simulation Name="SimulationDataGen">
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<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Combined Stiff Solver (IDA/CVODE)">
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<TimeBound StartTime="0.0" EndTime="2.0" />
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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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<Constant Name="Kr">1.0</Constant>
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<Constant Name="Kf">0.5</Constant>
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<Constant Name="s0_init_uM">2.5</Constant>
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</MathOverrides>
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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" currentValue="0.2" selected="true" />
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<parameterMappingSpec parameterReferenceAttribute="model.r0.Kr" lowLimit="0.2" highLimit="20.0" currentValue="0.3" selected="true" />
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<parameterMappingSpec parameterReferenceAttribute="Application0.s0_scs.initConc" lowLimit="0.0" highLimit="20.0" currentValue="2.0" selected="true" />
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<parameterMappingSpec parameterReferenceAttribute="Application0.s1_scs.initConc" lowLimit="0.0" highLimit="0.0" currentValue="0.0" selected="false" />
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<parameterMappingSpec parameterReferenceAttribute="Application0.c0_mapping.Size" lowLimit="5000.0" highLimit="500000.0" currentValue="50000.0" selected="false" />
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</parameterMappingSpecList>
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<referenceData numRows="25" 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>1.6535399245133132E-4 3.9995453382905546</dataRow>
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<dataRow>6.276635144329321E-4 3.998274743619277</dataRow>
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<dataRow>0.0034306276215528586 3.990590010029197</dataRow>
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<dataRow>0.00930981017033542 3.9745759499569466</dataRow>
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<dataRow>0.021379458033809823 3.942139223285978</dataRow>
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<dataRow>0.041873558753016286 3.8883895570062883</dataRow>
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<dataRow>0.07015716884832657 3.816872546080026</dataRow>
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<dataRow>0.12746580885899947 3.680942136818943</dataRow>
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<dataRow>0.18695226617648983 3.5516767175235633</dataRow>
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<dataRow>0.26645702476153477 3.3959732254044463</dataRow>
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<dataRow>0.35022514860447995 3.2508185754735517</dataRow>
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<dataRow>0.44678336822112563 3.104634800348445</dataRow>
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<dataRow>0.5798008594989622 2.9349739439153484</dataRow>
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<dataRow>0.7130335067221049 2.7957984782266956</dataRow>
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<dataRow>0.8462661539452475 2.681834033949502</dataRow>
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<dataRow>0.9794988011683902 2.588513744615282</dataRow>
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<dataRow>1.1127314483915325 2.5120980127515082</dataRow>
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<dataRow>1.2459640956146747 2.449524652625187</dataRow>
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<dataRow>1.379196742837817 2.398286179857271</dataRow>
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<dataRow>1.5124293900609591 2.356329329749134</dataRow>
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<dataRow>1.6456620372841013 2.3219727774172454</dataRow>
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<dataRow>1.7788946845072435 2.293839762543596</dataRow>
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<dataRow>1.9121273317303857 2.270802918851185</dataRow>
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<dataRow>2.0 2.257942965982347</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="3.0" />
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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#" 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> |