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Copasi_test.cps
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Copasi_test.cps
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<?xml version="1.0" encoding="UTF-8"?>
<!-- generated with COPASI 4.11 (Build 65) (http://www.copasi.org) at 2014-05-22 11:07:20 UTC -->
<?oxygen RNGSchema="http://www.copasi.org/static/schema/CopasiML.rng" type="xml"?>
<COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="11" versionDevel="65" copasiSourcesModified="0">
<ListOfFunctions>
<Function key="Function_40" name="Rate_R1" type="UserDefined" reversible="unspecified">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Function_40">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-05-21T17:03:19Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
k1
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_267" name="k1" order="0" role="constant"/>
</ListOfParameterDescriptions>
</Function>
<Function key="Function_42" name="Rate_R2" type="UserDefined" reversible="unspecified">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Function_42">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-05-21T17:03:37Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
k2*X*Y*Y
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_276" name="k2" order="0" role="constant"/>
<ParameterDescription key="FunctionParameter_275" name="X" order="1" role="substrate"/>
<ParameterDescription key="FunctionParameter_278" name="Y" order="2" role="product"/>
</ListOfParameterDescriptions>
</Function>
<Function key="Function_43" name="Rate_R3" type="UserDefined" reversible="unspecified">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Function_43">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-05-21T17:04:33Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
k3 * Y
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_270" name="Y" order="0" role="substrate"/>
<ParameterDescription key="FunctionParameter_272" name="k3" order="1" role="constant"/>
</ListOfParameterDescriptions>
</Function>
</ListOfFunctions>
<Model key="Model_1" name="New Model" simulationType="time" timeUnit="s" volumeUnit="ml" areaUnit="m²" lengthUnit="m" quantityUnit="mmol" type="deterministic" avogadroConstant="6.02214179e+023">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Model_1">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-05-21T17:01:05Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfCompartments>
<Compartment key="Compartment_0" name="compartment" simulationType="fixed" dimensionality="3">
</Compartment>
</ListOfCompartments>
<ListOfMetabolites>
<Metabolite key="Metabolite_0" name="X" simulationType="reactions" compartment="Compartment_0">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_0">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-05-21T17:01:25Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
<Metabolite key="Metabolite_1" name="Y" simulationType="reactions" compartment="Compartment_0">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_1">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-05-21T17:01:36Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
</Metabolite>
</ListOfMetabolites>
<ListOfReactions>
<Reaction key="Reaction_0" name="reaction_1" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_0">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-05-21T17:02:20Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfProducts>
<Product metabolite="Metabolite_0" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4265" name="k1" value="1.1"/>
</ListOfConstants>
<KineticLaw function="Function_40">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_267">
<SourceParameter reference="Parameter_4265"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_1" name="reaction_2" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_1">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-05-21T17:02:35Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_0" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4262" name="k2" value="1.1"/>
</ListOfConstants>
<KineticLaw function="Function_42">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_276">
<SourceParameter reference="Parameter_4262"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_275">
<SourceParameter reference="Metabolite_0"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_278">
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_2" name="reaction_3" reversible="false">
<MiriamAnnotation>
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Reaction_2">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-05-21T17:02:47Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_4291" name="k3" value="0.6"/>
</ListOfConstants>
<KineticLaw function="Function_43">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_270">
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_272">
<SourceParameter reference="Parameter_4291"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
</ListOfReactions>
<StateTemplate>
<StateTemplateVariable objectReference="Model_1"/>
<StateTemplateVariable objectReference="Metabolite_0"/>
<StateTemplateVariable objectReference="Metabolite_1"/>
<StateTemplateVariable objectReference="Compartment_0"/>
</StateTemplate>
<InitialState type="initialState">
0 1.204428358e+021 6.022141790000001e+020 1
</InitialState>
</Model>
<ListOfTasks>
<Task key="Task_14" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
<Report reference="Report_9" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="JacobianRequested" type="bool" value="1"/>
<Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
</Problem>
<Method name="Enhanced Newton" type="EnhancedNewton">
<Parameter name="Resolution" type="unsignedFloat" value="1e-009"/>
<Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
<Parameter name="Use Newton" type="bool" value="1"/>
<Parameter name="Use Integration" type="bool" value="1"/>
<Parameter name="Use Back Integration" type="bool" value="1"/>
<Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
<Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
<Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/>
<Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/>
</Method>
</Task>
<Task key="Task_15" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
<Problem>
<Parameter name="StepNumber" type="unsignedInteger" value="300"/>
<Parameter name="StepSize" type="float" value="0.1"/>
<Parameter name="Duration" type="float" value="30"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
<Parameter name="Output Event" type="bool" value="0"/>
</Problem>
<Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
<Parameter name="Integrate Reduced Model" type="bool" value="0"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-006"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-012"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
</Method>
</Task>
<Task key="Task_16" name="Scan" type="scan" scheduled="false" updateModel="false">
<Report reference="Report_8" target="scan_output.txt" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Subtask" type="unsignedInteger" value="0"/>
<ParameterGroup name="ScanItems">
</ParameterGroup>
<Parameter name="Output in subtask" type="bool" value="0"/>
<Parameter name="Adjust initial conditions" type="bool" value="0"/>
</Problem>
<Method name="Scan Framework" type="ScanFramework">
</Method>
</Task>
<Task key="Task_17" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
<Report reference="Report_10" target="" append="1" confirmOverwrite="1"/>
<Problem>
</Problem>
<Method name="EFM Algorithm" type="EFMAlgorithm">
</Method>
</Task>
<Task key="Task_18" name="Optimization" type="optimization" scheduled="false" updateModel="false">
<Report reference="Report_11" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
<ParameterText name="ObjectiveExpression" type="expression">
</ParameterText>
<Parameter name="Maximize" type="bool" value="0"/>
<Parameter name="Randomize Start Values" type="bool" value="0"/>
<Parameter name="Calculate Statistics" type="bool" value="1"/>
<ParameterGroup name="OptimizationItemList">
</ParameterGroup>
<ParameterGroup name="OptimizationConstraintList">
</ParameterGroup>
</Problem>
<Method name="Random Search" type="RandomSearch">
<Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
<Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
<Parameter name="Seed" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_19" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
<Report reference="Report_12" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Maximize" type="bool" value="0"/>
<Parameter name="Randomize Start Values" type="bool" value="0"/>
<Parameter name="Calculate Statistics" type="bool" value="1"/>
<ParameterGroup name="OptimizationItemList">
</ParameterGroup>
<ParameterGroup name="OptimizationConstraintList">
</ParameterGroup>
<Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
<Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
<ParameterGroup name="Experiment Set">
</ParameterGroup>
<ParameterGroup name="Validation Set">
<Parameter name="Weight" type="unsignedFloat" value="1"/>
<Parameter name="Threshold" type="unsignedInteger" value="5"/>
</ParameterGroup>
</Problem>
<Method name="Evolutionary Programming" type="EvolutionaryProgram">
<Parameter name="Number of Generations" type="unsignedInteger" value="200"/>
<Parameter name="Population Size" type="unsignedInteger" value="20"/>
<Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
<Parameter name="Seed" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_20" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_13" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Steady-State" type="key" value="Task_14"/>
</Problem>
<Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
<Parameter name="Modulation Factor" type="unsignedFloat" value="1e-009"/>
</Method>
</Task>
<Task key="Task_21" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
<Report reference="Report_14" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
<Parameter name="DivergenceRequested" type="bool" value="1"/>
<Parameter name="TransientTime" type="float" value="0"/>
</Problem>
<Method name="Wolf Method" type="WolfMethod">
<Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
<Parameter name="Overall time" type="unsignedFloat" value="1000"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-006"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-012"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
</Method>
</Task>
<Task key="Task_22" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_15" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="StepNumber" type="unsignedInteger" value="100"/>
<Parameter name="StepSize" type="float" value="0.01"/>
<Parameter name="Duration" type="float" value="1"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
</Problem>
<Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
<Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="1e-006"/>
</Method>
</Task>
<Task key="Task_23" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
<Report reference="Report_16" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="SubtaskType" type="unsignedInteger" value="1"/>
<ParameterGroup name="TargetFunctions">
<Parameter name="SingleObject" type="cn" value=""/>
<Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
</ParameterGroup>
<ParameterGroup name="ListOfVariables">
<ParameterGroup name="Variables">
<Parameter name="SingleObject" type="cn" value=""/>
<Parameter name="ObjectListType" type="unsignedInteger" value="41"/>
</ParameterGroup>
</ParameterGroup>
</Problem>
<Method name="Sensitivities Method" type="SensitivitiesMethod">
<Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
<Parameter name="Delta minimum" type="unsignedFloat" value="1e-012"/>
</Method>
</Task>
<Task key="Task_24" name="Moieties" type="moieties" scheduled="false" updateModel="false">
<Problem>
</Problem>
<Method name="Householder Reduction" type="Householder">
</Method>
</Task>
<Task key="Task_25" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
<Problem>
<Parameter name="StepNumber" type="unsignedInteger" value="100"/>
<Parameter name="StepSize" type="float" value="0.01"/>
<Parameter name="Duration" type="float" value="1"/>
<Parameter name="TimeSeriesRequested" type="bool" value="1"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
<Parameter name="Output Event" type="bool" value="0"/>
<Parameter name="LimitCrossings" type="bool" value="0"/>
<Parameter name="NumCrossingsLimit" type="unsignedInteger" value="0"/>
<Parameter name="LimitOutTime" type="bool" value="0"/>
<Parameter name="LimitOutCrossings" type="bool" value="0"/>
<Parameter name="PositiveDirection" type="bool" value="1"/>
<Parameter name="NumOutCrossingsLimit" type="unsignedInteger" value="0"/>
<Parameter name="LimitUntilConvergence" type="bool" value="0"/>
<Parameter name="ConvergenceTolerance" type="float" value="1e-006"/>
<Parameter name="Threshold" type="float" value="0"/>
<Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
<Parameter name="OutputConvergenceTolerance" type="float" value="1e-006"/>
<ParameterText name="TriggerExpression" type="expression">
</ParameterText>
<Parameter name="SingleVariable" type="cn" value=""/>
</Problem>
<Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
<Parameter name="Integrate Reduced Model" type="bool" value="0"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-006"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-012"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
</Method>
</Task>
<Task key="Task_26" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
<Report reference="Report_17" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Steady-State" type="key" value="Task_14"/>
</Problem>
<Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
</Method>
</Task>
</ListOfTasks>
<ListOfReports>
<Report key="Report_9" name="Steady-State" taskType="steadyState" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Footer>
<Object cn="CN=Root,Vector=TaskList[Steady-State]"/>
</Footer>
</Report>
<Report key="Report_10" name="Elementary Flux Modes" taskType="fluxMode" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Footer>
<Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/>
</Footer>
</Report>
<Report key="Report_11" name="Optimization" taskType="optimization" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Optimization],Object=Description"/>
<Object cn="String=\[Function Evaluations\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Value\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Parameters\]"/>
</Header>
<Body>
<Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations"/>
<Object cn="Separator=	"/>
<Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value"/>
<Object cn="Separator=	"/>
<Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Parameters"/>
</Body>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Optimization],Object=Result"/>
</Footer>
</Report>
<Report key="Report_12" name="Parameter Estimation" taskType="parameterFitting" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Description"/>
<Object cn="String=\[Function Evaluations\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Value\]"/>
<Object cn="Separator=	"/>
<Object cn="String=\[Best Parameters\]"/>
</Header>
<Body>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Function Evaluations"/>
<Object cn="Separator=	"/>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Value"/>
<Object cn="Separator=	"/>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Parameters"/>
</Body>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Result"/>
</Footer>
</Report>
<Report key="Report_13" name="Metabolic Control Analysis" taskType="metabolicControlAnalysis" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result"/>
</Footer>
</Report>
<Report key="Report_14" name="Lyapunov Exponents" taskType="lyapunovExponents" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result"/>
</Footer>
</Report>
<Report key="Report_15" name="Time Scale Separation Analysis" taskType="timeScaleSeparationAnalysis" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Result"/>
</Footer>
</Report>
<Report key="Report_16" name="Sensitivities" taskType="sensitivities" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Result"/>
</Footer>
</Report>
<Report key="Report_17" name="Linear Noise Approximation" taskType="linearNoiseApproximation" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Result"/>
</Footer>
</Report>
<Report key="Report_8" name="Scan Parameters, Time, Concentrations, Volumes, and Global Quantity Values" taskType="scan" separator="	" precision="6">
<Comment>
A table of scan parameters, time, variable species concentrations, variable compartment volumes, and variable global quantity values.
</Comment>
<Table printTitle="1">
<Object cn="CN=Root,Model=New Model,Vector=Reactions[reaction_1],ParameterGroup=Parameters,Parameter=k1,Reference=Value"/>
<Object cn="CN=Root,Model=New Model,Vector=Reactions[reaction_2],ParameterGroup=Parameters,Parameter=k2,Reference=Value"/>
<Object cn="CN=Root,Model=New Model,Vector=Reactions[reaction_3],ParameterGroup=Parameters,Parameter=k3,Reference=Value"/>
<Object cn="CN=Root,Model=New Model,Reference=Time"/>
<Object cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[X],Reference=Concentration"/>
<Object cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[Y],Reference=Concentration"/>
</Table>
</Report>
</ListOfReports>
<ListOfPlots>
<PlotSpecification name="Concentrations, Volumes, and Global Quantity Values" type="Plot2D" active="1">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<ListOfPlotItems>
<PlotItem name="[X]" type="Curve2D">
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=New Model,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[X],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[Y]" type="Curve2D">
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=New Model,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[Y],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
</ListOfPlotItems>
</PlotSpecification>
<PlotSpecification name="Scan of Concentrations, Volumes, and Global Quantity Values" type="Plot2D" active="1">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<ListOfPlotItems>
<PlotItem name="[X]" type="Curve2D">
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=New Model,Vector=Reactions[reaction_1],ParameterGroup=Parameters,Parameter=k1,Reference=Value"/>
<ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[X],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[Y]" type="Curve2D">
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=New Model,Vector=Reactions[reaction_1],ParameterGroup=Parameters,Parameter=k1,Reference=Value"/>
<ChannelSpec cn="CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[Y],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
</ListOfPlotItems>
</PlotSpecification>
</ListOfPlots>
<GUI>
</GUI>
<SBMLReference file="Copasi_test.xml">
<SBMLMap SBMLid="Rate_R1" COPASIkey="Function_40"/>
<SBMLMap SBMLid="Rate_R2" COPASIkey="Function_42"/>
<SBMLMap SBMLid="Rate_R3" COPASIkey="Function_43"/>
<SBMLMap SBMLid="compartment_1" COPASIkey="Compartment_0"/>
<SBMLMap SBMLid="reaction_1" COPASIkey="Reaction_0"/>
<SBMLMap SBMLid="reaction_2" COPASIkey="Reaction_1"/>
<SBMLMap SBMLid="reaction_3" COPASIkey="Reaction_2"/>
<SBMLMap SBMLid="species_1" COPASIkey="Metabolite_0"/>
<SBMLMap SBMLid="species_2" COPASIkey="Metabolite_1"/>
</SBMLReference>
</COPASI>