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prom_enzyme.cps
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<?xml version="1.0" encoding="UTF-8"?>
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<ListOfFunctions>
<Function key="Function_6" name="Constant flux (irreversible)" type="PreDefined" reversible="false">
<Expression>
v
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<ParameterDescription key="FunctionParameter_49" name="v" order="0" role="constant"/>
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<body xmlns="http://www.w3.org/1999/xhtml">
<b>Mass action rate law for irreversible reactions</b>
<p>
Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant.
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<Expression>
k1*PRODUCT<substrate_i>
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<Expression>
kcat*E*substrate/(substrate+Km)
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<ParameterDescription key="FunctionParameter_274" name="Km" order="3" role="constant"/>
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<Model key="Model_4" name="New Model" simulationType="time" timeUnit="s" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mol" type="deterministic" avogadroConstant="6.022140857e+23">
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<Compartment key="Compartment_1" name="Cell" simulationType="fixed" dimensionality="3">
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</ListOfCompartments>
<ListOfMetabolites>
<Metabolite key="Metabolite_1" name="Substrate" simulationType="reactions" compartment="Compartment_1">
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<Metabolite key="Metabolite_5" name="Co-product" simulationType="reactions" compartment="Compartment_1">
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<Metabolite key="Metabolite_7" name="Enzyme" simulationType="reactions" compartment="Compartment_1">
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</Metabolite>
<Metabolite key="Metabolite_9" name="Inducer" simulationType="reactions" compartment="Compartment_1">
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<Metabolite key="Metabolite_11" name="Activated_promoter" simulationType="reactions" compartment="Compartment_1">
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</Metabolite>
</ListOfMetabolites>
<ListOfReactions>
<Reaction key="Reaction_0" name="Induction" reversible="false" fast="false">
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<Substrate metabolite="Metabolite_9" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4417" name="Shalve" value="0.1"/>
<Constant key="Parameter_4418" name="V" value="1000"/>
<Constant key="Parameter_4419" name="h" value="4"/>
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<SourceParameter reference="Parameter_4418"/>
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<CallParameter functionParameter="FunctionParameter_51">
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</Reaction>
<Reaction key="Reaction_1" name="Expression" reversible="false" fast="false">
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<Product metabolite="Metabolite_7" stoichiometry="1"/>
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<Constant key="Parameter_4420" name="k1" value="1e+06"/>
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<CallParameter functionParameter="FunctionParameter_79">
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<Reaction key="Reaction_2" name="Leakage" reversible="false" fast="false">
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<Substrate metabolite="Metabolite_7" stoichiometry="1"/>
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<Constant key="Parameter_4422" name="k1" value="1e-06"/>
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<Substrate metabolite="Metabolite_1" stoichiometry="1"/>
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<Product metabolite="Metabolite_3" stoichiometry="1"/>
<Product metabolite="Metabolite_5" stoichiometry="1"/>
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<Constant key="Parameter_4253" name="kcat" value="0.1"/>
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<KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=New Model,Vector=Compartments[Cell]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_246">
<SourceParameter reference="Parameter_4253"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_254">
<SourceParameter reference="Metabolite_7"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_284">
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_274">
<SourceParameter reference="Parameter_4423"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
</ListOfReactions>
<ListOfModelParameterSets activeSet="ModelParameterSet_0">
<ModelParameterSet key="ModelParameterSet_0" name="Initial State">
<ModelParameterGroup cn="String=Initial Time" type="Group">
<ModelParameter cn="CN=Root,Model=New Model" value="0" type="Model" simulationType="time"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
<ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[Cell]" value="1" type="Compartment" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Species Values" type="Group">
<ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[Cell],Vector=Metabolites[Substrate]" value="6.022140856999882e+21" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[Cell],Vector=Metabolites[Product]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[Cell],Vector=Metabolites[Co-product]" value="6.022140856999882e+21" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[Cell],Vector=Metabolites[Enzyme]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[Cell],Vector=Metabolites[Inducer]" value="6.022140856999852e+20" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=New Model,Vector=Compartments[Cell],Vector=Metabolites[Activated_promoter]" value="0" type="Species" simulationType="reactions"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
</ModelParameterGroup>
<ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
<ModelParameterGroup cn="CN=Root,Model=New Model,Vector=Reactions[Induction]" type="Reaction">
<ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[Induction],ParameterGroup=Parameters,Parameter=Shalve" value="0.1" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[Induction],ParameterGroup=Parameters,Parameter=V" value="1000" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[Induction],ParameterGroup=Parameters,Parameter=h" value="4" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=New Model,Vector=Reactions[Expression]" type="Reaction">
<ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[Expression],ParameterGroup=Parameters,Parameter=k1" value="1000000" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=New Model,Vector=Reactions[Leakage]" type="Reaction">
<ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[Leakage],ParameterGroup=Parameters,Parameter=v" value="1e-09" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=New Model,Vector=Reactions[Degradation]" type="Reaction">
<ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[Degradation],ParameterGroup=Parameters,Parameter=k1" value="1e-06" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=New Model,Vector=Reactions[Catalysis]" type="Reaction">
<ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[Catalysis],ParameterGroup=Parameters,Parameter=Km" value="0.1" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=New Model,Vector=Reactions[Catalysis],ParameterGroup=Parameters,Parameter=kcat" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
</ModelParameterGroup>
</ModelParameterSet>
</ListOfModelParameterSets>
<StateTemplate>
<StateTemplateVariable objectReference="Model_4"/>
<StateTemplateVariable objectReference="Metabolite_7"/>
<StateTemplateVariable objectReference="Metabolite_11"/>
<StateTemplateVariable objectReference="Metabolite_5"/>
<StateTemplateVariable objectReference="Metabolite_9"/>
<StateTemplateVariable objectReference="Metabolite_1"/>
<StateTemplateVariable objectReference="Metabolite_3"/>
<StateTemplateVariable objectReference="Compartment_1"/>
</StateTemplate>
<InitialState type="initialState">
0 0 0 6.022140856999882e+21 6.022140856999852e+20 6.022140856999882e+21 0 1
</InitialState>
</Model>
<ListOfTasks>
<Task key="Task_12" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
<Report reference="Report_8" 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-09"/>
<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="0"/>
<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_11" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
<Problem>
<Parameter name="AutomaticStepSize" type="bool" value="0"/>
<Parameter name="StepNumber" type="unsignedInteger" value="3600"/>
<Parameter name="StepSize" type="float" value="1"/>
<Parameter name="Duration" type="float" value="3600"/>
<Parameter name="TimeSeriesRequested" type="bool" value="0"/>
<Parameter name="OutputStartTime" type="float" value="0"/>
<Parameter name="Output Event" type="bool" value="0"/>
<Parameter name="Start in Steady State" 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-06"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
<Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
</Method>
</Task>
<Task key="Task_10" name="Scan" type="scan" scheduled="false" updateModel="false">
<Problem>
<Parameter name="Subtask" type="unsignedInteger" value="1"/>
<ParameterGroup name="ScanItems">
</ParameterGroup>
<Parameter name="Output in subtask" type="bool" value="1"/>
<Parameter name="Adjust initial conditions" type="bool" value="0"/>
</Problem>
<Method name="Scan Framework" type="ScanFramework">
</Method>
</Task>
<Task key="Task_9" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
<Report reference="Report_7" target="" append="1" confirmOverwrite="1"/>
<Problem>
</Problem>
<Method name="EFM Algorithm" type="EFMAlgorithm">
</Method>
</Task>
<Task key="Task_8" name="Optimization" type="optimization" scheduled="false" updateModel="false">
<Report reference="Report_6" 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"/>
<Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_7" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
<Report reference="Report_5" 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]"/>
<Parameter name="Create Parameter Sets" type="bool" value="0"/>
<ParameterGroup name="Experiment Set">
</ParameterGroup>
<ParameterGroup name="Validation Set">
<Parameter name="Threshold" type="unsignedInteger" value="5"/>
<Parameter name="Weight" type="unsignedFloat" value="1"/>
</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"/>
<Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
<Parameter name="Stop after # Stalled Generations" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_6" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_4" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Steady-State" type="key" value="Task_12"/>
</Problem>
<Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
<Parameter name="Modulation Factor" type="unsignedFloat" value="1e-09"/>
<Parameter name="Use Reder" type="bool" value="1"/>
<Parameter name="Use Smallbone" type="bool" value="1"/>
</Method>
</Task>
<Task key="Task_5" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
<Report reference="Report_3" 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-06"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
</Method>
</Task>
<Task key="Task_4" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_2" 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="0.0001"/>
</Method>
</Task>
<Task key="Task_3" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
<Report reference="Report_1" 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 name="Variables">
<Parameter name="SingleObject" type="cn" value=""/>
<Parameter name="ObjectListType" type="unsignedInteger" value="0"/>
</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-12"/>
</Method>
</Task>
<Task key="Task_2" name="Moieties" type="moieties" scheduled="false" updateModel="false">
<Problem>
</Problem>
<Method name="Householder Reduction" type="Householder">
</Method>
</Task>
<Task key="Task_1" name="Cross Section" type="crosssection" scheduled="false" updateModel="false">
<Problem>
<Parameter name="AutomaticStepSize" type="bool" value="0"/>
<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="Start in Steady State" 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-06"/>
<Parameter name="Threshold" type="float" value="0"/>
<Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
<Parameter name="OutputConvergenceTolerance" type="float" value="1e-06"/>
<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-06"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
<Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
</Method>
</Task>
<Task key="Task_13" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
<Report reference="Report_0" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Steady-State" type="key" value=""/>
</Problem>
<Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
</Method>
</Task>
</ListOfTasks>
<ListOfReports>
<Report key="Report_8" 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_7" 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_6" 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_5" 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_4" 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_3" 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_2" 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_1" 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_0" 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>
</ListOfReports>
<ListOfPlots>
<PlotSpecification name="plot" type="Plot2D" active="1">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<ListOfPlotItems>
<PlotItem name="[Activated_promoter]|Time" 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[Cell],Vector=Metabolites[Activated_promoter],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[Enzyme]|Time" 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[Cell],Vector=Metabolites[Enzyme],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[Inducer]|Time" 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[Cell],Vector=Metabolites[Inducer],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[Product]|Time" 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[Cell],Vector=Metabolites[Product],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[Substrate]|Time" 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[Cell],Vector=Metabolites[Substrate],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
</ListOfPlotItems>
</PlotSpecification>
</ListOfPlots>
<GUI>
</GUI>
<SBMLReference file="prom_enzyme.xml">
<SBMLMap SBMLid="Activated_promoter" COPASIkey="Metabolite_11"/>
<SBMLMap SBMLid="Catalysis" COPASIkey="Reaction_4"/>
<SBMLMap SBMLid="Cell" COPASIkey="Compartment_1"/>
<SBMLMap SBMLid="Co_product" COPASIkey="Metabolite_5"/>
<SBMLMap SBMLid="Constant_flux__irreversible" COPASIkey="Function_6"/>
<SBMLMap SBMLid="Degradation" COPASIkey="Reaction_3"/>
<SBMLMap SBMLid="Enzyme" COPASIkey="Metabolite_7"/>
<SBMLMap SBMLid="Expression" COPASIkey="Reaction_1"/>
<SBMLMap SBMLid="Hill_Cooperativity" COPASIkey="Function_9"/>
<SBMLMap SBMLid="Inducer" COPASIkey="Metabolite_9"/>
<SBMLMap SBMLid="Induction" COPASIkey="Reaction_0"/>
<SBMLMap SBMLid="Leakage" COPASIkey="Reaction_2"/>
<SBMLMap SBMLid="Product" COPASIkey="Metabolite_3"/>
<SBMLMap SBMLid="Substrate" COPASIkey="Metabolite_1"/>
<SBMLMap SBMLid="function" COPASIkey="Function_41"/>
</SBMLReference>
<ListOfUnitDefinitions>
<UnitDefinition key="Unit_0" name="meter" symbol="m">
<Expression>
m
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_2" name="second" symbol="s">
<Expression>
s
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_6" name="Avogadro" symbol="Avogadro">
<Expression>
Avogadro
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_8" name="item" symbol="#">
<Expression>
#
</Expression>
</UnitDefinition>
</ListOfUnitDefinitions>
</COPASI>