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MichaelisMenten.cps
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<?xml version="1.0" encoding="UTF-8"?>
<!-- generated with COPASI 4.38 (Build 268) (http://www.copasi.org) at 2022-12-14T14:27:14Z -->
<?oxygen RNGSchema="http://www.copasi.org/static/schema/CopasiML.rng" type="xml"?>
<COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="38" versionDevel="268" copasiSourcesModified="0">
<ListOfFunctions>
<Function key="Function_8" name="Henri-Michaelis-Menten (irreversible)" type="PreDefined" 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="#Function_8">
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</MiriamAnnotation>
<Expression>
V*substrate/(Km+substrate)
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_47" name="substrate" order="0" role="substrate"/>
<ParameterDescription key="FunctionParameter_46" name="Km" order="1" role="constant"/>
<ParameterDescription key="FunctionParameter_45" name="V" order="2" role="constant"/>
</ListOfParameterDescriptions>
</Function>
</ListOfFunctions>
<Model key="Model_1" name="Michaelis-Menten enzyme kinetics" simulationType="time" timeUnit="s" volumeUnit="l" areaUnit="m²" lengthUnit="m" quantityUnit="mol" type="deterministic" avogadroConstant="6.0221408570000002e+23">
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<dcterms:creator>
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<vCard:EMAIL>[email protected]</vCard:EMAIL>
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<rdf:Description>
<vCard:Family>Mendes</vCard:Family>
<vCard:Given>Pedro</vCard:Given>
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<vCard:Orgname>University of Connecticut</vCard:Orgname>
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<Comment>
<body xmlns="http://www.w3.org/1999/xhtml"><h1>Michaelis-Menten enzyme kinetics</h1>
<p>This model simulates a typical enzyme kinetics experiment of an classic Michaelis-Menten enzyme</p>
<p>First, go to the <b>time course</b> task to simulate a single assay. If you set time to 50 seconds, and 100 intervals, you will see two plots. One shows the rate of reaction along time, the other the concentration of product along time (progress of reaction). You will notice that the initial rate decreases quickly, so we need a quick measurement to capture the initial rate propertly, 0.1 second may be good enough. Now let's set the end time back to 0.1 second, and set 2 intervals, as this is will allow us to estimate the initial rate of reaction to carry out the substrate-rate experiment. We hope that 0.1 second is fast enough to catch the initial rate, but if not this could be reduced (it is easy in simulations!...)</p>
<p>Then go to the <b>parameter scan</b> task to simulate the entire experiment with several assays at various concentrations of substrate. This will carry out 50 assays where the initial substrate concentration will change from 0.01 to 10 (we use a logarithmic spacing to have good resolution at low substrate concentration). The plot that appears when you run this task is the classical initial rate plot versus the initial substrate concentration.</p>
<p style="font-size:8pt"><b>CC0 1.0 Universal</b>: To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Creative Commons CC0">CC0 Public Domain Dedication</a> for more information.</p>
</body>
</Comment>
<ListOfCompartments>
<Compartment key="Compartment_0" name="compartment" simulationType="fixed" dimensionality="3" addNoise="false">
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</Compartment>
</ListOfCompartments>
<ListOfMetabolites>
<Metabolite key="Metabolite_2" name="P" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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</Metabolite>
<Metabolite key="Metabolite_3" name="S" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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</ListOfMetabolites>
<ListOfReactions>
<Reaction key="Reaction_3" name="Enzyme catalysis" reversible="false" fast="false" addNoise="false">
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<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_3">
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<ListOfSubstrates>
<Substrate metabolite="Metabolite_3" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_2" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4625" name="Km" value="0.1"/>
<Constant key="Parameter_6713" name="V" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_8" unitType="Default" scalingCompartment="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_47">
<SourceParameter reference="Metabolite_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_46">
<SourceParameter reference="Parameter_4625"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_45">
<SourceParameter reference="Parameter_6713"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
</ListOfReactions>
<ListOfModelParameterSets activeSet="ModelParameterSet_1">
<ModelParameterSet key="ModelParameterSet_1" name="Initial State">
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<ModelParameterGroup cn="String=Initial Time" type="Group">
<ModelParameter cn="CN=Root,Model=Michaelis-Menten enzyme kinetics" value="0" type="Model" simulationType="time"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
<ModelParameter cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment]" value="1" type="Compartment" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Species Values" type="Group">
<ModelParameter cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment],Vector=Metabolites[P]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment],Vector=Metabolites[S]" value="6.0221408570000002e+23" 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=Michaelis-Menten enzyme kinetics,Vector=Reactions[Enzyme catalysis]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Reactions[Enzyme catalysis],ParameterGroup=Parameters,Parameter=Km" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Reactions[Enzyme catalysis],ParameterGroup=Parameters,Parameter=V" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
</ModelParameterGroup>
</ModelParameterSet>
</ListOfModelParameterSets>
<StateTemplate>
<StateTemplateVariable objectReference="Model_1"/>
<StateTemplateVariable objectReference="Metabolite_2"/>
<StateTemplateVariable objectReference="Metabolite_3"/>
<StateTemplateVariable objectReference="Compartment_0"/>
</StateTemplate>
<InitialState type="initialState">
0 0 6.0221408570000002e+23 1
</InitialState>
</Model>
<ListOfTasks>
<Task key="Task_18" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
<Report reference="Report_11" 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="1.0000000000000001e-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"/>
<Parameter name="Target Criterion" type="string" value="Distance and Rate"/>
</Method>
</Task>
<Task key="Task_19" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
<Report reference="Report_10" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="AutomaticStepSize" type="bool" value="0"/>
<Parameter name="StepNumber" type="unsignedInteger" value="2"/>
<Parameter name="StepSize" type="float" value="0.050000000000000003"/>
<Parameter name="Duration" type="float" value="0.10000000000000001"/>
<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="Use Values" type="bool" value="0"/>
<Parameter name="Values" type="string" 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="9.9999999999999995e-07"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
<Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
</Method>
</Task>
<Task key="Task_20" name="Scan" type="scan" scheduled="false" updateModel="false">
<Problem>
<Parameter name="Subtask" type="unsignedInteger" value="1"/>
<ParameterGroup name="ScanItems">
<ParameterGroup name="ScanItem">
<Parameter name="Number of steps" type="unsignedInteger" value="50"/>
<Parameter name="Type" type="unsignedInteger" value="1"/>
<Parameter name="Object" type="cn" value="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment],Vector=Metabolites[S],Reference=InitialConcentration"/>
<Parameter name="Minimum" type="float" value="0.01"/>
<Parameter name="Maximum" type="float" value="1"/>
<Parameter name="log" type="bool" value="1"/>
<Parameter name="Values" type="string" value=""/>
<Parameter name="Use Values" type="bool" value="0"/>
</ParameterGroup>
</ParameterGroup>
<Parameter name="Output in subtask" type="bool" value="0"/>
<Parameter name="Adjust initial conditions" type="bool" value="0"/>
<Parameter name="Continue on Error" type="bool" value="0"/>
</Problem>
<Method name="Scan Framework" type="ScanFramework">
</Method>
</Task>
<Task key="Task_21" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
<Report reference="Report_13" target="" append="1" confirmOverwrite="1"/>
<Problem>
</Problem>
<Method name="EFM Algorithm" type="EFMAlgorithm">
</Method>
</Task>
<Task key="Task_22" name="Optimization" type="optimization" scheduled="false" updateModel="false">
<Report reference="Report_14" 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="Log Verbosity" type="unsignedInteger" value="0"/>
<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_32" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
<Report reference="Report_15" 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"/>
<Parameter name="Use Time Sens" type="bool" value="0"/>
<Parameter name="Time-Sens" type="cn" value=""/>
<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="Log Verbosity" type="unsignedInteger" value="0"/>
<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="Stop after # Stalled Generations" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_23" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_16" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Steady-State" type="key" value="Task_18"/>
</Problem>
<Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
<Parameter name="Modulation Factor" type="unsignedFloat" value="1.0000000000000001e-09"/>
<Parameter name="Use Reder" type="bool" value="1"/>
<Parameter name="Use Smallbone" type="bool" value="1"/>
</Method>
</Task>
<Task key="Task_24" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
<Report reference="Report_17" 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="9.9999999999999995e-07"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
</Method>
</Task>
<Task key="Task_25" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
<Report reference="Report_18" 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_33" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
<Report reference="Report_19" 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="9.9999999999999998e-13"/>
</Method>
</Task>
<Task key="Task_17" name="Moieties" type="moieties" scheduled="false" updateModel="false">
<Report reference="Report_20" target="" append="1" confirmOverwrite="1"/>
<Problem>
</Problem>
<Method name="Householder Reduction" type="Householder">
</Method>
</Task>
<Task key="Task_26" 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="Use Values" type="bool" value="0"/>
<Parameter name="Values" type="string" value=""/>
<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="9.9999999999999995e-07"/>
<Parameter name="Threshold" type="float" value="0"/>
<Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/>
<Parameter name="OutputConvergenceTolerance" type="float" value="9.9999999999999995e-07"/>
<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="9.9999999999999995e-07"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="100000"/>
<Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
</Method>
</Task>
<Task key="Task_27" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
<Report reference="Report_21" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="Steady-State" type="key" value="Task_18"/>
</Problem>
<Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
</Method>
</Task>
<Task key="Task_28" name="Time-Course Sensitivities" type="timeSensitivities" 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="Use Values" type="bool" value="0"/>
<Parameter name="Values" type="string" value=""/>
<ParameterGroup name="ListOfParameters">
</ParameterGroup>
<ParameterGroup name="ListOfTargets">
</ParameterGroup>
</Problem>
<Method name="LSODA Sensitivities" type="Sensitivities(LSODA)">
<Parameter name="Integrate Reduced Model" type="bool" value="0"/>
<Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-07"/>
<Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-13"/>
<Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
<Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/>
</Method>
</Task>
</ListOfTasks>
<ListOfReports>
<Report key="Report_11" 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_12" name="Time-Course" taskType="timeCourse" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Time-Course],Object=Description"/>
</Header>
<Footer>
<Object cn="CN=Root,Vector=TaskList[Time-Course],Object=Result"/>
</Footer>
</Report>
<Report key="Report_13" 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_14" 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_15" 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_16" 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_17" 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_18" 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_19" 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_20" name="Moieties" taskType="moieties" separator="	" precision="6">
<Comment>
Automatically generated report.
</Comment>
<Header>
<Object cn="CN=Root,Vector=TaskList[Moieties],Object=Description"/>
</Header>
<Footer>
<Object cn="String=
"/>
<Object cn="CN=Root,Vector=TaskList[Moieties],Object=Result"/>
</Footer>
</Report>
<Report key="Report_21" 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_10" name="Time, Concentrations, Volumes, and Global Quantity Values" taskType="timeCourse" separator="	" precision="6">
<Comment>
A table of time, variable species concentrations, variable compartment volumes, and variable global quantity values.
</Comment>
<Table printTitle="1">
<Object cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Reference=Time"/>
<Object cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment],Vector=Metabolites[P],Reference=Concentration"/>
<Object cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment],Vector=Metabolites[S],Reference=Concentration"/>
<Object cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment],Vector=Metabolites[Inhibitor],Reference=Concentration"/>
</Table>
</Report>
</ListOfReports>
<ListOfPlots>
<PlotSpecification name="Rate of reaction" type="Plot2D" active="1" taskTypes="Time-Course">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<ListOfPlotItems>
<PlotItem name="rate" type="Curve2D">
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Reactions[Enzyme catalysis],Reference=Flux"/>
</ListOfChannels>
</PlotItem>
</ListOfPlotItems>
</PlotSpecification>
<PlotSpecification name="Progress of reaction (time course)" type="Plot2D" active="1" taskTypes="Time-Course">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<ListOfPlotItems>
<PlotItem name="[P]" type="Curve2D">
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment],Vector=Metabolites[P],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
</ListOfPlotItems>
</PlotSpecification>
<PlotSpecification name="Initial rate kinetics" type="Plot2D" active="1" taskTypes="Scan">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<ListOfPlotItems>
<PlotItem name="initial rate" type="Curve2D">
<Parameter name="Line type" type="unsignedInteger" value="3"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Compartments[compartment],Vector=Metabolites[S],Reference=InitialConcentration"/>
<ChannelSpec cn="CN=Root,Model=Michaelis-Menten enzyme kinetics,Vector=Reactions[Enzyme catalysis],Reference=Flux"/>
</ListOfChannels>
</PlotItem>
</ListOfPlotItems>
</PlotSpecification>
</ListOfPlots>
<GUI>
</GUI>
<ListOfUnitDefinitions>
<UnitDefinition key="Unit_1" name="meter" symbol="m">
<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="#Unit_0">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
m
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_5" name="second" symbol="s">
<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="#Unit_4">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
s
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_13" name="Avogadro" symbol="Avogadro">
<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="#Unit_12">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
Avogadro
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_17" name="item" symbol="#">
<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="#Unit_16">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
#
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_35" name="liter" symbol="l">
<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="#Unit_34">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
0.001*m^3
</Expression>
</UnitDefinition>
<UnitDefinition key="Unit_41" name="mole" symbol="mol">
<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="#Unit_40">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
Avogadro*#
</Expression>
</UnitDefinition>
</ListOfUnitDefinitions>
</COPASI>