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Lotka.cps
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<?xml version="1.0" encoding="UTF-8"?>
<!-- generated with COPASI 4.44 (Build 295) (http://www.copasi.org) at 2024-07-08T19:19:20Z -->
<?oxygen RNGSchema="http://www.copasi.org/static/schema/CopasiML.rng" type="xml"?>
<COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="44" versionDevel="295" copasiSourcesModified="0">
<ListOfFunctions>
<Function key="Function_13" name="Mass action (irreversible)" type="MassAction" reversible="false">
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<Comment>
<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.
</p>
</body>
</Comment>
<Expression>
k1*PRODUCT<substrate_i>
</Expression>
<ListOfParameterDescriptions>
<ParameterDescription key="FunctionParameter_80" name="k1" order="0" role="constant"/>
<ParameterDescription key="FunctionParameter_81" name="substrate" order="1" role="substrate"/>
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</Function>
<Function key="Function_41" name="product activation" type="UserDefined" reversible="unspecified">
<Expression>
k * P
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<ParameterDescription key="FunctionParameter_281" name="k" order="0" role="constant"/>
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</Function>
<Function key="Function_45" name="predation" type="UserDefined" reversible="unspecified">
<Expression>
k * S * P
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<ParameterDescription key="FunctionParameter_287" name="k" order="0" role="constant"/>
<ParameterDescription key="FunctionParameter_286" name="S" order="1" role="substrate"/>
<ParameterDescription key="FunctionParameter_289" name="P" order="2" role="product"/>
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</Function>
</ListOfFunctions>
<Model key="Model_1" name="Lotka" simulationType="time" timeUnit="d" volumeUnit="l" areaUnit="km²" lengthUnit="m" quantityUnit="amol" type="deterministic" avogadroConstant="6.0221407599999999e+23">
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<rdf:Description rdf:about="#Model_1">
<dcterms:bibliographicCitation>
<rdf:Description>
<dcterms:description>Lotka AJ (1920) Analytical Note on Certain Rhythmic Relations in Organic Systems. PNAS 6:410–415</dcterms:description>
<CopasiMT:isDescribedBy rdf:resource="urn:miriam:doi:10.1073/pnas.6.7.410"/>
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<dcterms:W3CDTF>2024-07-08T17:38:27Z</dcterms:W3CDTF>
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<dcterms:creator>
<rdf:Description>
<vCard:EMAIL>[email protected]</vCard:EMAIL>
<vCard:N>
<rdf:Description>
<vCard:Family>Mendes</vCard:Family>
<vCard:Given>Pedro</vCard:Given>
</rdf:Description>
</vCard:N>
<vCard:ORG>
<rdf:Description>
<vCard:Orgname>University of Connecticut School of Medicine</vCard:Orgname>
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<Comment>
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<h1>Lotka model</h1>
<p>This is a famous model for oscillating reactions and population dynamics (1). This model was also developed independently by Volterra (ref 2, thus being better known as the "Lotka-Volterra model"). This uses the nomenclature used by Lotka (1) covering the special case where A2=B1 (the rate of predation is also the rate of growth of the predator, which assumes the prey being the only source for growth of the predator).</p>
<p><b>References</b></p>
<p>1 - <a href="https://doi.org/10.1073/pnas.6.7.410">Lotka AJ (1920) Analytical Note on Certain Rhythmic Relations in Organic Systems. <i>PNAS</i> 6:410–415</a><br/>
2 - Volterra V (1926) Variazioni e fluttuazioni del numero d’individui in specie animali conviventi. Memorie della R. Accademia Nazionale dei Lincei Roma 2:31–113
</p>
</body>
</Comment>
<ListOfCompartments>
<Compartment key="Compartment_0" name="terrain" simulationType="fixed" dimensionality="2" addNoise="false">
</Compartment>
</ListOfCompartments>
<ListOfMetabolites>
<Metabolite key="Metabolite_0" name="X1" simulationType="reactions" compartment="Compartment_0" addNoise="false">
</Metabolite>
<Metabolite key="Metabolite_1" name="X2" simulationType="reactions" compartment="Compartment_0" addNoise="false">
</Metabolite>
</ListOfMetabolites>
<ListOfModelValues>
<ModelValue key="ModelValue_0" name="A1" simulationType="fixed" addNoise="false">
</ModelValue>
<ModelValue key="ModelValue_1" name="B1" simulationType="fixed" addNoise="false">
</ModelValue>
<ModelValue key="ModelValue_3" name="B2" simulationType="fixed" addNoise="false">
</ModelValue>
</ListOfModelValues>
<ListOfReactions>
<Reaction key="Reaction_0" name="R1" reversible="false" fast="false" addNoise="false">
<ListOfProducts>
<Product metabolite="Metabolite_0" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_8518" name="k" value="1"/>
</ListOfConstants>
<KineticLaw function="Function_41" unitType="Default" scalingCompartment="CN=Root,Model=Lotka,Vector=Compartments[terrain]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_281">
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<CallParameter functionParameter="FunctionParameter_282">
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<Reaction key="Reaction_1" name="R2" reversible="false" fast="false" addNoise="false">
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<Substrate metabolite="Metabolite_0" stoichiometry="1"/>
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<ListOfProducts>
<Product metabolite="Metabolite_1" stoichiometry="1"/>
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<ListOfConstants>
<Constant key="Parameter_7495" name="k" value="1"/>
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<KineticLaw function="Function_45" unitType="Default" scalingCompartment="CN=Root,Model=Lotka,Vector=Compartments[terrain]">
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<CallParameter functionParameter="FunctionParameter_287">
<SourceParameter reference="ModelValue_1"/>
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<CallParameter functionParameter="FunctionParameter_289">
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</KineticLaw>
</Reaction>
<Reaction key="Reaction_2" name="R3" reversible="false" fast="false" addNoise="false">
<ListOfSubstrates>
<Substrate metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_8520" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Lotka,Vector=Compartments[terrain]">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_80">
<SourceParameter reference="ModelValue_3"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Metabolite_1"/>
</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=Lotka" value="0" type="Model" simulationType="time"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
<ModelParameter cn="CN=Root,Model=Lotka,Vector=Compartments[terrain]" value="1" type="Compartment" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Species Values" type="Group">
<ModelParameter cn="CN=Root,Model=Lotka,Vector=Compartments[terrain],Vector=Metabolites[X1]" value="1030.4037548373246" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Lotka,Vector=Compartments[terrain],Vector=Metabolites[X2]" value="5729306.2790304152" type="Species" simulationType="reactions"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
<ModelParameter cn="CN=Root,Model=Lotka,Vector=Values[A1]" value="0.26000000000000001" type="ModelValue" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Lotka,Vector=Values[B1]" value="0.13" type="ModelValue" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Lotka,Vector=Values[B2]" value="0.13" type="ModelValue" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
<ModelParameterGroup cn="CN=Root,Model=Lotka,Vector=Reactions[R1]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Lotka,Vector=Reactions[R1],ParameterGroup=Parameters,Parameter=k" value="0.26000000000000001" type="ReactionParameter" simulationType="assignment">
<InitialExpression>
<CN=Root,Model=Lotka,Vector=Values[A1],Reference=InitialValue>
</InitialExpression>
</ModelParameter>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Lotka,Vector=Reactions[R2]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Lotka,Vector=Reactions[R2],ParameterGroup=Parameters,Parameter=k" value="0.13" type="ReactionParameter" simulationType="assignment">
<InitialExpression>
<CN=Root,Model=Lotka,Vector=Values[B1],Reference=InitialValue>
</InitialExpression>
</ModelParameter>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Lotka,Vector=Reactions[R3]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Lotka,Vector=Reactions[R3],ParameterGroup=Parameters,Parameter=k1" value="0.13" type="ReactionParameter" simulationType="assignment">
<InitialExpression>
<CN=Root,Model=Lotka,Vector=Values[B2],Reference=InitialValue>
</InitialExpression>
</ModelParameter>
</ModelParameterGroup>
</ModelParameterGroup>
</ModelParameterSet>
</ListOfModelParameterSets>
<StateTemplate>
<StateTemplateVariable objectReference="Model_1"/>
<StateTemplateVariable objectReference="Metabolite_0"/>
<StateTemplateVariable objectReference="Metabolite_1"/>
<StateTemplateVariable objectReference="Compartment_0"/>
<StateTemplateVariable objectReference="ModelValue_0"/>
<StateTemplateVariable objectReference="ModelValue_1"/>
<StateTemplateVariable objectReference="ModelValue_3"/>
</StateTemplate>
<InitialState type="initialState">
0 1030.4037548373246 5729306.2790304152 1 0.26000000000000001 0.13 0.13
</InitialState>
</Model>
<ListOfTasks>
<Task key="Task_17" 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_18" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
<Report reference="Report_12" target="" append="1" confirmOverwrite="1"/>
<Problem>
<Parameter name="AutomaticStepSize" type="bool" value="1"/>
<Parameter name="StepNumber" type="unsignedInteger" value="2000"/>
<Parameter name="StepSize" type="float" value="0.10000000000000001"/>
<Parameter name="Duration" type="float" value="200"/>
<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_19" name="Scan" type="scan" scheduled="false" updateModel="false">
<Problem>
<Parameter name="Subtask" type="unsignedInteger" value="1"/>
<ParameterGroup name="ScanItems">
</ParameterGroup>
<Parameter name="Subtask Output" type="string" value="subTaskDuring"/>
<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_20" 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_21" 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"/>
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<Task key="Task_22" 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">
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<ParameterGroup name="OptimizationConstraintList">
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<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_17"/>
</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_26" 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_27" 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_28" 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_29" 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_17"/>
</Problem>
<Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
</Method>
</Task>
<Task key="Task_30" 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>
</ListOfReports>
<ListOfPlots>
<PlotSpecification name="Trajectory" type="Plot2D" active="1" taskTypes="">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<Parameter name="plot engine" type="string" value="QCustomPlot"/>
<Parameter name="x axis" type="string" value="time"/>
<Parameter name="y axis" type="string" value=""/>
<Parameter name="z axis" type="string" value=""/>
<ListOfPlotItems>
<PlotItem name="[X1]" 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="1.2"/>
<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=Lotka,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=Lotka,Vector=Compartments[terrain],Vector=Metabolites[X1],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[X2]" 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="1.2"/>
<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=Lotka,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=Lotka,Vector=Compartments[terrain],Vector=Metabolites[X2],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
</ListOfPlotItems>
</PlotSpecification>
<PlotSpecification name="phase plane" type="Plot2D" active="1" taskTypes="">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<Parameter name="x axis" type="string" value="[X1]"/>
<Parameter name="y axis" type="string" value="[X2]"/>
<Parameter name="z axis" type="string" value=""/>
<Parameter name="plot engine" type="string" value="QCustomPlot"/>
<ListOfPlotItems>
<PlotItem name="orbit" 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="1.2"/>
<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=Lotka,Vector=Compartments[terrain],Vector=Metabolites[X1],Reference=Concentration"/>
<ChannelSpec cn="CN=Root,Model=Lotka,Vector=Compartments[terrain],Vector=Metabolites[X2],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
</ListOfPlotItems>
</PlotSpecification>
</ListOfPlots>
<GUI>
<ListOfSliders>
<Slider key="Slider_0" associatedEntityKey="Task_18" objectCN="CN=Root,Model=Lotka,Vector=Values[A1],Reference=InitialValue" objectType="float" objectValue="0.26" minValue="0.2" maxValue="20" tickNumber="1000" tickFactor="100" scaling="logarithmic"/>
<Slider key="Slider_1" associatedEntityKey="Task_18" objectCN="CN=Root,Model=Lotka,Vector=Values[B1],Reference=InitialValue" objectType="float" objectValue="0.13" minValue="0.01" maxValue="10" tickNumber="1000" tickFactor="100" scaling="logarithmic"/>
<Slider key="Slider_2" associatedEntityKey="Task_18" objectCN="CN=Root,Model=Lotka,Vector=Values[B2],Reference=InitialValue" objectType="float" objectValue="0.13" minValue="0.01" maxValue="10" tickNumber="1000" tickFactor="100" scaling="logarithmic"/>
</ListOfSliders>
</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>
<UnitDefinition key="Unit_69" name="day" symbol="d">
<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_68">
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Expression>
86400*s
</Expression>
</UnitDefinition>
</ListOfUnitDefinitions>
</COPASI>