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| <!-- generated with COPASI 4.20 (Build 158) (http://www.copasi.org) at 2017-09-17 18:52:40 UTC --> | |
| <COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="20" versionDevel="158" copasiSourcesModified="0"> | |
| <ListOfFunctions> | |
| <Function key="Function_6" name="Constant flux (irreversible)" type="PreDefined" reversible="false"> | |
| <Expression> | |
| v | |
| </Expression> | |
| <ListOfParameterDescriptions> | |
| <ParameterDescription key="FunctionParameter_49" name="v" order="0" role="constant"/> | |
| </ListOfParameterDescriptions> | |
| </Function> | |
| <Function key="Function_13" name="Mass action (irreversible)" type="MassAction" reversible="false"> | |
| <MiriamAnnotation> | |
| <rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | |
| <rdf:Description rdf:about="#Function_13"> | |
| <CopasiMT:is rdf:resource="urn:miriam:obo.sbo:SBO:0000041" /> | |
| </rdf:Description> | |
| </rdf:RDF> | |
| </MiriamAnnotation> | |
| <Comment> | |
| <body xmlns="http://www.w3.org/1999/xhtml"> | |
| <b>Mass action rate law for first order 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_81" name="k1" order="0" role="constant"/> | |
| <ParameterDescription key="FunctionParameter_79" name="substrate" order="1" role="substrate"/> | |
| </ListOfParameterDescriptions> | |
| </Function> | |
| </ListOfFunctions> | |
| <Model key="Model_1" name="Simple test for parameter estimation in conjunction with simple_exp_data.txt." simulationType="time" timeUnit="s" volumeUnit="ml" areaUnit="m²" lengthUnit="m" quantityUnit="mmol" type="deterministic" avogadroConstant="6.0221417899999999e+023"> | |
| <MiriamAnnotation> | |
| <rdf:RDF | |
| xmlns:dcterms="http://purl.org/dc/terms/" | |
| xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | |
| <rdf:Description rdf:about="#Model_1"> | |
| <dcterms:created> | |
| <rdf:Description> | |
| <dcterms:W3CDTF>2013-07-31T10:49:40Z</dcterms:W3CDTF> | |
| </rdf:Description> | |
| </dcterms:created> | |
| </rdf:Description> | |
| </rdf:RDF> | |
| </MiriamAnnotation> | |
| <ListOfCompartments> | |
| <Compartment key="Compartment_0" name="compartment" simulationType="fixed" dimensionality="3"> | |
| </Compartment> | |
| </ListOfCompartments> | |
| <ListOfMetabolites> | |
| <Metabolite key="Metabolite_0" name="A" simulationType="reactions" compartment="Compartment_0"> | |
| <MiriamAnnotation> | |
| <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | |
| <rdf:Description rdf:about="#Metabolite_0"> | |
| <dcterms:created> | |
| <rdf:Description> | |
| <dcterms:W3CDTF>2013-07-31T10:55:14Z</dcterms:W3CDTF> | |
| </rdf:Description> | |
| </dcterms:created> | |
| </rdf:Description> | |
| </rdf:RDF> | |
| </MiriamAnnotation> | |
| </Metabolite> | |
| <Metabolite key="Metabolite_1" name="B" simulationType="reactions" compartment="Compartment_0"> | |
| <MiriamAnnotation> | |
| <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | |
| <rdf:Description rdf:about="#Metabolite_1"> | |
| <dcterms:created> | |
| <rdf:Description> | |
| <dcterms:W3CDTF>2013-07-31T10:55:18Z</dcterms:W3CDTF> | |
| </rdf:Description> | |
| </dcterms:created> | |
| </rdf:Description> | |
| </rdf:RDF> | |
| </MiriamAnnotation> | |
| </Metabolite> | |
| </ListOfMetabolites> | |
| <ListOfReactions> | |
| <Reaction key="Reaction_0" name="reaction_1" reversible="false" fast="false"> | |
| <MiriamAnnotation> | |
| <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | |
| <rdf:Description rdf:about="#Reaction_0"> | |
| <dcterms:created> | |
| <rdf:Description> | |
| <dcterms:W3CDTF>2013-07-31T10:54:29Z</dcterms:W3CDTF> | |
| </rdf:Description> | |
| </dcterms:created> | |
| </rdf:Description> | |
| </rdf:RDF> | |
| </MiriamAnnotation> | |
| <ListOfProducts> | |
| <Product metabolite="Metabolite_0" stoichiometry="1"/> | |
| </ListOfProducts> | |
| <ListOfConstants> | |
| <Constant key="Parameter_4953" name="v" value="1"/> | |
| </ListOfConstants> | |
| <KineticLaw function="Function_6" unitType="Default" scalingCompartment="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment]"> | |
| <ListOfCallParameters> | |
| <CallParameter functionParameter="FunctionParameter_49"> | |
| <SourceParameter reference="Parameter_4953"/> | |
| </CallParameter> | |
| </ListOfCallParameters> | |
| </KineticLaw> | |
| </Reaction> | |
| <Reaction key="Reaction_1" name="reaction_2" reversible="false" fast="false"> | |
| <MiriamAnnotation> | |
| <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | |
| <rdf:Description rdf:about="#Reaction_1"> | |
| <dcterms:created> | |
| <rdf:Description> | |
| <dcterms:W3CDTF>2013-07-31T10:54:52Z</dcterms:W3CDTF> | |
| </rdf:Description> | |
| </dcterms:created> | |
| </rdf:Description> | |
| </rdf:RDF> | |
| </MiriamAnnotation> | |
| <ListOfSubstrates> | |
| <Substrate metabolite="Metabolite_0" stoichiometry="1"/> | |
| </ListOfSubstrates> | |
| <ListOfProducts> | |
| <Product metabolite="Metabolite_1" stoichiometry="1"/> | |
| </ListOfProducts> | |
| <ListOfConstants> | |
| <Constant key="Parameter_4952" name="k1" value="0.25"/> | |
| </ListOfConstants> | |
| <KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment]"> | |
| <ListOfCallParameters> | |
| <CallParameter functionParameter="FunctionParameter_81"> | |
| <SourceParameter reference="Parameter_4952"/> | |
| </CallParameter> | |
| <CallParameter functionParameter="FunctionParameter_79"> | |
| <SourceParameter reference="Metabolite_0"/> | |
| </CallParameter> | |
| </ListOfCallParameters> | |
| </KineticLaw> | |
| </Reaction> | |
| <Reaction key="Reaction_2" name="reaction_3" reversible="false" fast="false"> | |
| <MiriamAnnotation> | |
| <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> | |
| <rdf:Description rdf:about="#Reaction_2"> | |
| <dcterms:created> | |
| <rdf:Description> | |
| <dcterms:W3CDTF>2013-07-31T10:56:59Z</dcterms:W3CDTF> | |
| </rdf:Description> | |
| </dcterms:created> | |
| </rdf:Description> | |
| </rdf:RDF> | |
| </MiriamAnnotation> | |
| <ListOfSubstrates> | |
| <Substrate metabolite="Metabolite_1" stoichiometry="1"/> | |
| </ListOfSubstrates> | |
| <ListOfConstants> | |
| <Constant key="Parameter_4951" name="k1" value="0.1"/> | |
| </ListOfConstants> | |
| <KineticLaw function="Function_13" unitType="Default" scalingCompartment="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment]"> | |
| <ListOfCallParameters> | |
| <CallParameter functionParameter="FunctionParameter_81"> | |
| <SourceParameter reference="Parameter_4951"/> | |
| </CallParameter> | |
| <CallParameter functionParameter="FunctionParameter_79"> | |
| <SourceParameter reference="Metabolite_1"/> | |
| </CallParameter> | |
| </ListOfCallParameters> | |
| </KineticLaw> | |
| </Reaction> | |
| </ListOfReactions> | |
| <ListOfModelParameterSets activeSet="ModelParameterSet_1"> | |
| <ModelParameterSet key="ModelParameterSet_1" name="Initial State"> | |
| <ModelParameterGroup cn="String=Initial Time" type="Group"> | |
| <ModelParameter cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt." value="0" type="Model" simulationType="time"/> | |
| </ModelParameterGroup> | |
| <ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group"> | |
| <ModelParameter cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment]" value="1" type="Compartment" simulationType="fixed"/> | |
| </ModelParameterGroup> | |
| <ModelParameterGroup cn="String=Initial Species Values" type="Group"> | |
| <ModelParameter cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment],Vector=Metabolites[A]" value="602214179" type="Species" simulationType="reactions"/> | |
| <ModelParameter cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment],Vector=Metabolites[B]" value="602214179" 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=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_1]" type="Reaction"> | |
| <ModelParameter cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_1],ParameterGroup=Parameters,Parameter=v" value="1" type="ReactionParameter" simulationType="fixed"/> | |
| </ModelParameterGroup> | |
| <ModelParameterGroup cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_2]" type="Reaction"> | |
| <ModelParameter cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_2],ParameterGroup=Parameters,Parameter=k1" value="0.25" type="ReactionParameter" simulationType="fixed"/> | |
| </ModelParameterGroup> | |
| <ModelParameterGroup cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_3]" type="Reaction"> | |
| <ModelParameter cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_3],ParameterGroup=Parameters,Parameter=k1" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/> | |
| </ModelParameterGroup> | |
| </ModelParameterGroup> | |
| </ModelParameterSet> | |
| </ListOfModelParameterSets> | |
| <StateTemplate> | |
| <StateTemplateVariable objectReference="Model_1"/> | |
| <StateTemplateVariable objectReference="Metabolite_0"/> | |
| <StateTemplateVariable objectReference="Metabolite_1"/> | |
| <StateTemplateVariable objectReference="Compartment_0"/> | |
| </StateTemplate> | |
| <InitialState type="initialState"> | |
| 0 602214179 602214179 1 | |
| </InitialState> | |
| </Model> | |
| <ListOfTasks> | |
| <Task key="Task_14" name="Steady-State" type="steadyState" scheduled="false" updateModel="false"> | |
| <Report reference="Report_9" target="" append="1" confirmOverwrite="1"/> | |
| <Problem> | |
| <Parameter name="JacobianRequested" type="bool" value="1"/> | |
| <Parameter name="StabilityAnalysisRequested" type="bool" value="1"/> | |
| </Problem> | |
| <Method name="Enhanced Newton" type="EnhancedNewton"> | |
| <Parameter name="Resolution" type="unsignedFloat" value="1.0000000000000001e-009"/> | |
| <Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/> | |
| <Parameter name="Use Newton" type="bool" value="1"/> | |
| <Parameter name="Use Integration" type="bool" value="1"/> | |
| <Parameter name="Use Back Integration" type="bool" value="1"/> | |
| <Parameter name="Accept Negative Concentrations" type="bool" value="0"/> | |
| <Parameter name="Iteration Limit" type="unsignedInteger" value="50"/> | |
| <Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1000000000"/> | |
| <Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1000000"/> | |
| </Method> | |
| </Task> | |
| <Task key="Task_15" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false"> | |
| <Problem> | |
| <Parameter name="AutomaticStepSize" type="bool" value="0"/> | |
| <Parameter name="StepNumber" type="unsignedInteger" value="1000"/> | |
| <Parameter name="StepSize" type="float" value="0.10000000000000001"/> | |
| <Parameter name="Duration" type="float" value="100"/> | |
| <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="Continue on Simultaneous Events" 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="9.9999999999999995e-007"/> | |
| <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-013"/> | |
| <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/> | |
| <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/> | |
| </Method> | |
| </Task> | |
| <Task key="Task_16" 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_17" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false"> | |
| <Report reference="Report_10" target="" append="1" confirmOverwrite="1"/> | |
| <Problem> | |
| </Problem> | |
| <Method name="EFM Algorithm" type="EFMAlgorithm"> | |
| </Method> | |
| </Task> | |
| <Task key="Task_18" name="Optimization" type="optimization" scheduled="false" updateModel="false"> | |
| <Report reference="Report_11" target="" append="1" confirmOverwrite="1"/> | |
| <Problem> | |
| <Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/> | |
| <ParameterText name="ObjectiveExpression" type="expression"> | |
| <CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_2],Reference=Flux> | |
| </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 name="OptimizationItem"> | |
| <Parameter name="LowerBound" type="cn" value="1e-06"/> | |
| <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_1],ParameterGroup=Parameters,Parameter=v,Reference=Value"/> | |
| <Parameter name="StartValue" type="float" value="1"/> | |
| <Parameter name="UpperBound" type="cn" value="1e+06"/> | |
| </ParameterGroup> | |
| <ParameterGroup name="OptimizationItem"> | |
| <Parameter name="LowerBound" type="cn" value="1e-06"/> | |
| <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_3],ParameterGroup=Parameters,Parameter=k1,Reference=Value"/> | |
| <Parameter name="StartValue" type="float" value="0.10000000000000001"/> | |
| <Parameter name="UpperBound" type="cn" value="1e+06"/> | |
| </ParameterGroup> | |
| </ParameterGroup> | |
| <ParameterGroup name="OptimizationConstraintList"> | |
| </ParameterGroup> | |
| </Problem> | |
| <Method name="Particle Swarm" type="ParticleSwarm"> | |
| <Parameter name="Iteration Limit" type="unsignedInteger" value="2000"/> | |
| <Parameter name="Swarm Size" type="unsignedInteger" value="50"/> | |
| <Parameter name="Std. Deviation" type="unsignedFloat" value="9.9999999999999995e-007"/> | |
| <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/> | |
| <Parameter name="Seed" type="unsignedInteger" value="0"/> | |
| </Method> | |
| </Task> | |
| <Task key="Task_19" name="Parameter Estimation" type="parameterFitting" scheduled="true" updateModel="false"> | |
| <Report reference="Report_12" target="" append="1" confirmOverwrite="1"/> | |
| <Problem> | |
| <Parameter name="Maximize" type="bool" value="0"/> | |
| <Parameter name="Randomize Start Values" type="bool" value="0"/> | |
| <Parameter name="Calculate Statistics" type="bool" value="1"/> | |
| <ParameterGroup name="OptimizationItemList"> | |
| <ParameterGroup name="FitItem"> | |
| <ParameterGroup name="Affected Cross Validation Experiments"> | |
| </ParameterGroup> | |
| <ParameterGroup name="Affected Experiments"> | |
| </ParameterGroup> | |
| <Parameter name="LowerBound" type="cn" value="1e-06"/> | |
| <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_1],ParameterGroup=Parameters,Parameter=v,Reference=Value"/> | |
| <Parameter name="StartValue" type="float" value="1"/> | |
| <Parameter name="UpperBound" type="cn" value="1e+06"/> | |
| </ParameterGroup> | |
| <ParameterGroup name="FitItem"> | |
| <ParameterGroup name="Affected Cross Validation Experiments"> | |
| </ParameterGroup> | |
| <ParameterGroup name="Affected Experiments"> | |
| </ParameterGroup> | |
| <Parameter name="LowerBound" type="cn" value="1e-06"/> | |
| <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_2],ParameterGroup=Parameters,Parameter=k1,Reference=Value"/> | |
| <Parameter name="StartValue" type="float" value="0.25"/> | |
| <Parameter name="UpperBound" type="cn" value="1e+06"/> | |
| </ParameterGroup> | |
| <ParameterGroup name="FitItem"> | |
| <ParameterGroup name="Affected Cross Validation Experiments"> | |
| </ParameterGroup> | |
| <ParameterGroup name="Affected Experiments"> | |
| </ParameterGroup> | |
| <Parameter name="LowerBound" type="cn" value="1e-06"/> | |
| <Parameter name="ObjectCN" type="cn" value="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Reactions[reaction_3],ParameterGroup=Parameters,Parameter=k1,Reference=Value"/> | |
| <Parameter name="StartValue" type="float" value="0.10000000000000001"/> | |
| <Parameter name="UpperBound" type="cn" value="1e+06"/> | |
| </ParameterGroup> | |
| </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 name="Experiment_1"> | |
| <Parameter name="Data is Row Oriented" type="bool" value="1"/> | |
| <Parameter name="Experiment Type" type="unsignedInteger" value="1"/> | |
| <Parameter name="File Name" type="file" value="test_paramest_exp_data.txt"/> | |
| <Parameter name="First Row" type="unsignedInteger" value="1"/> | |
| <Parameter name="Key" type="key" value="Experiment_0"/> | |
| <Parameter name="Last Row" type="unsignedInteger" value="5"/> | |
| <Parameter name="Normalize Weights per Experiment" type="bool" value="1"/> | |
| <Parameter name="Number of Columns" type="unsignedInteger" value="3"/> | |
| <ParameterGroup name="Object Map"> | |
| <ParameterGroup name="0"> | |
| <Parameter name="Role" type="unsignedInteger" value="3"/> | |
| </ParameterGroup> | |
| <ParameterGroup name="1"> | |
| <Parameter name="Object CN" type="cn" value="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=Concentration"/> | |
| <Parameter name="Role" type="unsignedInteger" value="2"/> | |
| <Parameter name="Weight" type="unsignedFloat" value="1"/> | |
| </ParameterGroup> | |
| <ParameterGroup name="2"> | |
| <Parameter name="Object CN" type="cn" value="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment],Vector=Metabolites[B],Reference=Concentration"/> | |
| <Parameter name="Role" type="unsignedInteger" value="2"/> | |
| </ParameterGroup> | |
| </ParameterGroup> | |
| <Parameter name="Row containing Names" type="unsignedInteger" value="1"/> | |
| <Parameter name="Separator" type="string" value="	"/> | |
| <Parameter name="Weight Method" type="unsignedInteger" value="0"/> | |
| </ParameterGroup> | |
| </ParameterGroup> | |
| <ParameterGroup name="Validation Set"> | |
| <Parameter name="Threshold" type="unsignedInteger" value="5"/> | |
| <Parameter name="Weight" type="unsignedFloat" value="1"/> | |
| </ParameterGroup> | |
| </Problem> | |
| <Method name="Levenberg - Marquardt" type="LevenbergMarquardt"> | |
| <Parameter name="Iteration Limit" type="unsignedInteger" value="2000"/> | |
| <Parameter name="Tolerance" type="float" value="9.9999999999999995e-007"/> | |
| </Method> | |
| </Task> | |
| <Task key="Task_20" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false"> | |
| <Report reference="Report_13" target="" append="1" confirmOverwrite="1"/> | |
| <Problem> | |
| <Parameter name="Steady-State" type="key" value="Task_14"/> | |
| </Problem> | |
| <Method name="MCA Method (Reder)" type="MCAMethod(Reder)"> | |
| <Parameter name="Modulation Factor" type="unsignedFloat" value="1.0000000000000001e-009"/> | |
| <Parameter name="Use Reder" type="bool" value="1"/> | |
| <Parameter name="Use Smallbone" type="bool" value="1"/> | |
| </Method> | |
| </Task> | |
| <Task key="Task_21" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false"> | |
| <Report reference="Report_14" target="" append="1" confirmOverwrite="1"/> | |
| <Problem> | |
| <Parameter name="ExponentNumber" type="unsignedInteger" value="3"/> | |
| <Parameter name="DivergenceRequested" type="bool" value="1"/> | |
| <Parameter name="TransientTime" type="float" value="0"/> | |
| </Problem> | |
| <Method name="Wolf Method" type="WolfMethod"> | |
| <Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/> | |
| <Parameter name="Overall time" type="unsignedFloat" value="1000"/> | |
| <Parameter name="Relative Tolerance" type="unsignedFloat" value="9.9999999999999995e-007"/> | |
| <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-013"/> | |
| <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/> | |
| </Method> | |
| </Task> | |
| <Task key="Task_22" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false"> | |
| <Report reference="Report_15" target="" append="1" confirmOverwrite="1"/> | |
| <Problem> | |
| <Parameter name="StepNumber" type="unsignedInteger" value="100"/> | |
| <Parameter name="StepSize" type="float" value="0.01"/> | |
| <Parameter name="Duration" type="float" value="1"/> | |
| <Parameter name="TimeSeriesRequested" type="bool" value="1"/> | |
| <Parameter name="OutputStartTime" type="float" value="0"/> | |
| </Problem> | |
| <Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Modified)"> | |
| <Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="9.9999999999999995e-007"/> | |
| </Method> | |
| </Task> | |
| <Task key="Task_23" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false"> | |
| <Report reference="Report_16" target="" append="1" confirmOverwrite="1"/> | |
| <Problem> | |
| <Parameter name="SubtaskType" type="unsignedInteger" value="1"/> | |
| <ParameterGroup name="TargetFunctions"> | |
| <Parameter name="SingleObject" type="cn" value=""/> | |
| <Parameter name="ObjectListType" type="unsignedInteger" value="7"/> | |
| </ParameterGroup> | |
| <ParameterGroup name="ListOfVariables"> | |
| <ParameterGroup name="Variables"> | |
| <Parameter name="SingleObject" type="cn" value=""/> | |
| <Parameter name="ObjectListType" type="unsignedInteger" value="41"/> | |
| </ParameterGroup> | |
| <ParameterGroup 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-013"/> | |
| </Method> | |
| </Task> | |
| <Task key="Task_24" name="Moieties" type="moieties" scheduled="false" updateModel="false"> | |
| <Problem> | |
| </Problem> | |
| <Method name="Householder Reduction" type="Householder"> | |
| </Method> | |
| </Task> | |
| <Task key="Task_25" name="Cross Section" type="crosssection" scheduled="false" updateModel="false"> | |
| <Problem> | |
| <Parameter name="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="0"/> | |
| <Parameter name="Threshold" type="float" value="0"/> | |
| <Parameter name="DelayOutputUntilConvergence" type="bool" value="0"/> | |
| <Parameter name="OutputConvergenceTolerance" type="float" value="0"/> | |
| <ParameterText name="TriggerExpression" type="expression"> | |
| </ParameterText> | |
| <Parameter name="SingleVariable" type="cn" value=""/> | |
| <Parameter name="Continue on Simultaneous Events" 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="9.9999999999999995e-007"/> | |
| <Parameter name="Absolute Tolerance" type="unsignedFloat" value="9.9999999999999998e-013"/> | |
| <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/> | |
| <Parameter name="Max Internal Step Size" type="unsignedFloat" value="0"/> | |
| </Method> | |
| </Task> | |
| <Task key="Task_26" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false"> | |
| <Report reference="Report_17" target="" append="1" confirmOverwrite="1"/> | |
| <Problem> | |
| <Parameter name="Steady-State" type="key" value="Task_14"/> | |
| </Problem> | |
| <Method name="Linear Noise Approximation" type="LinearNoiseApproximation"> | |
| </Method> | |
| </Task> | |
| </ListOfTasks> | |
| <ListOfReports> | |
| <Report key="Report_9" name="Steady-State" taskType="steadyState" separator="	" precision="6"> | |
| <Comment> | |
| Automatically generated report. | |
| </Comment> | |
| <Footer> | |
| <Object cn="CN=Root,Vector=TaskList[Steady-State]"/> | |
| </Footer> | |
| </Report> | |
| <Report key="Report_10" name="Elementary Flux Modes" taskType="fluxMode" separator="	" precision="6"> | |
| <Comment> | |
| Automatically generated report. | |
| </Comment> | |
| <Footer> | |
| <Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/> | |
| </Footer> | |
| </Report> | |
| <Report key="Report_11" name="Optimization" taskType="optimization" separator="	" precision="6"> | |
| <Comment> | |
| Automatically generated report. | |
| </Comment> | |
| <Header> | |
| <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Description"/> | |
| <Object cn="String=\[Function Evaluations\]"/> | |
| <Object cn="Separator=	"/> | |
| <Object cn="String=\[Best Value\]"/> | |
| <Object cn="Separator=	"/> | |
| <Object cn="String=\[Best Parameters\]"/> | |
| </Header> | |
| <Body> | |
| <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations"/> | |
| <Object cn="Separator=	"/> | |
| <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value"/> | |
| <Object cn="Separator=	"/> | |
| <Object cn="CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Parameters"/> | |
| </Body> | |
| <Footer> | |
| <Object cn="String=
"/> | |
| <Object cn="CN=Root,Vector=TaskList[Optimization],Object=Result"/> | |
| </Footer> | |
| </Report> | |
| <Report key="Report_12" name="Parameter Estimation" taskType="parameterFitting" separator="	" precision="6"> | |
| <Comment> | |
| Automatically generated report. | |
| </Comment> | |
| <Header> | |
| <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Description"/> | |
| <Object cn="String=\[Function Evaluations\]"/> | |
| <Object cn="Separator=	"/> | |
| <Object cn="String=\[Best Value\]"/> | |
| <Object cn="Separator=	"/> | |
| <Object cn="String=\[Best Parameters\]"/> | |
| </Header> | |
| <Body> | |
| <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Function Evaluations"/> | |
| <Object cn="Separator=	"/> | |
| <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Value"/> | |
| <Object cn="Separator=	"/> | |
| <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Parameters"/> | |
| </Body> | |
| <Footer> | |
| <Object cn="String=
"/> | |
| <Object cn="CN=Root,Vector=TaskList[Parameter Estimation],Object=Result"/> | |
| </Footer> | |
| </Report> | |
| <Report key="Report_13" name="Metabolic Control Analysis" taskType="metabolicControlAnalysis" separator="	" precision="6"> | |
| <Comment> | |
| Automatically generated report. | |
| </Comment> | |
| <Header> | |
| <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Description"/> | |
| </Header> | |
| <Footer> | |
| <Object cn="String=
"/> | |
| <Object cn="CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result"/> | |
| </Footer> | |
| </Report> | |
| <Report key="Report_14" name="Lyapunov Exponents" taskType="lyapunovExponents" separator="	" precision="6"> | |
| <Comment> | |
| Automatically generated report. | |
| </Comment> | |
| <Header> | |
| <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Description"/> | |
| </Header> | |
| <Footer> | |
| <Object cn="String=
"/> | |
| <Object cn="CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result"/> | |
| </Footer> | |
| </Report> | |
| <Report key="Report_15" name="Time Scale Separation Analysis" taskType="timeScaleSeparationAnalysis" separator="	" precision="6"> | |
| <Comment> | |
| Automatically generated report. | |
| </Comment> | |
| <Header> | |
| <Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Description"/> | |
| </Header> | |
| <Footer> | |
| <Object cn="String=
"/> | |
| <Object cn="CN=Root,Vector=TaskList[Time Scale Separation Analysis],Object=Result"/> | |
| </Footer> | |
| </Report> | |
| <Report key="Report_16" name="Sensitivities" taskType="sensitivities" separator="	" precision="6"> | |
| <Comment> | |
| Automatically generated report. | |
| </Comment> | |
| <Header> | |
| <Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Description"/> | |
| </Header> | |
| <Footer> | |
| <Object cn="String=
"/> | |
| <Object cn="CN=Root,Vector=TaskList[Sensitivities],Object=Result"/> | |
| </Footer> | |
| </Report> | |
| <Report key="Report_17" name="Linear Noise Approximation" taskType="linearNoiseApproximation" separator="	" precision="6"> | |
| <Comment> | |
| Automatically generated report. | |
| </Comment> | |
| <Header> | |
| <Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Description"/> | |
| </Header> | |
| <Footer> | |
| <Object cn="String=
"/> | |
| <Object cn="CN=Root,Vector=TaskList[Linear Noise Approximation],Object=Result"/> | |
| </Footer> | |
| </Report> | |
| </ListOfReports> | |
| <ListOfPlots> | |
| <PlotSpecification name="Concentrations, Volumes, and Global Quantity Values" type="Plot2D" active="1"> | |
| <Parameter name="log X" type="bool" value="0"/> | |
| <Parameter name="log Y" type="bool" value="0"/> | |
| <ListOfPlotItems> | |
| <PlotItem name="[A]" 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=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Reference=Time"/> | |
| <ChannelSpec cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=Concentration"/> | |
| </ListOfChannels> | |
| </PlotItem> | |
| <PlotItem name="[B]" 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=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Reference=Time"/> | |
| <ChannelSpec cn="CN=Root,Model=Simple test for parameter estimation in conjunction with simple_exp_data.txt.,Vector=Compartments[compartment],Vector=Metabolites[B],Reference=Concentration"/> | |
| </ListOfChannels> | |
| </PlotItem> | |
| </ListOfPlotItems> | |
| </PlotSpecification> | |
| <PlotSpecification name="Parameter Estimation Result" type="Plot2D" active="1"> | |
| <Parameter name="log X" type="bool" value="0"/> | |
| <Parameter name="log Y" type="bool" value="0"/> | |
| <ListOfPlotItems> | |
| <PlotItem name="Experiment,[A](Measured Value)" type="Curve2D"> | |
| <Parameter name="Color" type="string" value="#FF0000"/> | |
| <Parameter name="Line subtype" type="unsignedInteger" value="1"/> | |
| <Parameter name="Line type" type="unsignedInteger" value="3"/> | |
| <Parameter name="Line width" type="unsignedFloat" value="1"/> | |
| <Parameter name="Recording Activity" type="string" value="after"/> | |
| <Parameter name="Symbol subtype" type="unsignedInteger" value="1"/> | |
| <ListOfChannels> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[0],Reference=Independent Value"/> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[0],Reference=Measured Value"/> | |
| </ListOfChannels> | |
| </PlotItem> | |
| <PlotItem name="Experiment,[A](Fitted Value)" type="Curve2D"> | |
| <Parameter name="Color" type="string" value="#FF0000"/> | |
| <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="after"/> | |
| <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/> | |
| <ListOfChannels> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[0],Reference=Independent Value"/> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[0],Reference=Fitted Value"/> | |
| </ListOfChannels> | |
| </PlotItem> | |
| <PlotItem name="Experiment,[A](Weighted Error)" type="Curve2D"> | |
| <Parameter name="Color" type="string" value="#FF0000"/> | |
| <Parameter name="Line subtype" type="unsignedInteger" value="0"/> | |
| <Parameter name="Line type" type="unsignedInteger" value="2"/> | |
| <Parameter name="Line width" type="unsignedFloat" value="1"/> | |
| <Parameter name="Recording Activity" type="string" value="after"/> | |
| <Parameter name="Symbol subtype" type="unsignedInteger" value="2"/> | |
| <ListOfChannels> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[0],Reference=Independent Value"/> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[0],Reference=Weighted Error"/> | |
| </ListOfChannels> | |
| </PlotItem> | |
| <PlotItem name="Experiment,[B](Measured Value)" type="Curve2D"> | |
| <Parameter name="Color" type="string" value="#0000FF"/> | |
| <Parameter name="Line subtype" type="unsignedInteger" value="1"/> | |
| <Parameter name="Line type" type="unsignedInteger" value="3"/> | |
| <Parameter name="Line width" type="unsignedFloat" value="1"/> | |
| <Parameter name="Recording Activity" type="string" value="after"/> | |
| <Parameter name="Symbol subtype" type="unsignedInteger" value="1"/> | |
| <ListOfChannels> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[0],Reference=Independent Value"/> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[1],Reference=Measured Value"/> | |
| </ListOfChannels> | |
| </PlotItem> | |
| <PlotItem name="Experiment,[B](Fitted Value)" type="Curve2D"> | |
| <Parameter name="Color" type="string" value="#0000FF"/> | |
| <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="after"/> | |
| <Parameter name="Symbol subtype" type="unsignedInteger" value="0"/> | |
| <ListOfChannels> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[0],Reference=Independent Value"/> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[1],Reference=Fitted Value"/> | |
| </ListOfChannels> | |
| </PlotItem> | |
| <PlotItem name="Experiment,[B](Weighted Error)" type="Curve2D"> | |
| <Parameter name="Color" type="string" value="#0000FF"/> | |
| <Parameter name="Line subtype" type="unsignedInteger" value="0"/> | |
| <Parameter name="Line type" type="unsignedInteger" value="2"/> | |
| <Parameter name="Line width" type="unsignedFloat" value="1"/> | |
| <Parameter name="Recording Activity" type="string" value="after"/> | |
| <Parameter name="Symbol subtype" type="unsignedInteger" value="2"/> | |
| <ListOfChannels> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[0],Reference=Independent Value"/> | |
| <ChannelSpec cn="CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment_1,Vector=Fitted Points[1],Reference=Weighted Error"/> | |
| </ListOfChannels> | |
| </PlotItem> | |
| </ListOfPlotItems> | |
| </PlotSpecification> | |
| </ListOfPlots> | |
| <GUI> | |
| </GUI> | |
| <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> | |
| </ListOfUnitDefinitions> | |
| </COPASI> | |