<?xml version="1.0" encoding="UTF-8"?>
<!-- generated with COPASI 4.5 (Build 30) (http://www.copasi.org) at 2011-09-04 21:00:10 UTC -->
<COPASI xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.copasi.org/static/schema.xsd" versionMajor="1" versionMinor="0" versionDevel="30">
  <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">
      <Expression>
        k1*PRODUCT&lt;substrate_i&gt;
      </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="Constitutively expressed gene" timeUnit="min" volumeUnit="dimensionless" quantityUnit="#" type="deterministic">
    <Comment>
      <body xmlns="http://www.w3.org/1999/xhtml">
        
      </body>
    </Comment>
    <ListOfCompartments>
      <Compartment key="Compartment_0" name="compartment" simulationType="fixed">
      </Compartment>
    </ListOfCompartments>
    <ListOfMetabolites>
      <Metabolite key="Metabolite_0" name="P" simulationType="reactions" compartment="Compartment_0">
      </Metabolite>
    </ListOfMetabolites>
    <ListOfReactions>
      <Reaction key="Reaction_0" name="P-production" reversible="false">
        <ListOfProducts>
          <Product metabolite="Metabolite_0" stoichiometry="1"/>
        </ListOfProducts>
        <ListOfConstants>
          <Constant key="Parameter_740" name="v" value="1"/>
        </ListOfConstants>
        <KineticLaw function="Function_6">
          <ListOfCallParameters>
            <CallParameter functionParameter="FunctionParameter_49">
              <SourceParameter reference="Parameter_740"/>
            </CallParameter>
          </ListOfCallParameters>
        </KineticLaw>
      </Reaction>
      <Reaction key="Reaction_1" name="P-degradation" reversible="false">
        <ListOfSubstrates>
          <Substrate metabolite="Metabolite_0" stoichiometry="1"/>
        </ListOfSubstrates>
        <ListOfConstants>
          <Constant key="Parameter_739" name="k1" value="0.01"/>
        </ListOfConstants>
        <KineticLaw function="Function_13">
          <ListOfCallParameters>
            <CallParameter functionParameter="FunctionParameter_81">
              <SourceParameter reference="Parameter_739"/>
            </CallParameter>
            <CallParameter functionParameter="FunctionParameter_79">
              <SourceParameter reference="Metabolite_0"/>
            </CallParameter>
          </ListOfCallParameters>
        </KineticLaw>
      </Reaction>
    </ListOfReactions>
    <StateTemplate>
      <StateTemplateVariable objectReference="Model_1"/>
      <StateTemplateVariable objectReference="Metabolite_0"/>
      <StateTemplateVariable objectReference="Compartment_0"/>
    </StateTemplate>
    <InitialState type="initialState">
      0 10 1
    </InitialState>
  </Model>
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    <Task key="Task_11" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
      <Report reference="Report_8" target="" append="1"/>
      <Problem>
        <Parameter name="JacobianRequested" type="bool" value="1"/>
        <Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
      </Problem>
      <Method name="Enhanced Newton" type="EnhancedNewton">
        <Parameter name="Resolution" type="unsignedFloat" value="1e-09"/>
        <Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
        <Parameter name="Use Newton" type="bool" value="1"/>
        <Parameter name="Use Integration" type="bool" value="1"/>
        <Parameter name="Use Back Integration" type="bool" value="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="1e+09"/>
        <Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1e+06"/>
      </Method>
    </Task>
    <Task key="Task_12" name="Time-Course" type="timeCourse" scheduled="false" updateModel="false">
      <Problem>
        <Parameter name="StepNumber" type="unsignedInteger" value="1000"/>
        <Parameter name="StepSize" type="float" value="1"/>
        <Parameter name="Duration" type="float" value="1000"/>
        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
        <Parameter name="OutputStartTime" type="float" value="0"/>
      </Problem>
      <Method name="Stochastic (Gibson + Bruck)" type="Stochastic">
        <Parameter name="Max Internal Steps" type="integer" value="1000000"/>
        <Parameter name="Subtype" type="unsignedInteger" value="2"/>
        <Parameter name="Use Random Seed" type="bool" value="0"/>
        <Parameter name="Random Seed" type="unsignedInteger" value="1"/>
      </Method>
    </Task>
    <Task key="Task_13" 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">
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    <Task key="Task_14" name="Elementary Flux Modes" type="fluxMode" scheduled="false" updateModel="false">
      <Report reference="Report_9" target="" append="1"/>
      <Problem>
      </Problem>
      <Method name="EFM Algorithm" type="EFMAlgorithm">
      </Method>
    </Task>
    <Task key="Task_15" name="Optimization" type="optimization" scheduled="false" updateModel="false">
      <Report reference="Report_10" target="" append="1"/>
      <Problem>
        <Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
        <Parameter name="ObjectiveFunction" type="key" value=""/>
        <Parameter name="Maximize" type="bool" value="0"/>
        <ParameterGroup name="OptimizationItemList">
        </ParameterGroup>
        <ParameterGroup name="OptimizationConstraintList">
        </ParameterGroup>
        <Parameter name="Steady-State" type="string" value=""/>
        <Parameter name="Time-Course" type="string" value=""/>
      </Problem>
      <Method name="Random Search" type="RandomSearch">
        <Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
        <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
        <Parameter name="Seed" type="unsignedInteger" value="0"/>
      </Method>
    </Task>
    <Task key="Task_16" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
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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]"/>
        <ParameterGroup name="Experiment Set">
        </ParameterGroup>
      </Problem>
      <Method name="Evolutionary Programming" type="EvolutionaryProgram">
        <Parameter name="Number of Generations" type="unsignedInteger" value="200"/>
        <Parameter name="Population Size" type="unsignedInteger" value="20"/>
        <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
        <Parameter name="Seed" type="unsignedInteger" value="0"/>
      </Method>
    </Task>
    <Task key="Task_17" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
      <Report reference="Report_12" target="" append="1"/>
      <Problem>
        <Parameter name="Steady-State" type="key" value="Task_11"/>
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      <Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
        <Parameter name="Modulation Factor" type="unsignedFloat" value="1e-09"/>
      </Method>
    </Task>
    <Task key="Task_18" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
      <Report reference="Report_13" target="" append="1"/>
      <Problem>
        <Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
        <Parameter name="DivergenceRequested" type="bool" value="1"/>
        <Parameter name="TransientTime" type="float" value="0"/>
      </Problem>
      <Method name="Wolf Method" type="WolfMethod">
        <Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
        <Parameter name="Overall time" type="unsignedFloat" value="1000"/>
        <Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-06"/>
        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
        <Parameter name="Adams Max Order" type="unsignedInteger" value="12"/>
        <Parameter name="BDF Max Order" type="unsignedInteger" value="5"/>
        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
      </Method>
    </Task>
    <Task key="Task_19" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
      <Report reference="Report_14" target="" append="1"/>
      <Problem>
        <Parameter name="Deuflhard Tolerance" type="float" value="1e-06"/>
        <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="Integrate Reduced Model" type="bool" value="1"/>
        <Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-06"/>
        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-12"/>
        <Parameter name="Adams Max Order" type="unsignedInteger" value="12"/>
        <Parameter name="BDF Max Order" type="unsignedInteger" value="5"/>
        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
      </Method>
    </Task>
    <Task key="Task_20" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
      <Report reference="Report_15" target="" append="1"/>
      <Problem>
        <Parameter name="SubtaskType" type="unsignedInteger" value="1"/>
        <ParameterGroup name="TargetFunctions">
          <Parameter name="SingleObject" type="cn" value=""/>
          <Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
        </ParameterGroup>
        <ParameterGroup name="ListOfVariables">
          <ParameterGroup name="Variables">
            <Parameter name="SingleObject" type="cn" value=""/>
            <Parameter name="ObjectListType" type="unsignedInteger" value="41"/>
          </ParameterGroup>
        </ParameterGroup>
      </Problem>
      <Method name="Sensitivities Method" type="SensitivitiesMethod">
        <Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
        <Parameter name="Delta minimum" type="unsignedFloat" value="1e-12"/>
      </Method>
    </Task>
    <Task key="Task_21" name="Moieties" type="moieties" scheduled="false" updateModel="false">
      <Problem>
      </Problem>
      <Method name="Householder Reduction" type="Householder">
      </Method>
    </Task>
  </ListOfTasks>
  <ListOfReports>
    <Report key="Report_8" name="Steady-State" taskType="steadyState" separator="&#x09;" precision="6">
      <Comment>
        <body xmlns="http://www.w3.org/1999/xhtml">
          Automatically generated report.
        </body>
      </Comment>
      <Footer>
        <Object cn="CN=Root,Vector=TaskList[Steady-State]"/>
      </Footer>
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    <Report key="Report_9" name="Elementary Flux Modes" taskType="fluxMode" separator="&#x09;" precision="6">
      <Comment>
        <body xmlns="http://www.w3.org/1999/xhtml">
          Automatically generated report.
        </body>
      </Comment>
      <Footer>
        <Object cn="CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result"/>
      </Footer>
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    <Report key="Report_10" name="Optimization" taskType="optimization" separator="&#x09;" precision="6">
      <Comment>
        <body xmlns="http://www.w3.org/1999/xhtml">
          Automatically generated report.
        </body>
      </Comment>
      <Header>
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        <Object cn="String=\[Function Evaluations\]"/>
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      <Comment>
        <body xmlns="http://www.w3.org/1999/xhtml">
          Automatically generated report.
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      <Comment>
        <body xmlns="http://www.w3.org/1999/xhtml">
          Automatically generated report.
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      <Comment>
        <body xmlns="http://www.w3.org/1999/xhtml">
          Automatically generated report.
        </body>
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      <Comment>
        <body xmlns="http://www.w3.org/1999/xhtml">
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        </body>
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        </body>
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  </ListOfReports>
  <ListOfPlots>
    <PlotSpecification name="P particle numbers-deterministic" type="Plot2D" active="0">
      <Parameter name="log X" type="bool" value="0"/>
      <Parameter name="log Y" type="bool" value="0"/>
      <ListOfPlotItems>
        <PlotItem name="P.ParticleNumber|Time" type="Curve2D">
          <Parameter name="Line type" type="unsignedInteger" value="0"/>
          <Parameter name="Recording Activity" type="string" value="during"/>
          <ListOfChannels>
            <ChannelSpec cn="CN=Root,Model=Constitutively expressed gene,Reference=Time"/>
            <ChannelSpec cn="CN=Root,Model=Constitutively expressed gene,Vector=Compartments[compartment],Vector=Metabolites[P],Reference=ParticleNumber"/>
          </ListOfChannels>
        </PlotItem>
      </ListOfPlotItems>
    </PlotSpecification>
    <PlotSpecification name="P particle numbers, stochastic" type="Plot2D" active="1">
      <Parameter name="log X" type="bool" value="0"/>
      <Parameter name="log Y" type="bool" value="0"/>
      <ListOfPlotItems>
        <PlotItem name="P.ParticleNumber|Time" type="Curve2D">
          <Parameter name="Line type" type="unsignedInteger" value="0"/>
          <Parameter name="Recording Activity" type="string" value="during"/>
          <ListOfChannels>
            <ChannelSpec cn="CN=Root,Model=Constitutively expressed gene,Reference=Time"/>
            <ChannelSpec cn="CN=Root,Model=Constitutively expressed gene,Vector=Compartments[compartment],Vector=Metabolites[P],Reference=ParticleNumber"/>
          </ListOfChannels>
        </PlotItem>
      </ListOfPlotItems>
    </PlotSpecification>
    <PlotSpecification name="P-Histogram, stochastic" type="Plot2D" active="1">
      <Parameter name="log X" type="bool" value="0"/>
      <Parameter name="log Y" type="bool" value="0"/>
      <ListOfPlotItems>
        <PlotItem name="Histogram: P.ParticleNumber" type="Histogram1DItem">
          <Parameter name="Recording Activity" type="string" value="during"/>
          <Parameter name="increment" type="float" value="1"/>
          <ListOfChannels>
            <ChannelSpec cn="CN=Root,Model=Constitutively expressed gene,Vector=Compartments[compartment],Vector=Metabolites[P],Reference=ParticleNumber"/>
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        </PlotItem>
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  <GUI>
    <ListOfSliders>
      <Slider key="Slider_0" associatedEntityKey="Model_1" objectCN="CN=Root,Model=Constitutively expressed gene,Vector=Reactions[P-production],ParameterGroup=Parameters,Parameter=v,Reference=Value" objectType="float" objectValue="100" minValue="0.001" maxValue="100" tickNumber="1000" tickFactor="100" scaling="logarithmic"/>
    </ListOfSliders>
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</COPASI>
