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<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R15_DyingFibroblast_death],ParameterGroup=Parameters,Parameter=k1" value="0.20000000000000001" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R16_Healthy_to_Dying_fibroblast]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R16_Healthy_to_Dying_fibroblast],ParameterGroup=Parameters,Parameter=k1" value="4.9999999999999998e-07" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R17_HealthyBacteriaProduction]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R17_HealthyBacteriaProduction],ParameterGroup=Parameters,Parameter=k1" value="0.01" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R18_HealthyFibProduction]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R18_HealthyFibProduction],ParameterGroup=Parameters,Parameter=k1" value="4.8500000000000002e-07" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R19_MMP7_release_HealthyFibr]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R19_MMP7_release_HealthyFibr],ParameterGroup=Parameters,Parameter=k1" value="1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R20_MMP8_release_HealthyFibr]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R20_MMP8_release_HealthyFibr],ParameterGroup=Parameters,Parameter=k1" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R21_Healthy_to_Dying_Bacteria]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R21_Healthy_to_Dying_Bacteria],ParameterGroup=Parameters,Parameter=k1" value="0.0050000000000000001" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R22_CRA_binding]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R22_CRA_binding],ParameterGroup=Parameters,Parameter=k1" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R22_CRA_binding],ParameterGroup=Parameters,Parameter=k2" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R23_FLC_binding]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R23_FLC_binding],ParameterGroup=Parameters,Parameter=k1" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R23_FLC_binding],ParameterGroup=Parameters,Parameter=k2" value="0.10000000000000001" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R24_TNFalpha_production]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R24_TNFalpha_production],ParameterGroup=Parameters,Parameter=k1" value="5000" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R25_Protease_production]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R25_Protease_production],ParameterGroup=Parameters,Parameter=k1" value="65" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R26_DyingBacteria secrete CRA]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R26_DyingBacteria secrete CRA],ParameterGroup=Parameters,Parameter=k1" value="10" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R27_Dyingbacteria die]" type="Reaction">
<ModelParameter cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Reactions[R27_Dyingbacteria die],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="Metabolite_3"/>
<StateTemplateVariable objectReference="Metabolite_9"/>
<StateTemplateVariable objectReference="Metabolite_5"/>
<StateTemplateVariable objectReference="Metabolite_4"/>
<StateTemplateVariable objectReference="Metabolite_11"/>
<StateTemplateVariable objectReference="Metabolite_15"/>
<StateTemplateVariable objectReference="Metabolite_10"/>
<StateTemplateVariable objectReference="Metabolite_16"/>
<StateTemplateVariable objectReference="Metabolite_17"/>
<StateTemplateVariable objectReference="Metabolite_13"/>
<StateTemplateVariable objectReference="Metabolite_6"/>
<StateTemplateVariable objectReference="Metabolite_7"/>
<StateTemplateVariable objectReference="Metabolite_8"/>
<StateTemplateVariable objectReference="Metabolite_12"/>
<StateTemplateVariable objectReference="Metabolite_14"/>
<StateTemplateVariable objectReference="Metabolite_18"/>
<StateTemplateVariable objectReference="Metabolite_2"/>
<StateTemplateVariable objectReference="Compartment_0"/>
<StateTemplateVariable objectReference="ModelValue_0"/>
</StateTemplate>
<InitialState type="initialState">
0 6018600.77062748 601918491838111 601860.07706274802 0 602214179 60191909405229 286149293.72199798 60125.304517031604 601918491838.11096 600.89894323306453 60160714.710756794 295687161.88905972 602214179 0 0 0 0 602214179000 602214179 1 16.699999999999999
</InitialState>
</Model>
<ListOfTasks>
<Task key="Task_14" name="Steady-State" type="steadyState" scheduled="false" updateModel="false">
<Report reference="Report_10" 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="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="100"/>
<Parameter name="StepSize" type="float" value="200"/>
<Parameter name="Duration" type="float" value="20000"/>
<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-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>
<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">
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<Problem>
</Problem>
<Method name="EFM Algorithm" type="EFMAlgorithm">
</Method>
</Task>
<Task key="Task_18" name="Optimization" type="optimization" scheduled="false" updateModel="false">
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<Problem>
<Parameter name="Subtask" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
<ParameterText name="ObjectiveExpression" type="expression">
</ParameterText>
<Parameter name="Maximize" type="bool" value="0"/>
<Parameter name="Randomize Start Values" type="bool" value="0"/>
<Parameter name="Calculate Statistics" type="bool" value="1"/>
<ParameterGroup name="OptimizationItemList">
</ParameterGroup>
<ParameterGroup name="OptimizationConstraintList">
</ParameterGroup>
</Problem>
<Method name="Random Search" type="RandomSearch">
<Parameter name="Log Verbosity" type="unsignedInteger" value="0"/>
<Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
<Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
<Parameter name="Seed" type="unsignedInteger" value="0"/>
</Method>
</Task>
<Task key="Task_19" name="Parameter Estimation" type="parameterFitting" scheduled="false" updateModel="false">
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<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"/>
<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_20" name="Metabolic Control Analysis" type="metabolicControlAnalysis" scheduled="false" updateModel="false">
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<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-09"/>
<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">
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<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_22" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
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<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="9.9999999999999995e-07"/>
</Method>
</Task>
<Task key="Task_23" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
<Report reference="Report_17" 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_24" name="Moieties" type="moieties" scheduled="false" updateModel="false">
<Report reference="Report_19" target="" append="1" confirmOverwrite="1"/>
<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="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=""/>
<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-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>
<Task key="Task_26" name="Linear Noise Approximation" type="linearNoiseApproximation" scheduled="false" updateModel="false">
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<Problem>
<Parameter name="Steady-State" type="key" value="Task_14"/>
</Problem>
<Method name="Linear Noise Approximation" type="LinearNoiseApproximation">
</Method>
</Task>
</ListOfTasks>
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</ListOfReports>
<ListOfPlots>
<PlotSpecification name="Concentrations, Volumes, and Global Quantity Values" type="Plot2D" active="1" taskTypes="">
<Parameter name="log X" type="bool" value="0"/>
<Parameter name="log Y" type="bool" value="0"/>
<ListOfPlotItems>
<PlotItem name="[BAFF]" type="Curve2D">
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Compartments[compartment],Vector=Metabolites[CRA],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[MMP8]" type="Curve2D">
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Recording Activity" type="string" value="during"/>
<ListOfChannels>
<ChannelSpec cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Reference=Time"/>
<ChannelSpec cn="CN=Root,Model=acute case used for generating control analysis in supplemental material Kolodkin et al,Vector=Compartments[compartment],Vector=Metabolites[MMP8],Reference=Concentration"/>
</ListOfChannels>
</PlotItem>
<PlotItem name="[washout]" type="Curve2D">
<Parameter name="Line type" type="unsignedInteger" value="0"/>
<Parameter name="Line subtype" type="unsignedInteger" value="0"/>
<Parameter name="Line width" type="unsignedFloat" value="1"/>
<Parameter name="Symbol subtype" type="unsignedInteger" value="0"/>
<Parameter name="Color" type="string" value="auto"/>
<Parameter name="Recording Activity" type="string" value="during"/>
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