├── .gitattributes ├── .gitignore ├── .travis.yml ├── .vscode └── settings.json ├── FernMLSchema.xsd ├── INSTALL.md ├── LICENSE.txt ├── MyLog4j.properties ├── README.md ├── UserGuidelines.md ├── dev ├── diagrams │ ├── README.md │ ├── comp-model-simulation │ │ ├── COMP_Model_Simulation_Sequence_Diagram.png │ │ └── COMP_Model_Simulation_Sequence_Diagram.txt │ ├── fbc-model-simulation │ │ ├── FBC_Model_Simulation_Sequence_Diagram.png │ │ └── FBC_Model_Simulation_Sequence_Diagram.txt │ ├── sbml-model-simulation │ │ ├── SBML_Model_Simulation_Sequence_Diagram.png │ │ └── SBML_Model_Simulation_Sequence_Diagram.txt │ └── stochastic-simulation │ │ ├── Stochastic_Simulation_Sequence_Diagram.png │ │ └── Stochastic_Simulation_Sequence_Diagram.txt └── formatting-guidelines │ ├── README.md │ ├── eclipse-java-codestyle.xml │ └── intellij-java-codestyle.xml ├── docs ├── VLN-Retreat │ ├── VLN_poster_abstract.doc │ └── VLN_poster_abstract.pdf ├── apidocs │ ├── allclasses-frame.html │ ├── allclasses-noframe.html │ ├── constant-values.html │ ├── deprecated-list.html │ ├── fern │ │ ├── Start.html │ │ ├── analysis │ │ │ ├── AnalysisBase.html │ │ │ ├── AutocatalyticNetworkDetection.html │ │ │ ├── IntQueue.html │ │ │ ├── IntSearchStructure.html │ │ │ ├── IntStack.html │ │ │ ├── NetworkSearchAction.NeighborType.html │ │ │ ├── NetworkSearchAction.html │ │ │ ├── NodeChecker.html │ │ │ ├── NodeCheckerByAnnotation.html │ │ │ ├── ShortestPath.Path.html │ │ │ ├── ShortestPath.html │ │ │ ├── class-use │ │ │ │ ├── AnalysisBase.html │ │ │ │ ├── AutocatalyticNetworkDetection.html │ │ │ │ ├── IntQueue.html │ │ │ │ ├── IntSearchStructure.html │ │ │ │ ├── IntStack.html │ │ │ │ ├── NetworkSearchAction.NeighborType.html │ │ │ │ ├── NetworkSearchAction.html │ │ │ │ ├── NodeChecker.html │ │ │ │ ├── NodeCheckerByAnnotation.html │ │ │ │ ├── ShortestPath.Path.html │ │ │ │ └── ShortestPath.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ ├── benchmark │ │ │ ├── Benchmark.html │ │ │ ├── RandomNumber.html │ │ │ ├── SimulatorCorrectness.html │ │ │ ├── SimulatorFireTypes.html │ │ │ ├── SimulatorPerformance.html │ │ │ ├── SimulatorRandomNumbers.html │ │ │ ├── SimulatorTime.html │ │ │ ├── class-use │ │ │ │ ├── Benchmark.html │ │ │ │ ├── RandomNumber.html │ │ │ │ ├── SimulatorCorrectness.html │ │ │ │ ├── SimulatorFireTypes.html │ │ │ │ ├── SimulatorPerformance.html │ │ │ │ ├── SimulatorRandomNumbers.html │ │ │ │ └── SimulatorTime.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ ├── class-use │ │ │ └── Start.html │ │ ├── example │ │ │ ├── AutocatalyticNetworkExample.html │ │ │ ├── CellGrowthObserver.html │ │ │ ├── CompositionRejectionStressTest.html │ │ │ ├── DecayingDimerizingHistogramDistances.html │ │ │ ├── DecayingDimerizingInteractive.html │ │ │ ├── DecayingDimerizingPlots.html │ │ │ ├── Dsmts.html │ │ │ ├── ExamplePath.html │ │ │ ├── HistogramDistanceTestSet.html │ │ │ ├── IrreversibleIsomerization.html │ │ │ ├── LacYComplete.html │ │ │ ├── LacYHistogramDistances.html │ │ │ ├── LacZ.html │ │ │ ├── Mapk.html │ │ │ ├── MapkBenchmark.html │ │ │ ├── MichaelisMentenKinetic.html │ │ │ ├── SBMLMathTreeTest.html │ │ │ ├── class-use │ │ │ │ ├── AutocatalyticNetworkExample.html │ │ │ │ ├── CellGrowthObserver.html │ │ │ │ ├── CompositionRejectionStressTest.html │ │ │ │ ├── DecayingDimerizingHistogramDistances.html │ │ │ │ ├── DecayingDimerizingInteractive.html │ │ │ │ ├── DecayingDimerizingPlots.html │ │ │ │ ├── Dsmts.html │ │ │ │ ├── ExamplePath.html │ │ │ │ ├── HistogramDistanceTestSet.html │ │ │ │ ├── IrreversibleIsomerization.html │ │ │ │ ├── LacYComplete.html │ │ │ │ ├── LacYHistogramDistances.html │ │ │ │ ├── LacZ.html │ │ │ │ ├── Mapk.html │ │ │ │ ├── MapkBenchmark.html │ │ │ │ ├── MichaelisMentenKinetic.html │ │ │ │ └── SBMLMathTreeTest.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ ├── network │ │ │ ├── AbstractKineticConstantPropensityCalculator.html │ │ │ ├── AbstractNetworkImpl.html │ │ │ ├── AmountManager.html │ │ │ ├── AnnotationManager.html │ │ │ ├── AnnotationManagerImpl.html │ │ │ ├── ArrayKineticConstantPropensityCalculator.html │ │ │ ├── ComplexDependenciesPropensityCalculator.html │ │ │ ├── ConstantAmountManager.html │ │ │ ├── DefaultAmountManager.html │ │ │ ├── FeatureNotSupportedException.html │ │ │ ├── KineticConstantPropensityCalculator.html │ │ │ ├── Network.html │ │ │ ├── NetworkLoader.html │ │ │ ├── PartialDerivativePropensityCalculator.html │ │ │ ├── PropensityCalculator.html │ │ │ ├── class-use │ │ │ │ ├── AbstractKineticConstantPropensityCalculator.html │ │ │ │ ├── AbstractNetworkImpl.html │ │ │ │ ├── AmountManager.html │ │ │ │ ├── AnnotationManager.html │ │ │ │ ├── AnnotationManagerImpl.html │ │ │ │ ├── ArrayKineticConstantPropensityCalculator.html │ │ │ │ ├── ComplexDependenciesPropensityCalculator.html │ │ │ │ ├── ConstantAmountManager.html │ │ │ │ ├── DefaultAmountManager.html │ │ │ │ ├── FeatureNotSupportedException.html │ │ │ │ ├── KineticConstantPropensityCalculator.html │ │ │ │ ├── Network.html │ │ │ │ ├── NetworkLoader.html │ │ │ │ ├── PartialDerivativePropensityCalculator.html │ │ │ │ └── PropensityCalculator.html │ │ │ ├── creation │ │ │ │ ├── AutocatalyticNetwork.html │ │ │ │ ├── CatalystIterator.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AutocatalyticNetwork.html │ │ │ │ │ └── CatalystIterator.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── fernml │ │ │ │ ├── FernMLAnnotationManager.html │ │ │ │ ├── FernMLNetwork.html │ │ │ │ ├── class-use │ │ │ │ │ ├── FernMLAnnotationManager.html │ │ │ │ │ └── FernMLNetwork.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── modification │ │ │ │ ├── CatalysedNetwork.html │ │ │ │ ├── ExtractSubNetwork.html │ │ │ │ ├── ModifierNetwork.html │ │ │ │ ├── ReversibleNetwork.html │ │ │ │ ├── class-use │ │ │ │ │ ├── CatalysedNetwork.html │ │ │ │ │ ├── ExtractSubNetwork.html │ │ │ │ │ ├── ModifierNetwork.html │ │ │ │ │ └── ReversibleNetwork.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ ├── package-use.html │ │ │ └── sbml │ │ │ │ ├── MathTree.html │ │ │ │ ├── SBMLEventHandlerObserver.html │ │ │ │ ├── SBMLNetwork.html │ │ │ │ ├── SBMLPropensityCalculator.html │ │ │ │ ├── class-use │ │ │ │ ├── MathTree.html │ │ │ │ ├── SBMLEventHandlerObserver.html │ │ │ │ ├── SBMLNetwork.html │ │ │ │ └── SBMLPropensityCalculator.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ ├── package-frame.html │ │ ├── package-summary.html │ │ ├── package-tree.html │ │ ├── package-use.html │ │ ├── simulation │ │ │ ├── Simulator.FireType.html │ │ │ ├── Simulator.html │ │ │ ├── algorithm │ │ │ │ ├── AbstractBaseTauLeaping.html │ │ │ │ ├── AbstractTauLeapingPropensityBoundSimulator.html │ │ │ │ ├── CompositionRejection.html │ │ │ │ ├── DependencyGraph.html │ │ │ │ ├── GibsonBruckSimulator.html │ │ │ │ ├── GillespieEnhanced.html │ │ │ │ ├── GillespieSimple.html │ │ │ │ ├── GroupContainer.html │ │ │ │ ├── HybridMaximalTimeStep.html │ │ │ │ ├── IndexedPriorityQueue.html │ │ │ │ ├── TauLeapingAbsoluteBoundSimulator.html │ │ │ │ ├── TauLeapingRelativeBoundSimulator.html │ │ │ │ ├── TauLeapingSpeciesPopulationBoundSimulator.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AbstractBaseTauLeaping.html │ │ │ │ │ ├── AbstractTauLeapingPropensityBoundSimulator.html │ │ │ │ │ ├── CompositionRejection.html │ │ │ │ │ ├── DependencyGraph.html │ │ │ │ │ ├── GibsonBruckSimulator.html │ │ │ │ │ ├── GillespieEnhanced.html │ │ │ │ │ ├── GillespieSimple.html │ │ │ │ │ ├── GroupContainer.html │ │ │ │ │ ├── HybridMaximalTimeStep.html │ │ │ │ │ ├── IndexedPriorityQueue.html │ │ │ │ │ ├── TauLeapingAbsoluteBoundSimulator.html │ │ │ │ │ ├── TauLeapingRelativeBoundSimulator.html │ │ │ │ │ └── TauLeapingSpeciesPopulationBoundSimulator.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── class-use │ │ │ │ ├── Simulator.FireType.html │ │ │ │ └── Simulator.html │ │ │ ├── controller │ │ │ │ ├── AmountLowerThanController.html │ │ │ │ ├── AndController.html │ │ │ │ ├── DefaultController.html │ │ │ │ ├── OrController.html │ │ │ │ ├── SimulationController.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AmountLowerThanController.html │ │ │ │ │ ├── AndController.html │ │ │ │ │ ├── DefaultController.html │ │ │ │ │ ├── OrController.html │ │ │ │ │ └── SimulationController.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── observer │ │ │ │ ├── AmountAtMomentObserver.html │ │ │ │ ├── AmountIntervalObserver.html │ │ │ │ ├── FireTypeObserver.html │ │ │ │ ├── GnuPlotObserver.html │ │ │ │ ├── InstantOutputObserver.html │ │ │ │ ├── IntervalObserver.html │ │ │ │ ├── LeapObserver.html │ │ │ │ ├── MultiAmountIntervalObserver.html │ │ │ │ ├── Observer.html │ │ │ │ ├── RandomNumberGeneratorCallObserver.html │ │ │ │ ├── ReactionIntervalObserver.html │ │ │ │ ├── TriggerObserver.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AmountAtMomentObserver.html │ │ │ │ │ ├── AmountIntervalObserver.html │ │ │ │ │ ├── FireTypeObserver.html │ │ │ │ │ ├── GnuPlotObserver.html │ │ │ │ │ ├── InstantOutputObserver.html │ │ │ │ │ ├── IntervalObserver.html │ │ │ │ │ ├── LeapObserver.html │ │ │ │ │ ├── MultiAmountIntervalObserver.html │ │ │ │ │ ├── Observer.html │ │ │ │ │ ├── RandomNumberGeneratorCallObserver.html │ │ │ │ │ ├── ReactionIntervalObserver.html │ │ │ │ │ └── TriggerObserver.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ └── tools │ │ │ ├── ColorSpectrum.html │ │ │ ├── ConfigReader.html │ │ │ ├── NetworkTools.html │ │ │ ├── NumberTools.html │ │ │ ├── Stochastics.html │ │ │ ├── class-use │ │ │ ├── ColorSpectrum.html │ │ │ ├── ConfigReader.html │ │ │ ├── NetworkTools.html │ │ │ ├── NumberTools.html │ │ │ └── Stochastics.html │ │ │ ├── functions │ │ │ ├── Probability.Constant.html │ │ │ ├── Probability.ReactionProbability.html │ │ │ ├── Probability.html │ │ │ ├── class-use │ │ │ │ ├── Probability.Constant.html │ │ │ │ ├── Probability.ReactionProbability.html │ │ │ │ └── Probability.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ │ ├── gnuplot │ │ │ ├── ArrayMatrixAxes.html │ │ │ ├── Axes.html │ │ │ ├── CollectionAxes.html │ │ │ ├── GnuPlot.html │ │ │ ├── TransposedArrayMatrixAxes.html │ │ │ ├── class-use │ │ │ │ ├── ArrayMatrixAxes.html │ │ │ │ ├── Axes.html │ │ │ │ ├── CollectionAxes.html │ │ │ │ ├── GnuPlot.html │ │ │ │ └── TransposedArrayMatrixAxes.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ ├── help-doc.html │ ├── index-all.html │ ├── index.html │ ├── org │ │ ├── simulator │ │ │ ├── About.html │ │ │ ├── class-use │ │ │ │ └── About.html │ │ │ ├── comp │ │ │ │ ├── CompSimulator.html │ │ │ │ ├── class-use │ │ │ │ │ └── CompSimulator.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── examples │ │ │ │ ├── BiomodelsExample.html │ │ │ │ ├── CompExample.html │ │ │ │ ├── ConstraintExample.html │ │ │ │ ├── FBAExample.html │ │ │ │ ├── OMEXExample.html │ │ │ │ ├── SEDMLExample.html │ │ │ │ ├── SimulatorExample.html │ │ │ │ ├── class-use │ │ │ │ │ ├── BiomodelsExample.html │ │ │ │ │ ├── CompExample.html │ │ │ │ │ ├── ConstraintExample.html │ │ │ │ │ ├── FBAExample.html │ │ │ │ │ ├── OMEXExample.html │ │ │ │ │ ├── SEDMLExample.html │ │ │ │ │ └── SimulatorExample.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── fba │ │ │ │ ├── FluxBalanceAnalysis.html │ │ │ │ ├── NewGLPKSolver.html │ │ │ │ ├── class-use │ │ │ │ │ ├── FluxBalanceAnalysis.html │ │ │ │ │ └── NewGLPKSolver.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── io │ │ │ │ ├── CSVImporter.html │ │ │ │ ├── class-use │ │ │ │ │ └── CSVImporter.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── math │ │ │ │ ├── ArithmeticMean.html │ │ │ │ ├── DistanceSum.html │ │ │ │ ├── EuclideanDistance.html │ │ │ │ ├── ManhattanDistance.html │ │ │ │ ├── Mathematics.html │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ ├── MatrixOperations.html │ │ │ │ ├── MaxAbsDistance.html │ │ │ │ ├── MaxDivergenceTolerance.html │ │ │ │ ├── MeanFunction.html │ │ │ │ ├── N_Metric.html │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ ├── QualityMeasure.html │ │ │ │ ├── RNG.html │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ ├── RelativeMaxDistance.html │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ ├── Relative_N_Metric.html │ │ │ │ ├── class-use │ │ │ │ │ ├── ArithmeticMean.html │ │ │ │ │ ├── DistanceSum.html │ │ │ │ │ ├── EuclideanDistance.html │ │ │ │ │ ├── ManhattanDistance.html │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ ├── MaxAbsDistance.html │ │ │ │ │ ├── MaxDivergenceTolerance.html │ │ │ │ │ ├── MeanFunction.html │ │ │ │ │ ├── N_Metric.html │ │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ │ ├── QualityMeasure.html │ │ │ │ │ ├── RNG.html │ │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ │ ├── RelativeMaxDistance.html │ │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ │ └── Relative_N_Metric.html │ │ │ │ ├── odes │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ ├── DESystem.html │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── omex │ │ │ │ ├── OMEXArchive.html │ │ │ │ ├── class-use │ │ │ │ │ └── OMEXArchive.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ ├── package-use.html │ │ │ ├── plot │ │ │ │ ├── PlotMultiTable.html │ │ │ │ ├── PlotProcessedSedmlResults.html │ │ │ │ ├── class-use │ │ │ │ │ ├── PlotMultiTable.html │ │ │ │ │ └── PlotProcessedSedmlResults.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── sbml │ │ │ │ ├── AddMetaInfo.html │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ ├── ConstraintEvent.html │ │ │ │ ├── ConstraintListener.html │ │ │ │ ├── EquationSystem.html │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ ├── SimpleConstraintListener.html │ │ │ │ ├── astnode │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ ├── TimesValue.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ │ └── TimesValue.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AddMetaInfo.html │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── ConstraintEvent.html │ │ │ │ │ ├── ConstraintListener.html │ │ │ │ │ ├── EquationSystem.html │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ │ └── SimpleConstraintListener.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ └── sedml │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── FileModelResolver.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── ProcessSedMLResults.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ ├── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── class-use │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── FileModelResolver.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── ProcessSedMLResults.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ └── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ └── testsuite │ │ │ ├── SBMLTestSuiteRunnerWrapper.html │ │ │ ├── class-use │ │ │ └── SBMLTestSuiteRunnerWrapper.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ ├── overview-frame.html │ ├── overview-summary.html │ ├── overview-tree.html │ ├── package-list │ ├── script.js │ ├── serialized-form.html │ └── stylesheet.css ├── ci-management.html ├── css │ ├── apache-maven-fluido-1.7.min.css │ ├── maven-base.css │ ├── maven-theme.css │ ├── print.css │ └── site.css ├── dependencies.html ├── dependency-info.html ├── distribution-management.html ├── fonts │ ├── glyphicons-halflings-regular.eot │ ├── glyphicons-halflings-regular.svg │ ├── glyphicons-halflings-regular.ttf │ └── glyphicons-halflings-regular.woff ├── images │ ├── Calvin-Benson-Cycle.jpg │ ├── Fluxes_during_glycolytic-oscillations.jpg │ ├── Oscilating_concentrations_in_glycolysis.jpg │ ├── SCL_icon.png │ ├── accessories-text-editor.png │ ├── add.gif │ ├── apache-maven-project-2.png │ ├── application-certificate.png │ ├── close.gif │ ├── collapsed.gif │ ├── contact-new.png │ ├── document-properties.png │ ├── drive-harddisk.png │ ├── expanded.gif │ ├── external.png │ ├── fix.gif │ ├── icon_error_sml.gif │ ├── icon_help_sml.gif │ ├── icon_info_sml.gif │ ├── icon_success_sml.gif │ ├── icon_warning_sml.gif │ ├── image-x-generic.png │ ├── internet-web-browser.png │ ├── logos │ │ ├── build-by-maven-black.png │ │ ├── build-by-maven-white.png │ │ └── maven-feather.png │ ├── network-server.png │ ├── newwindow.png │ ├── package-x-generic.png │ ├── profiles │ │ ├── pre-release.png │ │ ├── retired.png │ │ └── sandbox.png │ ├── remove.gif │ ├── rss.png │ ├── update.gif │ └── window-new.png ├── img │ ├── glyphicons-halflings-white.png │ └── glyphicons-halflings.png ├── index.html ├── issue-management.html ├── js │ └── apache-maven-fluido-1.7.min.js ├── licenses.html ├── old_javadoc │ ├── version_1.0 │ │ ├── allclasses-frame.html │ │ ├── allclasses-noframe.html │ │ ├── constant-values.html │ │ ├── deprecated-list.html │ │ ├── help-doc.html │ │ ├── index-files │ │ │ ├── index-1.html │ │ │ ├── index-10.html │ │ │ ├── index-11.html │ │ │ ├── index-12.html │ │ │ ├── index-13.html │ │ │ ├── index-14.html │ │ │ ├── index-15.html │ │ │ ├── index-16.html │ │ │ ├── index-17.html │ │ │ ├── index-18.html │ │ │ ├── index-19.html │ │ │ ├── index-2.html │ │ │ ├── index-20.html │ │ │ ├── index-21.html │ │ │ ├── index-22.html │ │ │ ├── index-23.html │ │ │ ├── index-24.html │ │ │ ├── index-3.html │ │ │ ├── index-4.html │ │ │ ├── index-5.html │ │ │ ├── index-6.html │ │ │ ├── index-7.html │ │ │ ├── index-8.html │ │ │ └── index-9.html │ │ ├── index.html │ │ ├── org │ │ │ └── simulator │ │ │ │ ├── SimulatorTest.html │ │ │ │ ├── class-use │ │ │ │ └── SimulatorTest.html │ │ │ │ ├── math │ │ │ │ ├── Mathematics.html │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ ├── MatrixOperations.html │ │ │ │ ├── RNG.html │ │ │ │ ├── class-use │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ └── RNG.html │ │ │ │ ├── odes │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ ├── DESAssignment.html │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ ├── DESystem.html │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESAssignment.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ ├── package-use.html │ │ │ │ └── sbml │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ ├── EfficientASTNodeInterpreter.html │ │ │ │ ├── EventInProcess.html │ │ │ │ ├── EventInProcessWithDelay.html │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ ├── SpecialASTNodeValue.html │ │ │ │ ├── ValueHolder.html │ │ │ │ ├── astnode │ │ │ │ ├── ASTNodeInterpreterWithTime.html │ │ │ │ ├── ASTNodeObject.html │ │ │ │ ├── AssignmentRuleObject.html │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ ├── FunctionValue.html │ │ │ │ ├── LocalParameterValue.html │ │ │ │ ├── NamedValue.html │ │ │ │ ├── RateRuleObject.html │ │ │ │ ├── ReactionValue.html │ │ │ │ ├── RootFunctionValue.html │ │ │ │ ├── RuleObject.html │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ ├── SpeciesValue.html │ │ │ │ ├── StoichiometryObject.html │ │ │ │ ├── class-use │ │ │ │ │ ├── ASTNodeInterpreterWithTime.html │ │ │ │ │ ├── ASTNodeObject.html │ │ │ │ │ ├── AssignmentRuleObject.html │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ ├── RateRuleObject.html │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ ├── RuleObject.html │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ └── StoichiometryObject.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── class-use │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ ├── EfficientASTNodeInterpreter.html │ │ │ │ ├── EventInProcess.html │ │ │ │ ├── EventInProcessWithDelay.html │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ ├── SpecialASTNodeValue.html │ │ │ │ └── ValueHolder.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ ├── overview-frame.html │ │ ├── overview-summary.html │ │ ├── overview-tree.html │ │ ├── package-list │ │ ├── resources │ │ │ └── inherit.gif │ │ ├── serialized-form.html │ │ └── stylesheet.css │ ├── version_1.1 │ │ ├── allclasses-frame.html │ │ ├── allclasses-noframe.html │ │ ├── constant-values.html │ │ ├── deprecated-list.html │ │ ├── help-doc.html │ │ ├── index-files │ │ │ ├── index-1.html │ │ │ ├── index-10.html │ │ │ ├── index-11.html │ │ │ ├── index-12.html │ │ │ ├── index-13.html │ │ │ ├── index-14.html │ │ │ ├── index-15.html │ │ │ ├── index-16.html │ │ │ ├── index-17.html │ │ │ ├── index-18.html │ │ │ ├── index-19.html │ │ │ ├── index-2.html │ │ │ ├── index-20.html │ │ │ ├── index-21.html │ │ │ ├── index-22.html │ │ │ ├── index-23.html │ │ │ ├── index-3.html │ │ │ ├── index-4.html │ │ │ ├── index-5.html │ │ │ ├── index-6.html │ │ │ ├── index-7.html │ │ │ ├── index-8.html │ │ │ └── index-9.html │ │ ├── index.html │ │ ├── org │ │ │ └── simulator │ │ │ │ ├── About.html │ │ │ │ ├── SimulatorTest.html │ │ │ │ ├── class-use │ │ │ │ ├── About.html │ │ │ │ └── SimulatorTest.html │ │ │ │ ├── math │ │ │ │ ├── Mathematics.html │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ ├── MatrixOperations.html │ │ │ │ ├── RNG.html │ │ │ │ ├── class-use │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ └── RNG.html │ │ │ │ ├── odes │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ ├── DESystem.html │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ ├── package-use.html │ │ │ │ ├── sbml │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ ├── astnode │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ └── StoichiometryValue.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ └── SBMLinterpreter.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ └── sedml │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ ├── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── class-use │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ └── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ ├── overview-frame.html │ │ ├── overview-summary.html │ │ ├── overview-tree.html │ │ ├── package-list │ │ ├── resources │ │ │ └── inherit.gif │ │ ├── serialized-form.html │ │ └── stylesheet.css │ ├── version_1.2 │ │ ├── allclasses-frame.html │ │ ├── allclasses-noframe.html │ │ ├── constant-values.html │ │ ├── deprecated-list.html │ │ ├── help-doc.html │ │ ├── index-files │ │ │ ├── index-1.html │ │ │ ├── index-10.html │ │ │ ├── index-11.html │ │ │ ├── index-12.html │ │ │ ├── index-13.html │ │ │ ├── index-14.html │ │ │ ├── index-15.html │ │ │ ├── index-16.html │ │ │ ├── index-17.html │ │ │ ├── index-18.html │ │ │ ├── index-19.html │ │ │ ├── index-2.html │ │ │ ├── index-20.html │ │ │ ├── index-21.html │ │ │ ├── index-22.html │ │ │ ├── index-23.html │ │ │ ├── index-24.html │ │ │ ├── index-3.html │ │ │ ├── index-4.html │ │ │ ├── index-5.html │ │ │ ├── index-6.html │ │ │ ├── index-7.html │ │ │ ├── index-8.html │ │ │ └── index-9.html │ │ ├── index.html │ │ ├── javadoc-style.css │ │ ├── org │ │ │ └── simulator │ │ │ │ ├── About.html │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ ├── SimulatorTest.html │ │ │ │ ├── TestBiomodels.html │ │ │ │ ├── class-use │ │ │ │ ├── About.html │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ ├── SimulatorTest.html │ │ │ │ └── TestBiomodels.html │ │ │ │ ├── gui │ │ │ │ ├── img │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── io │ │ │ │ ├── CSVImporter.html │ │ │ │ ├── class-use │ │ │ │ │ └── CSVImporter.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── math │ │ │ │ ├── ArithmeticMean.html │ │ │ │ ├── DistanceSum.html │ │ │ │ ├── EuclideanDistance.html │ │ │ │ ├── ManhattanDistance.html │ │ │ │ ├── Mathematics.html │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ ├── MatrixOperations.html │ │ │ │ ├── MeanFunction.html │ │ │ │ ├── N_Metric.html │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ ├── QualityMeasure.html │ │ │ │ ├── RNG.html │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ ├── Relative_N_Metric.html │ │ │ │ ├── class-use │ │ │ │ │ ├── ArithmeticMean.html │ │ │ │ │ ├── DistanceSum.html │ │ │ │ │ ├── EuclideanDistance.html │ │ │ │ │ ├── ManhattanDistance.html │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ ├── MeanFunction.html │ │ │ │ │ ├── N_Metric.html │ │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ │ ├── QualityMeasure.html │ │ │ │ │ ├── RNG.html │ │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ │ └── Relative_N_Metric.html │ │ │ │ ├── odes │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ ├── DESystem.html │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ ├── package-use.html │ │ │ │ ├── sbml │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ ├── astnode │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ ├── TimesValue.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ │ └── TimesValue.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ └── SBMLinterpreter.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ └── sedml │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ ├── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── class-use │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ └── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ ├── overview-frame.html │ │ ├── overview-summary.html │ │ ├── overview-tree.html │ │ ├── package-list │ │ ├── resources │ │ │ └── inherit.gif │ │ └── serialized-form.html │ ├── version_1.3 │ │ ├── allclasses-frame.html │ │ ├── allclasses-noframe.html │ │ ├── constant-values.html │ │ ├── deprecated-list.html │ │ ├── help-doc.html │ │ ├── index-files │ │ │ ├── index-1.html │ │ │ ├── index-10.html │ │ │ ├── index-11.html │ │ │ ├── index-12.html │ │ │ ├── index-13.html │ │ │ ├── index-14.html │ │ │ ├── index-15.html │ │ │ ├── index-16.html │ │ │ ├── index-17.html │ │ │ ├── index-18.html │ │ │ ├── index-19.html │ │ │ ├── index-2.html │ │ │ ├── index-20.html │ │ │ ├── index-21.html │ │ │ ├── index-22.html │ │ │ ├── index-23.html │ │ │ ├── index-24.html │ │ │ ├── index-3.html │ │ │ ├── index-4.html │ │ │ ├── index-5.html │ │ │ ├── index-6.html │ │ │ ├── index-7.html │ │ │ ├── index-8.html │ │ │ └── index-9.html │ │ ├── index.html │ │ ├── javadoc-style.css │ │ ├── org │ │ │ └── simulator │ │ │ │ ├── About.html │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ ├── SimulatorTest.html │ │ │ │ ├── TestBiomodels.html │ │ │ │ ├── class-use │ │ │ │ ├── About.html │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ ├── SimulatorTest.html │ │ │ │ └── TestBiomodels.html │ │ │ │ ├── gui │ │ │ │ ├── img │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── io │ │ │ │ ├── CSVImporter.html │ │ │ │ ├── class-use │ │ │ │ │ └── CSVImporter.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── math │ │ │ │ ├── ArithmeticMean.html │ │ │ │ ├── DistanceSum.html │ │ │ │ ├── EuclideanDistance.html │ │ │ │ ├── ManhattanDistance.html │ │ │ │ ├── Mathematics.html │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ ├── MatrixOperations.html │ │ │ │ ├── MeanFunction.html │ │ │ │ ├── N_Metric.html │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ ├── QualityMeasure.html │ │ │ │ ├── RNG.html │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ ├── Relative_N_Metric.html │ │ │ │ ├── class-use │ │ │ │ │ ├── ArithmeticMean.html │ │ │ │ │ ├── DistanceSum.html │ │ │ │ │ ├── EuclideanDistance.html │ │ │ │ │ ├── ManhattanDistance.html │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ ├── MeanFunction.html │ │ │ │ │ ├── N_Metric.html │ │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ │ ├── QualityMeasure.html │ │ │ │ │ ├── RNG.html │ │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ │ └── Relative_N_Metric.html │ │ │ │ ├── odes │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ ├── DESystem.html │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ ├── package-use.html │ │ │ │ ├── sbml │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ ├── ConstraintEvent.html │ │ │ │ ├── ConstraintListener.html │ │ │ │ ├── ConstraintTest.html │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ ├── SimpleConstraintListener.html │ │ │ │ ├── astnode │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ ├── TimesValue.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ │ └── TimesValue.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── ConstraintEvent.html │ │ │ │ │ ├── ConstraintListener.html │ │ │ │ │ ├── ConstraintTest.html │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ │ └── SimpleConstraintListener.html │ │ │ │ ├── data │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ └── sedml │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ ├── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── class-use │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ └── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ ├── overview-frame.html │ │ ├── overview-summary.html │ │ ├── overview-tree.html │ │ ├── package-list │ │ ├── resources │ │ │ ├── SCL_icon.png │ │ │ └── inherit.gif │ │ └── serialized-form.html │ └── version_1.4 │ │ ├── allclasses-frame.html │ │ ├── allclasses-noframe.html │ │ ├── constant-values.html │ │ ├── deprecated-list.html │ │ ├── help-doc.html │ │ ├── index-files │ │ ├── index-1.html │ │ ├── index-10.html │ │ ├── index-11.html │ │ ├── index-12.html │ │ ├── index-13.html │ │ ├── index-14.html │ │ ├── index-15.html │ │ ├── index-16.html │ │ ├── index-17.html │ │ ├── index-18.html │ │ ├── index-19.html │ │ ├── index-2.html │ │ ├── index-20.html │ │ ├── index-21.html │ │ ├── index-22.html │ │ ├── index-23.html │ │ ├── index-24.html │ │ ├── index-3.html │ │ ├── index-4.html │ │ ├── index-5.html │ │ ├── index-6.html │ │ ├── index-7.html │ │ ├── index-8.html │ │ └── index-9.html │ │ ├── index.html │ │ ├── javadoc-style.css │ │ ├── org │ │ └── simulator │ │ │ ├── About.html │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ ├── SimulatorTest.html │ │ │ ├── TestBiomodels.html │ │ │ ├── class-use │ │ │ ├── About.html │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ ├── SimulatorTest.html │ │ │ └── TestBiomodels.html │ │ │ ├── gui │ │ │ ├── img │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ │ ├── io │ │ │ ├── CSVImporter.html │ │ │ ├── class-use │ │ │ │ └── CSVImporter.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ │ ├── math │ │ │ ├── ArithmeticMean.html │ │ │ ├── DistanceSum.html │ │ │ ├── EuclideanDistance.html │ │ │ ├── ManhattanDistance.html │ │ │ ├── Mathematics.html │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ ├── MatrixOperations.html │ │ │ ├── MeanFunction.html │ │ │ ├── N_Metric.html │ │ │ ├── PearsonCorrelation.html │ │ │ ├── QualityMeasure.html │ │ │ ├── RNG.html │ │ │ ├── RelativeEuclideanDistance.html │ │ │ ├── RelativeManhattanDistance.html │ │ │ ├── RelativeSquaredError.html │ │ │ ├── Relative_N_Metric.html │ │ │ ├── class-use │ │ │ │ ├── ArithmeticMean.html │ │ │ │ ├── DistanceSum.html │ │ │ │ ├── EuclideanDistance.html │ │ │ │ ├── ManhattanDistance.html │ │ │ │ ├── Mathematics.html │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ ├── MatrixOperations.html │ │ │ │ ├── MeanFunction.html │ │ │ │ ├── N_Metric.html │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ ├── QualityMeasure.html │ │ │ │ ├── RNG.html │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ └── Relative_N_Metric.html │ │ │ ├── odes │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ ├── DESSolver.html │ │ │ │ ├── DESystem.html │ │ │ │ ├── DelayValueHolder.html │ │ │ │ ├── DelayedDESystem.html │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ ├── EulerMethod.html │ │ │ │ ├── EventDESystem.html │ │ │ │ ├── EventInProgress.html │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ ├── MultiTable.Block.html │ │ │ │ ├── MultiTable.html │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ ├── RichDESystem.html │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ ├── DESystem.html │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ ├── package-use.html │ │ │ ├── sbml │ │ │ ├── AlgebraicRuleConverter.html │ │ │ ├── ConstraintEvent.html │ │ │ ├── ConstraintListener.html │ │ │ ├── ConstraintTest.html │ │ │ ├── SBMLEventInProgress.html │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ ├── SBMLValueHolder.html │ │ │ ├── SBMLinterpreter.html │ │ │ ├── SimpleConstraintListener.html │ │ │ ├── astnode │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ ├── ASTNodeValue.html │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ ├── DivideValue.html │ │ │ │ ├── FunctionValue.html │ │ │ │ ├── IntegerValue.html │ │ │ │ ├── LocalParameterValue.html │ │ │ │ ├── MinusValue.html │ │ │ │ ├── NamedValue.html │ │ │ │ ├── PlusValue.html │ │ │ │ ├── PowerValue.html │ │ │ │ ├── RateRuleValue.html │ │ │ │ ├── ReactionValue.html │ │ │ │ ├── RootFunctionValue.html │ │ │ │ ├── RuleValue.html │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ ├── SpeciesValue.html │ │ │ │ ├── StoichiometryValue.html │ │ │ │ ├── TimesValue.html │ │ │ │ ├── class-use │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ └── TimesValue.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── class-use │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ ├── ConstraintEvent.html │ │ │ │ ├── ConstraintListener.html │ │ │ │ ├── ConstraintTest.html │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ └── SimpleConstraintListener.html │ │ │ ├── data │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ │ └── sedml │ │ │ ├── ExecutionException.html │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ ├── SEDMLExecutor.html │ │ │ ├── SEDMLExecutorTest.html │ │ │ ├── SEDMLWriter.html │ │ │ ├── SEDMLWriterTest.html │ │ │ ├── SedMLSBMLSimulatorExecutor.html │ │ │ ├── class-use │ │ │ ├── ExecutionException.html │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ ├── SEDMLExecutor.html │ │ │ ├── SEDMLExecutorTest.html │ │ │ ├── SEDMLWriter.html │ │ │ ├── SEDMLWriterTest.html │ │ │ └── SedMLSBMLSimulatorExecutor.html │ │ │ ├── package-frame.html │ │ │ ├── package-summary.html │ │ │ ├── package-tree.html │ │ │ └── package-use.html │ │ ├── overview-frame.html │ │ ├── overview-summary.html │ │ ├── overview-tree.html │ │ ├── package-list │ │ ├── resources │ │ ├── SCL_icon.png │ │ └── inherit.gif │ │ └── serialized-form.html ├── plugin-management.html ├── plugins.html ├── posters │ └── VLN-Retreat │ │ ├── VLN_poster_abstract.doc │ │ └── VLN_poster_abstract.pdf ├── project-info.html ├── project-reports.html ├── publications │ ├── 2012_BMC_SystBiol │ │ ├── Review │ │ │ ├── Point2PointList.rtf │ │ │ ├── Reviewer1_comment.pdf │ │ │ ├── Reviewer2_comment.pdf │ │ │ └── Submitted_article.pdf │ │ ├── Review2 │ │ │ └── Point2PointList.rtf │ │ ├── bmc_article.bib │ │ ├── bmc_article.bst │ │ ├── bmc_article.cls │ │ ├── bmc_article.tex │ │ ├── img │ │ │ ├── Figure1.tex │ │ │ ├── Figure2.tex │ │ │ ├── Figure3.tex │ │ │ ├── Figure4.tex │ │ │ ├── Figure5.tex │ │ │ ├── Figure6.pdf │ │ │ ├── Figure7.pdf │ │ │ └── Figure8.pdf │ │ ├── macros.tex │ │ ├── plots │ │ │ ├── BIOMODEL206.txt │ │ │ ├── BIOMODEL390.txt │ │ │ ├── plot.R │ │ │ └── test.pdf │ │ ├── readme.html │ │ ├── software_matrix.xls │ │ └── table_runningTimes.tex │ └── 2012_Bioinformatics │ │ ├── Cover_Letter.pdf │ │ ├── Decision.txt │ │ ├── PLAIN.BST │ │ ├── alltt.sty │ │ ├── array.sty │ │ ├── bioinfo.cls │ │ ├── chngpage.sty │ │ ├── color.sty │ │ ├── crop.cfg │ │ ├── crop.sty │ │ ├── document.bib │ │ ├── document.pdf │ │ ├── document.tex │ │ ├── documentation.doc │ │ ├── float.sty │ │ ├── flushend.sty │ │ ├── graphicx.sty │ │ ├── img │ │ ├── DESystems.pdf │ │ ├── SBMLInterpreter.pdf │ │ ├── Solvers.pdf │ │ ├── Solvers_and_DESystem.pdf │ │ ├── UML_Solvers_and_Systems.pdf │ │ └── UML_Solvers_and_Systems_1.pdf │ │ ├── landscap.sty │ │ ├── natbib.bst │ │ ├── natbib.sty │ │ ├── s1-ln1219595195844769-1939656818Hwf-2084541201IdV-107833966812195951PDF_HI0001.pdf │ │ ├── stfloats.sty │ │ ├── times.sty │ │ └── url.sty ├── scm.html ├── summary.html └── team.html ├── modules ├── cellDesigner │ ├── CellDesignerNetworkWrapper.java │ ├── CellDesignerPropensityCalculator.java │ ├── FernCellDesignerPlugin.java │ └── ui │ │ ├── ExtendedPane.java │ │ ├── MainFrame.java │ │ └── OverviewPane.java ├── cytoscape │ ├── ColorCalculator.java │ ├── CytoscapeAnnotationManager.java │ ├── CytoscapeColorChangeObserver.java │ ├── CytoscapeNetworkWrapper.java │ ├── CytoscapeVisualizer.java │ ├── FernVisualStyle.java │ ├── NetworkChecker.java │ └── ui │ │ ├── ColorPicker.java │ │ ├── ExtendedPane.java │ │ ├── MainFrame.java │ │ └── OverviewPane.java └── lib │ ├── celldesigner_fern.jar │ └── cytoscape_fern.jar ├── pom.xml └── src ├── assembly └── assembly.xml ├── lib ├── maven │ ├── kisao │ │ └── libkisao │ │ │ ├── 1.0.3.1-rc │ │ │ ├── libkisao-1.0.3.1-rc.jar │ │ │ ├── libkisao-1.0.3.1-rc.jar.md5 │ │ │ ├── libkisao-1.0.3.1-rc.jar.sha1 │ │ │ ├── libkisao-1.0.3.1-rc.pom │ │ │ ├── libkisao-1.0.3.1-rc.pom.md5 │ │ │ └── libkisao-1.0.3.1-rc.pom.sha1 │ │ │ ├── maven-metadata-local.xml │ │ │ ├── maven-metadata-local.xml.md5 │ │ │ └── maven-metadata-local.xml.sha1 │ └── scpsolver │ │ ├── GLPKSolverPack │ │ ├── 4.35v2 │ │ │ ├── GLPKSolverPack-4.35v2.jar │ │ │ ├── GLPKSolverPack-4.35v2.jar.md5 │ │ │ ├── GLPKSolverPack-4.35v2.jar.sha1 │ │ │ ├── GLPKSolverPack-4.35v2.pom │ │ │ ├── GLPKSolverPack-4.35v2.pom.md5 │ │ │ └── GLPKSolverPack-4.35v2.pom.sha1 │ │ ├── maven-metadata-local.xml │ │ ├── maven-metadata-local.xml.md5 │ │ └── maven-metadata-local.xml.sha1 │ │ ├── LPSOLVESolverPack │ │ ├── 5.5.2.5 │ │ │ ├── LPSOLVESolverPack-5.5.2.5.jar │ │ │ ├── LPSOLVESolverPack-5.5.2.5.jar.md5 │ │ │ ├── LPSOLVESolverPack-5.5.2.5.jar.sha1 │ │ │ ├── LPSOLVESolverPack-5.5.2.5.pom │ │ │ ├── LPSOLVESolverPack-5.5.2.5.pom.md5 │ │ │ └── LPSOLVESolverPack-5.5.2.5.pom.sha1 │ │ ├── maven-metadata-local.xml │ │ ├── maven-metadata-local.xml.md5 │ │ └── maven-metadata-local.xml.sha1 │ │ └── SCPSolver │ │ ├── 1.0v2 │ │ ├── SCPSolver-1.0v2.jar │ │ ├── SCPSolver-1.0v2.jar.md5 │ │ ├── SCPSolver-1.0v2.jar.sha1 │ │ ├── SCPSolver-1.0v2.pom │ │ ├── SCPSolver-1.0v2.pom.md5 │ │ └── SCPSolver-1.0v2.pom.sha1 │ │ ├── maven-metadata-local.xml │ │ ├── maven-metadata-local.xml.md5 │ │ └── maven-metadata-local.xml.sha1 ├── register_maven_jars.sh └── sbml_test_runner_wrapper │ ├── GLPKSolverPack-4.35v2.jar │ ├── LPSOLVESolverPack-5.5.2.5.jar │ ├── SCPSolver-1.0v2.jar │ ├── commons-math-2.2.jar │ ├── jigsaw-2.2.6.jar │ ├── jsbml-1.5.jar │ ├── jsbml-arrays-1.5.jar │ ├── jsbml-comp-1.5.jar │ ├── jsbml-core-1.5.jar │ ├── jsbml-distrib-1.5.jar │ ├── jsbml-dyn-1.5.jar │ ├── jsbml-fbc-1.5.jar │ ├── jsbml-groups-1.5.jar │ ├── jsbml-layout-1.5.jar │ ├── jsbml-qual-1.5.jar │ ├── jsbml-render-1.5.jar │ ├── jsbml-spatial-1.5.jar │ ├── libkisao-1.0.3.1-rc.jar │ ├── log4j-1.2-api-2.3.jar │ ├── log4j-api-2.3.jar │ ├── log4j-core-2.3.jar │ ├── stax2-api-3.1.4.jar │ └── woodstox-core-5.0.1.jar ├── main ├── java │ ├── fern │ │ ├── Start.java │ │ ├── analysis │ │ │ ├── AnalysisBase.java │ │ │ ├── AutocatalyticNetworkDetection.java │ │ │ ├── IntQueue.java │ │ │ ├── IntSearchStructure.java │ │ │ ├── IntStack.java │ │ │ ├── NetworkSearchAction.java │ │ │ ├── NodeChecker.java │ │ │ ├── NodeCheckerByAnnotation.java │ │ │ └── ShortestPath.java │ │ ├── benchmark │ │ │ ├── Benchmark.java │ │ │ ├── RandomNumber.java │ │ │ ├── SimulatorCorrectness.java │ │ │ ├── SimulatorFireTypes.java │ │ │ ├── SimulatorPerformance.java │ │ │ ├── SimulatorRandomNumbers.java │ │ │ └── SimulatorTime.java │ │ ├── example │ │ │ ├── AutocatalyticNetworkExample.java │ │ │ ├── CellGrowthObserver.java │ │ │ ├── CompositionRejectionStressTest.java │ │ │ ├── DecayingDimerizingHistogramDistances.java │ │ │ ├── DecayingDimerizingInteractive.java │ │ │ ├── DecayingDimerizingPlots.java │ │ │ ├── Dsmts.java │ │ │ ├── ExamplePath.java │ │ │ ├── HistogramDistanceTestSet.java │ │ │ ├── IrreversibleIsomerization.java │ │ │ ├── LacYComplete.java │ │ │ ├── LacYHistogramDistances.java │ │ │ ├── LacZ.java │ │ │ ├── Mapk.java │ │ │ ├── MapkBenchmark.java │ │ │ ├── MichaelisMentenKinetic.java │ │ │ └── SBMLMathTreeTest.java │ │ ├── network │ │ │ ├── AbstractKineticConstantPropensityCalculator.java │ │ │ ├── AbstractNetworkImpl.java │ │ │ ├── AmountManager.java │ │ │ ├── AnnotationManager.java │ │ │ ├── AnnotationManagerImpl.java │ │ │ ├── ArrayKineticConstantPropensityCalculator.java │ │ │ ├── ComplexDependenciesPropensityCalculator.java │ │ │ ├── ConstantAmountManager.java │ │ │ ├── DefaultAmountManager.java │ │ │ ├── FeatureNotSupportedException.java │ │ │ ├── KineticConstantPropensityCalculator.java │ │ │ ├── Network.java │ │ │ ├── NetworkLoader.java │ │ │ ├── PartialDerivativePropensityCalculator.java │ │ │ ├── PropensityCalculator.java │ │ │ ├── creation │ │ │ │ ├── AutocatalyticNetwork.java │ │ │ │ └── CatalystIterator.java │ │ │ ├── fernml │ │ │ │ ├── FernMLAnnotationManager.java │ │ │ │ └── FernMLNetwork.java │ │ │ ├── modification │ │ │ │ ├── CatalysedNetwork.java │ │ │ │ ├── ExtractSubNetwork.java │ │ │ │ ├── ModifierNetwork.java │ │ │ │ └── ReversibleNetwork.java │ │ │ └── sbml │ │ │ │ ├── MathTree.java │ │ │ │ ├── SBMLEventHandlerObserver.java │ │ │ │ ├── SBMLNetwork.java │ │ │ │ └── SBMLPropensityCalculator.java │ │ ├── simulation │ │ │ ├── Simulator.java │ │ │ ├── algorithm │ │ │ │ ├── AbstractBaseTauLeaping.java │ │ │ │ ├── AbstractTauLeapingPropensityBoundSimulator.java │ │ │ │ ├── CompositionRejection.java │ │ │ │ ├── DependencyGraph.java │ │ │ │ ├── GibsonBruckSimulator.java │ │ │ │ ├── GillespieEnhanced.java │ │ │ │ ├── GillespieSimple.java │ │ │ │ ├── GroupContainer.java │ │ │ │ ├── HybridMaximalTimeStep.java │ │ │ │ ├── IndexedPriorityQueue.java │ │ │ │ ├── TauLeapingAbsoluteBoundSimulator.java │ │ │ │ ├── TauLeapingRelativeBoundSimulator.java │ │ │ │ └── TauLeapingSpeciesPopulationBoundSimulator.java │ │ │ ├── controller │ │ │ │ ├── AmountLowerThanController.java │ │ │ │ ├── AndController.java │ │ │ │ ├── DefaultController.java │ │ │ │ ├── OrController.java │ │ │ │ └── SimulationController.java │ │ │ └── observer │ │ │ │ ├── AmountAtMomentObserver.java │ │ │ │ ├── AmountIntervalObserver.java │ │ │ │ ├── FireTypeObserver.java │ │ │ │ ├── GnuPlotObserver.java │ │ │ │ ├── InstantOutputObserver.java │ │ │ │ ├── IntervalObserver.java │ │ │ │ ├── LeapObserver.java │ │ │ │ ├── MultiAmountIntervalObserver.java │ │ │ │ ├── Observer.java │ │ │ │ ├── RandomNumberGeneratorCallObserver.java │ │ │ │ ├── ReactionIntervalObserver.java │ │ │ │ └── TriggerObserver.java │ │ └── tools │ │ │ ├── ColorSpectrum.java │ │ │ ├── ConfigReader.java │ │ │ ├── NetworkTools.java │ │ │ ├── NumberTools.java │ │ │ ├── Stochastics.java │ │ │ ├── functions │ │ │ └── Probability.java │ │ │ └── gnuplot │ │ │ ├── ArrayMatrixAxes.java │ │ │ ├── Axes.java │ │ │ ├── CollectionAxes.java │ │ │ ├── GnuPlot.java │ │ │ └── TransposedArrayMatrixAxes.java │ └── org │ │ ├── simulator │ │ ├── About.java │ │ ├── comp │ │ │ └── CompSimulator.java │ │ ├── examples │ │ │ ├── BiomodelsExample.java │ │ │ ├── CompExample.java │ │ │ ├── ConstraintExample.java │ │ │ ├── FBAExample.java │ │ │ ├── OMEXExample.java │ │ │ ├── SEDMLExample.java │ │ │ └── SimulatorExample.java │ │ ├── fba │ │ │ ├── FluxBalanceAnalysis.java │ │ │ ├── NewGLPKSolver.java │ │ │ └── package-info.java │ │ ├── io │ │ │ ├── CSVImporter.java │ │ │ └── package-info.java │ │ ├── math │ │ │ ├── ArithmeticMean.java │ │ │ ├── DistanceSum.java │ │ │ ├── EuclideanDistance.java │ │ │ ├── ManhattanDistance.java │ │ │ ├── Mathematics.java │ │ │ ├── MatrixOperations.java │ │ │ ├── MaxAbsDistance.java │ │ │ ├── MaxDivergenceTolerance.java │ │ │ ├── MeanFunction.java │ │ │ ├── N_Metric.java │ │ │ ├── PearsonCorrelation.java │ │ │ ├── QualityMeasure.java │ │ │ ├── RelativeEuclideanDistance.java │ │ │ ├── RelativeManhattanDistance.java │ │ │ ├── RelativeMaxDistance.java │ │ │ ├── RelativeSquaredError.java │ │ │ ├── Relative_N_Metric.java │ │ │ ├── odes │ │ │ │ ├── .LCKLSODAIntegrator.java~ │ │ │ │ ├── AbstractDESSolver.java │ │ │ │ ├── AdamsBashforthSolver.java │ │ │ │ ├── AdamsMoultonSolver.java │ │ │ │ ├── AdaptiveStepsizeIntegrator.java │ │ │ │ ├── DESSolver.java │ │ │ │ ├── DESystem.java │ │ │ │ ├── DelayValueHolder.java │ │ │ │ ├── DelayedDESystem.java │ │ │ │ ├── DormandPrince54Solver.java │ │ │ │ ├── DormandPrince853Solver.java │ │ │ │ ├── EulerMethod.java │ │ │ │ ├── EventDESystem.java │ │ │ │ ├── EventInProgress.java │ │ │ │ ├── FastProcessDESystem.java │ │ │ │ ├── FirstOrderSolver.java │ │ │ │ ├── GraggBulirschStoerSolver.java │ │ │ │ ├── HighamHall54Solver.java │ │ │ │ ├── LSODA │ │ │ │ │ ├── LSODACommon.java │ │ │ │ │ ├── LSODACommonContext.java │ │ │ │ │ ├── LSODAContext.java │ │ │ │ │ ├── LSODAIntegrator.java │ │ │ │ │ ├── LSODAOptions.java │ │ │ │ │ ├── LSODAStepper.java │ │ │ │ │ └── howToUse.md │ │ │ │ ├── MultiTable.java │ │ │ │ ├── ParameterizedDESystem.java │ │ │ │ ├── RichDESystem.java │ │ │ │ ├── RosenbrockSolver.java │ │ │ │ ├── RungeKutta_EventSolver.java │ │ │ │ ├── exception │ │ │ │ │ ├── ErrorWeightException.java │ │ │ │ │ ├── IllegalInputException.java │ │ │ │ │ ├── IllegalTException.java │ │ │ │ │ ├── IntdyException.java │ │ │ │ │ ├── MaxStepExceededException.java │ │ │ │ │ ├── MembersNotInitializedException.java │ │ │ │ │ ├── TestFailException.java │ │ │ │ │ ├── TooMuchAccuracyException.java │ │ │ │ │ └── UnsupportedMethodException.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── omex │ │ │ ├── OMEXArchive.java │ │ │ └── package-info.java │ │ ├── package-info.java │ │ ├── plot │ │ │ ├── PlotMultiTable.java │ │ │ ├── PlotProcessedSedmlResults.java │ │ │ └── package-info.java │ │ ├── sbml │ │ │ ├── AddMetaInfo.java │ │ │ ├── AlgebraicRuleConverter.java │ │ │ ├── ConstraintEvent.java │ │ │ ├── ConstraintListener.java │ │ │ ├── EquationSystem.java │ │ │ ├── SBMLEventInProgress.java │ │ │ ├── SBMLEventInProgressWithDelay.java │ │ │ ├── SBMLValueHolder.java │ │ │ ├── SBMLinterpreter.java │ │ │ ├── SimpleConstraintListener.java │ │ │ ├── astnode │ │ │ │ ├── ASTNodeInterpreter.java │ │ │ │ ├── ASTNodeValue.java │ │ │ │ ├── AssignmentRuleValue.java │ │ │ │ ├── CompartmentOrParameterValue.java │ │ │ │ ├── DivideValue.java │ │ │ │ ├── FunctionValue.java │ │ │ │ ├── IntegerValue.java │ │ │ │ ├── LocalParameterValue.java │ │ │ │ ├── MinusValue.java │ │ │ │ ├── NamedValue.java │ │ │ │ ├── PlusValue.java │ │ │ │ ├── PowerValue.java │ │ │ │ ├── RateRuleValue.java │ │ │ │ ├── ReactionValue.java │ │ │ │ ├── RootFunctionValue.java │ │ │ │ ├── RuleValue.java │ │ │ │ ├── SpeciesReferenceValue.java │ │ │ │ ├── SpeciesValue.java │ │ │ │ ├── StoichiometryValue.java │ │ │ │ ├── TimesValue.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ └── sedml │ │ │ ├── ExecutionException.java │ │ │ ├── FileModelResolver.java │ │ │ ├── IProcessedSedMLSimulationResultsWrapper.java │ │ │ ├── MultTableSEDMLWrapper.java │ │ │ ├── ProcessSedMLResults.java │ │ │ ├── SEDMLWriter.java │ │ │ ├── SedMLSBMLSimulatorExecutor.java │ │ │ └── package-info.java │ │ └── testsuite │ │ ├── SBMLTestSuiteRunnerWrapper.java │ │ └── SBMLTestSuiteRunnerWrapper_LSODA.java ├── javadoc │ └── overview.html └── resources │ ├── examples │ ├── decaydimer.xml │ ├── isomerization.xml │ ├── isomerization_sbml.xml │ ├── lacy.xml │ ├── lacy1000.xml │ ├── lacy1000_sbml.xml │ ├── lacy_sbml.xml │ ├── lacy_sbmll1v2.xml │ ├── lacz.xml │ ├── lacz_sbml.xml │ ├── mapk.xml │ ├── mapk_sbml.xml │ ├── mapk_sbmll1v2.xml │ ├── mm.xml │ └── mm_sbml.xml │ └── org │ └── simulator │ └── gui │ ├── img │ ├── SCL_icon.png │ └── package-info.java │ └── package-info.java ├── site ├── markdown │ └── index.md ├── resources │ ├── css │ │ └── site.css │ ├── images │ │ ├── Calvin-Benson-Cycle.jpg │ │ ├── Fluxes_during_glycolytic-oscillations.jpg │ │ ├── Oscilating_concentrations_in_glycolysis.jpg │ │ └── SCL_icon.png │ ├── old_javadoc │ │ ├── version_1.0 │ │ │ ├── allclasses-frame.html │ │ │ ├── allclasses-noframe.html │ │ │ ├── constant-values.html │ │ │ ├── deprecated-list.html │ │ │ ├── help-doc.html │ │ │ ├── index-files │ │ │ │ ├── index-1.html │ │ │ │ ├── index-10.html │ │ │ │ ├── index-11.html │ │ │ │ ├── index-12.html │ │ │ │ ├── index-13.html │ │ │ │ ├── index-14.html │ │ │ │ ├── index-15.html │ │ │ │ ├── index-16.html │ │ │ │ ├── index-17.html │ │ │ │ ├── index-18.html │ │ │ │ ├── index-19.html │ │ │ │ ├── index-2.html │ │ │ │ ├── index-20.html │ │ │ │ ├── index-21.html │ │ │ │ ├── index-22.html │ │ │ │ ├── index-23.html │ │ │ │ ├── index-24.html │ │ │ │ ├── index-3.html │ │ │ │ ├── index-4.html │ │ │ │ ├── index-5.html │ │ │ │ ├── index-6.html │ │ │ │ ├── index-7.html │ │ │ │ ├── index-8.html │ │ │ │ └── index-9.html │ │ │ ├── index.html │ │ │ ├── org │ │ │ │ └── simulator │ │ │ │ │ ├── SimulatorTest.html │ │ │ │ │ ├── class-use │ │ │ │ │ └── SimulatorTest.html │ │ │ │ │ ├── math │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ ├── RNG.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ │ └── RNG.html │ │ │ │ │ ├── odes │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESAssignment.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ │ ├── class-use │ │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ │ ├── DESAssignment.html │ │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ ├── package-use.html │ │ │ │ │ └── sbml │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── EfficientASTNodeInterpreter.html │ │ │ │ │ ├── EventInProcess.html │ │ │ │ │ ├── EventInProcessWithDelay.html │ │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ │ ├── SpecialASTNodeValue.html │ │ │ │ │ ├── ValueHolder.html │ │ │ │ │ ├── astnode │ │ │ │ │ ├── ASTNodeInterpreterWithTime.html │ │ │ │ │ ├── ASTNodeObject.html │ │ │ │ │ ├── AssignmentRuleObject.html │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ ├── RateRuleObject.html │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ ├── RuleObject.html │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ ├── StoichiometryObject.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── ASTNodeInterpreterWithTime.html │ │ │ │ │ │ ├── ASTNodeObject.html │ │ │ │ │ │ ├── AssignmentRuleObject.html │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ ├── RateRuleObject.html │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ ├── RuleObject.html │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ └── StoichiometryObject.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── class-use │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── EfficientASTNodeInterpreter.html │ │ │ │ │ ├── EventInProcess.html │ │ │ │ │ ├── EventInProcessWithDelay.html │ │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ │ ├── SpecialASTNodeValue.html │ │ │ │ │ └── ValueHolder.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ ├── overview-frame.html │ │ │ ├── overview-summary.html │ │ │ ├── overview-tree.html │ │ │ ├── package-list │ │ │ ├── resources │ │ │ │ └── inherit.gif │ │ │ ├── serialized-form.html │ │ │ └── stylesheet.css │ │ ├── version_1.1 │ │ │ ├── allclasses-frame.html │ │ │ ├── allclasses-noframe.html │ │ │ ├── constant-values.html │ │ │ ├── deprecated-list.html │ │ │ ├── help-doc.html │ │ │ ├── index-files │ │ │ │ ├── index-1.html │ │ │ │ ├── index-10.html │ │ │ │ ├── index-11.html │ │ │ │ ├── index-12.html │ │ │ │ ├── index-13.html │ │ │ │ ├── index-14.html │ │ │ │ ├── index-15.html │ │ │ │ ├── index-16.html │ │ │ │ ├── index-17.html │ │ │ │ ├── index-18.html │ │ │ │ ├── index-19.html │ │ │ │ ├── index-2.html │ │ │ │ ├── index-20.html │ │ │ │ ├── index-21.html │ │ │ │ ├── index-22.html │ │ │ │ ├── index-23.html │ │ │ │ ├── index-3.html │ │ │ │ ├── index-4.html │ │ │ │ ├── index-5.html │ │ │ │ ├── index-6.html │ │ │ │ ├── index-7.html │ │ │ │ ├── index-8.html │ │ │ │ └── index-9.html │ │ │ ├── index.html │ │ │ ├── org │ │ │ │ └── simulator │ │ │ │ │ ├── About.html │ │ │ │ │ ├── SimulatorTest.html │ │ │ │ │ ├── class-use │ │ │ │ │ ├── About.html │ │ │ │ │ └── SimulatorTest.html │ │ │ │ │ ├── math │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ ├── RNG.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ │ └── RNG.html │ │ │ │ │ ├── odes │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ │ ├── class-use │ │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ ├── package-use.html │ │ │ │ │ ├── sbml │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ │ ├── astnode │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ │ ├── class-use │ │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ │ └── StoichiometryValue.html │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ │ └── SBMLinterpreter.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ └── sedml │ │ │ │ │ ├── ExecutionException.html │ │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ │ ├── SEDMLWriter.html │ │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ │ ├── SedMLSBMLSimulatorExecutor.html │ │ │ │ │ ├── class-use │ │ │ │ │ ├── ExecutionException.html │ │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ │ ├── SEDMLWriter.html │ │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ │ └── SedMLSBMLSimulatorExecutor.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ ├── overview-frame.html │ │ │ ├── overview-summary.html │ │ │ ├── overview-tree.html │ │ │ ├── package-list │ │ │ ├── resources │ │ │ │ └── inherit.gif │ │ │ ├── serialized-form.html │ │ │ └── stylesheet.css │ │ ├── version_1.2 │ │ │ ├── allclasses-frame.html │ │ │ ├── allclasses-noframe.html │ │ │ ├── constant-values.html │ │ │ ├── deprecated-list.html │ │ │ ├── help-doc.html │ │ │ ├── index-files │ │ │ │ ├── index-1.html │ │ │ │ ├── index-10.html │ │ │ │ ├── index-11.html │ │ │ │ ├── index-12.html │ │ │ │ ├── index-13.html │ │ │ │ ├── index-14.html │ │ │ │ ├── index-15.html │ │ │ │ ├── index-16.html │ │ │ │ ├── index-17.html │ │ │ │ ├── index-18.html │ │ │ │ ├── index-19.html │ │ │ │ ├── index-2.html │ │ │ │ ├── index-20.html │ │ │ │ ├── index-21.html │ │ │ │ ├── index-22.html │ │ │ │ ├── index-23.html │ │ │ │ ├── index-24.html │ │ │ │ ├── index-3.html │ │ │ │ ├── index-4.html │ │ │ │ ├── index-5.html │ │ │ │ ├── index-6.html │ │ │ │ ├── index-7.html │ │ │ │ ├── index-8.html │ │ │ │ └── index-9.html │ │ │ ├── index.html │ │ │ ├── javadoc-style.css │ │ │ ├── org │ │ │ │ └── simulator │ │ │ │ │ ├── About.html │ │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ │ ├── SimulatorTest.html │ │ │ │ │ ├── TestBiomodels.html │ │ │ │ │ ├── class-use │ │ │ │ │ ├── About.html │ │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ │ ├── SimulatorTest.html │ │ │ │ │ └── TestBiomodels.html │ │ │ │ │ ├── gui │ │ │ │ │ ├── img │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── io │ │ │ │ │ ├── CSVImporter.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ └── CSVImporter.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── math │ │ │ │ │ ├── ArithmeticMean.html │ │ │ │ │ ├── DistanceSum.html │ │ │ │ │ ├── EuclideanDistance.html │ │ │ │ │ ├── ManhattanDistance.html │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ ├── MeanFunction.html │ │ │ │ │ ├── N_Metric.html │ │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ │ ├── QualityMeasure.html │ │ │ │ │ ├── RNG.html │ │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ │ ├── Relative_N_Metric.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── ArithmeticMean.html │ │ │ │ │ │ ├── DistanceSum.html │ │ │ │ │ │ ├── EuclideanDistance.html │ │ │ │ │ │ ├── ManhattanDistance.html │ │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ │ ├── MeanFunction.html │ │ │ │ │ │ ├── N_Metric.html │ │ │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ │ │ ├── QualityMeasure.html │ │ │ │ │ │ ├── RNG.html │ │ │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ │ │ └── Relative_N_Metric.html │ │ │ │ │ ├── odes │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ │ ├── class-use │ │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ ├── package-use.html │ │ │ │ │ ├── sbml │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ │ ├── astnode │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ │ ├── TimesValue.html │ │ │ │ │ │ ├── class-use │ │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ │ │ └── TimesValue.html │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ │ └── SBMLinterpreter.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ └── sedml │ │ │ │ │ ├── ExecutionException.html │ │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ │ ├── SEDMLWriter.html │ │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ │ ├── SedMLSBMLSimulatorExecutor.html │ │ │ │ │ ├── class-use │ │ │ │ │ ├── ExecutionException.html │ │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ │ ├── SEDMLWriter.html │ │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ │ └── SedMLSBMLSimulatorExecutor.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ ├── overview-frame.html │ │ │ ├── overview-summary.html │ │ │ ├── overview-tree.html │ │ │ ├── package-list │ │ │ ├── resources │ │ │ │ └── inherit.gif │ │ │ └── serialized-form.html │ │ ├── version_1.3 │ │ │ ├── allclasses-frame.html │ │ │ ├── allclasses-noframe.html │ │ │ ├── constant-values.html │ │ │ ├── deprecated-list.html │ │ │ ├── help-doc.html │ │ │ ├── index-files │ │ │ │ ├── index-1.html │ │ │ │ ├── index-10.html │ │ │ │ ├── index-11.html │ │ │ │ ├── index-12.html │ │ │ │ ├── index-13.html │ │ │ │ ├── index-14.html │ │ │ │ ├── index-15.html │ │ │ │ ├── index-16.html │ │ │ │ ├── index-17.html │ │ │ │ ├── index-18.html │ │ │ │ ├── index-19.html │ │ │ │ ├── index-2.html │ │ │ │ ├── index-20.html │ │ │ │ ├── index-21.html │ │ │ │ ├── index-22.html │ │ │ │ ├── index-23.html │ │ │ │ ├── index-24.html │ │ │ │ ├── index-3.html │ │ │ │ ├── index-4.html │ │ │ │ ├── index-5.html │ │ │ │ ├── index-6.html │ │ │ │ ├── index-7.html │ │ │ │ ├── index-8.html │ │ │ │ └── index-9.html │ │ │ ├── index.html │ │ │ ├── javadoc-style.css │ │ │ ├── org │ │ │ │ └── simulator │ │ │ │ │ ├── About.html │ │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ │ ├── SimulatorTest.html │ │ │ │ │ ├── TestBiomodels.html │ │ │ │ │ ├── class-use │ │ │ │ │ ├── About.html │ │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ │ ├── SimulatorTest.html │ │ │ │ │ └── TestBiomodels.html │ │ │ │ │ ├── gui │ │ │ │ │ ├── img │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── io │ │ │ │ │ ├── CSVImporter.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ └── CSVImporter.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── math │ │ │ │ │ ├── ArithmeticMean.html │ │ │ │ │ ├── DistanceSum.html │ │ │ │ │ ├── EuclideanDistance.html │ │ │ │ │ ├── ManhattanDistance.html │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ ├── MeanFunction.html │ │ │ │ │ ├── N_Metric.html │ │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ │ ├── QualityMeasure.html │ │ │ │ │ ├── RNG.html │ │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ │ ├── Relative_N_Metric.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── ArithmeticMean.html │ │ │ │ │ │ ├── DistanceSum.html │ │ │ │ │ │ ├── EuclideanDistance.html │ │ │ │ │ │ ├── ManhattanDistance.html │ │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ │ ├── MeanFunction.html │ │ │ │ │ │ ├── N_Metric.html │ │ │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ │ │ ├── QualityMeasure.html │ │ │ │ │ │ ├── RNG.html │ │ │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ │ │ └── Relative_N_Metric.html │ │ │ │ │ ├── odes │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ │ ├── class-use │ │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ ├── package-use.html │ │ │ │ │ ├── sbml │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── ConstraintEvent.html │ │ │ │ │ ├── ConstraintListener.html │ │ │ │ │ ├── ConstraintTest.html │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ │ ├── SimpleConstraintListener.html │ │ │ │ │ ├── astnode │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ │ ├── TimesValue.html │ │ │ │ │ │ ├── class-use │ │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ │ │ └── TimesValue.html │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ │ ├── ConstraintEvent.html │ │ │ │ │ │ ├── ConstraintListener.html │ │ │ │ │ │ ├── ConstraintTest.html │ │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ │ │ └── SimpleConstraintListener.html │ │ │ │ │ ├── data │ │ │ │ │ │ ├── package-frame.html │ │ │ │ │ │ ├── package-summary.html │ │ │ │ │ │ ├── package-tree.html │ │ │ │ │ │ └── package-use.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ │ └── sedml │ │ │ │ │ ├── ExecutionException.html │ │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ │ ├── SEDMLWriter.html │ │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ │ ├── SedMLSBMLSimulatorExecutor.html │ │ │ │ │ ├── class-use │ │ │ │ │ ├── ExecutionException.html │ │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ │ ├── SEDMLWriter.html │ │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ │ └── SedMLSBMLSimulatorExecutor.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ ├── overview-frame.html │ │ │ ├── overview-summary.html │ │ │ ├── overview-tree.html │ │ │ ├── package-list │ │ │ ├── resources │ │ │ │ ├── SCL_icon.png │ │ │ │ └── inherit.gif │ │ │ └── serialized-form.html │ │ └── version_1.4 │ │ │ ├── allclasses-frame.html │ │ │ ├── allclasses-noframe.html │ │ │ ├── constant-values.html │ │ │ ├── deprecated-list.html │ │ │ ├── help-doc.html │ │ │ ├── index-files │ │ │ ├── index-1.html │ │ │ ├── index-10.html │ │ │ ├── index-11.html │ │ │ ├── index-12.html │ │ │ ├── index-13.html │ │ │ ├── index-14.html │ │ │ ├── index-15.html │ │ │ ├── index-16.html │ │ │ ├── index-17.html │ │ │ ├── index-18.html │ │ │ ├── index-19.html │ │ │ ├── index-2.html │ │ │ ├── index-20.html │ │ │ ├── index-21.html │ │ │ ├── index-22.html │ │ │ ├── index-23.html │ │ │ ├── index-24.html │ │ │ ├── index-3.html │ │ │ ├── index-4.html │ │ │ ├── index-5.html │ │ │ ├── index-6.html │ │ │ ├── index-7.html │ │ │ ├── index-8.html │ │ │ └── index-9.html │ │ │ ├── index.html │ │ │ ├── javadoc-style.css │ │ │ ├── org │ │ │ └── simulator │ │ │ │ ├── About.html │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ ├── SimulatorTest.html │ │ │ │ ├── TestBiomodels.html │ │ │ │ ├── class-use │ │ │ │ ├── About.html │ │ │ │ ├── SBMLTestSuiteRunner.Options.html │ │ │ │ ├── SBMLTestSuiteRunner.html │ │ │ │ ├── SBMLTestSuiteWrapper.html │ │ │ │ ├── SimulatorTest.html │ │ │ │ └── TestBiomodels.html │ │ │ │ ├── gui │ │ │ │ ├── img │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── io │ │ │ │ ├── CSVImporter.html │ │ │ │ ├── class-use │ │ │ │ │ └── CSVImporter.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── math │ │ │ │ ├── ArithmeticMean.html │ │ │ │ ├── DistanceSum.html │ │ │ │ ├── EuclideanDistance.html │ │ │ │ ├── ManhattanDistance.html │ │ │ │ ├── Mathematics.html │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ ├── MatrixOperations.html │ │ │ │ ├── MeanFunction.html │ │ │ │ ├── N_Metric.html │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ ├── QualityMeasure.html │ │ │ │ ├── RNG.html │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ ├── Relative_N_Metric.html │ │ │ │ ├── class-use │ │ │ │ │ ├── ArithmeticMean.html │ │ │ │ │ ├── DistanceSum.html │ │ │ │ │ ├── EuclideanDistance.html │ │ │ │ │ ├── ManhattanDistance.html │ │ │ │ │ ├── Mathematics.html │ │ │ │ │ ├── MatrixOperations.MatrixException.html │ │ │ │ │ ├── MatrixOperations.html │ │ │ │ │ ├── MeanFunction.html │ │ │ │ │ ├── N_Metric.html │ │ │ │ │ ├── PearsonCorrelation.html │ │ │ │ │ ├── QualityMeasure.html │ │ │ │ │ ├── RNG.html │ │ │ │ │ ├── RelativeEuclideanDistance.html │ │ │ │ │ ├── RelativeManhattanDistance.html │ │ │ │ │ ├── RelativeSquaredError.html │ │ │ │ │ └── Relative_N_Metric.html │ │ │ │ ├── odes │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ ├── DESystem.html │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ ├── RungeKutta_EventSolver.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── AbstractDESSolver.html │ │ │ │ │ │ ├── AdamsBashforthSolver.html │ │ │ │ │ │ ├── AdamsMoultonSolver.html │ │ │ │ │ │ ├── AdaptiveStepsizeIntegrator.html │ │ │ │ │ │ ├── DESSolver.html │ │ │ │ │ │ ├── DESystem.html │ │ │ │ │ │ ├── DelayValueHolder.html │ │ │ │ │ │ ├── DelayedDESystem.html │ │ │ │ │ │ ├── DormandPrince54Solver.html │ │ │ │ │ │ ├── DormandPrince853Solver.html │ │ │ │ │ │ ├── EulerMethod.html │ │ │ │ │ │ ├── EventDESystem.html │ │ │ │ │ │ ├── EventInProgress.html │ │ │ │ │ │ ├── FastProcessDESystem.html │ │ │ │ │ │ ├── FirstOrderSolver.html │ │ │ │ │ │ ├── GraggBulirschStoerSolver.html │ │ │ │ │ │ ├── HighamHall54Solver.html │ │ │ │ │ │ ├── MultiTable.Block.Column.html │ │ │ │ │ │ ├── MultiTable.Block.html │ │ │ │ │ │ ├── MultiTable.html │ │ │ │ │ │ ├── ParameterizedDESystem.html │ │ │ │ │ │ ├── RichDESystem.html │ │ │ │ │ │ ├── RosenbrockSolver.html │ │ │ │ │ │ └── RungeKutta_EventSolver.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ ├── package-use.html │ │ │ │ ├── sbml │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ ├── ConstraintEvent.html │ │ │ │ ├── ConstraintListener.html │ │ │ │ ├── ConstraintTest.html │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ ├── SimpleConstraintListener.html │ │ │ │ ├── astnode │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ ├── TimesValue.html │ │ │ │ │ ├── class-use │ │ │ │ │ │ ├── ASTNodeInterpreter.html │ │ │ │ │ │ ├── ASTNodeValue.html │ │ │ │ │ │ ├── AssignmentRuleValue.html │ │ │ │ │ │ ├── CompartmentOrParameterValue.html │ │ │ │ │ │ ├── DivideValue.html │ │ │ │ │ │ ├── FunctionValue.html │ │ │ │ │ │ ├── IntegerValue.html │ │ │ │ │ │ ├── LocalParameterValue.html │ │ │ │ │ │ ├── MinusValue.html │ │ │ │ │ │ ├── NamedValue.html │ │ │ │ │ │ ├── PlusValue.html │ │ │ │ │ │ ├── PowerValue.html │ │ │ │ │ │ ├── RateRuleValue.html │ │ │ │ │ │ ├── ReactionValue.html │ │ │ │ │ │ ├── RootFunctionValue.html │ │ │ │ │ │ ├── RuleValue.html │ │ │ │ │ │ ├── SpeciesReferenceValue.html │ │ │ │ │ │ ├── SpeciesValue.html │ │ │ │ │ │ ├── StoichiometryValue.html │ │ │ │ │ │ └── TimesValue.html │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── class-use │ │ │ │ │ ├── AlgebraicRuleConverter.html │ │ │ │ │ ├── ConstraintEvent.html │ │ │ │ │ ├── ConstraintListener.html │ │ │ │ │ ├── ConstraintTest.html │ │ │ │ │ ├── SBMLEventInProgress.html │ │ │ │ │ ├── SBMLEventInProgressWithDelay.html │ │ │ │ │ ├── SBMLValueHolder.html │ │ │ │ │ ├── SBMLinterpreter.html │ │ │ │ │ └── SimpleConstraintListener.html │ │ │ │ ├── data │ │ │ │ │ ├── package-frame.html │ │ │ │ │ ├── package-summary.html │ │ │ │ │ ├── package-tree.html │ │ │ │ │ └── package-use.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ │ └── sedml │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ ├── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── class-use │ │ │ │ ├── ExecutionException.html │ │ │ │ ├── MultTableSEDMLWrapper.html │ │ │ │ ├── SEDMLExecutor.html │ │ │ │ ├── SEDMLExecutorTest.html │ │ │ │ ├── SEDMLWriter.html │ │ │ │ ├── SEDMLWriterTest.html │ │ │ │ └── SedMLSBMLSimulatorExecutor.html │ │ │ │ ├── package-frame.html │ │ │ │ ├── package-summary.html │ │ │ │ ├── package-tree.html │ │ │ │ └── package-use.html │ │ │ ├── overview-frame.html │ │ │ ├── overview-summary.html │ │ │ ├── overview-tree.html │ │ │ ├── package-list │ │ │ ├── resources │ │ │ ├── SCL_icon.png │ │ │ └── inherit.gif │ │ │ └── serialized-form.html │ ├── posters │ │ └── VLN-Retreat │ │ │ ├── VLN_poster_abstract.doc │ │ │ └── VLN_poster_abstract.pdf │ └── publications │ │ ├── 2012_BMC_SystBiol │ │ ├── Review │ │ │ ├── Point2PointList.rtf │ │ │ ├── Reviewer1_comment.pdf │ │ │ ├── Reviewer2_comment.pdf │ │ │ └── Submitted_article.pdf │ │ ├── Review2 │ │ │ └── Point2PointList.rtf │ │ ├── bmc_article.bib │ │ ├── bmc_article.bst │ │ ├── bmc_article.cls │ │ ├── bmc_article.tex │ │ ├── img │ │ │ ├── Figure1.tex │ │ │ ├── Figure2.tex │ │ │ ├── Figure3.tex │ │ │ ├── Figure4.tex │ │ │ ├── Figure5.tex │ │ │ ├── Figure6.pdf │ │ │ ├── Figure7.pdf │ │ │ └── Figure8.pdf │ │ ├── macros.tex │ │ ├── plots │ │ │ ├── BIOMODEL206.txt │ │ │ ├── BIOMODEL390.txt │ │ │ ├── plot.R │ │ │ └── test.pdf │ │ ├── readme.html │ │ ├── software_matrix.xls │ │ └── table_runningTimes.tex │ │ └── 2012_Bioinformatics │ │ ├── Cover_Letter.pdf │ │ ├── Decision.txt │ │ ├── PLAIN.BST │ │ ├── alltt.sty │ │ ├── array.sty │ │ ├── bioinfo.cls │ │ ├── chngpage.sty │ │ ├── color.sty │ │ ├── crop.cfg │ │ ├── crop.sty │ │ ├── document.bib │ │ ├── document.pdf │ │ ├── document.tex │ │ ├── documentation.doc │ │ ├── float.sty │ │ ├── flushend.sty │ │ ├── graphicx.sty │ │ ├── img │ │ ├── DESystems.pdf │ │ ├── SBMLInterpreter.pdf │ │ ├── Solvers.pdf │ │ ├── Solvers_and_DESystem.pdf │ │ ├── UML_Solvers_and_Systems.pdf │ │ └── UML_Solvers_and_Systems_1.pdf │ │ ├── landscap.sty │ │ ├── natbib.bst │ │ ├── natbib.sty │ │ ├── s1-ln1219595195844769-1939656818Hwf-2084541201IdV-107833966812195951PDF_HI0001.pdf │ │ ├── stfloats.sty │ │ ├── times.sty │ │ └── url.sty └── site.xml └── test ├── java ├── GnuplotTest.java ├── LSODAIntegratorTest.java ├── LSODASystemTest.java ├── RungeKutta_EventSolverTest.java ├── SBMLTestSuiteRunnerWrapper.java ├── ToolsTest.java └── org │ └── simulator │ ├── TestUtils.java │ ├── biomodels │ └── BioModelsTest.java │ ├── comp │ └── CompSimulatorTest.java │ ├── distance │ ├── MaxAbsDistanceTest.java │ ├── MaxDivergenceToleranceTest.java │ └── MaxRelDistanceTest.java │ ├── fba │ ├── BiGGTest.java │ ├── FluxBalanceAnalysisConvertToCPLEXTest.java │ └── FluxBalanceAnalysisTest.java │ ├── omex │ └── OMEXArchiveTest.java │ ├── oven │ └── SCPSolverIssue.java │ ├── sbml │ ├── SBMLTestSuiteRunner.java │ ├── SBMLTestSuiteTest.java │ ├── SBMLTestSuiteWrapper.java │ └── SimulatorTest.java │ ├── sedml │ ├── SEDMLExecutorTest.java │ └── SEDMLWriterTest.java │ └── stochastic │ └── StochasticTestSuiteTest.java ├── resources ├── bigg │ ├── bigg_reference_solutions.csv │ └── sbscl_bigg_model_solutions.csv ├── comp │ ├── test1.xml │ ├── test10.xml │ ├── test2.xml │ ├── test3.xml │ ├── test4.xml │ ├── test5.xml │ ├── test6.xml │ ├── test7.xml │ ├── test8.xml │ └── test9.xml ├── distance │ ├── test1 │ │ ├── a.csv │ │ ├── abs_result.csv │ │ ├── b.csv │ │ ├── max_div_tol_result.csv │ │ └── rel_result.csv │ └── test2 │ │ ├── a.csv │ │ ├── abs_result.csv │ │ ├── b.csv │ │ ├── max_div_tol_result.csv │ │ └── rel_result.csv ├── fba │ ├── e_coli_core.xml │ └── e_coli_core.xml.gz ├── omex │ └── 12859_2014_369_MOESM1_ESM.omex ├── sbml │ ├── 00001 │ │ ├── 00001-model.html │ │ ├── 00001-model.m │ │ ├── 00001-plot.jpg │ │ ├── 00001-plot.svg │ │ ├── 00001-results.csv │ │ ├── 00001-sbml-l1v2-sedml.xml │ │ ├── 00001-sbml-l1v2.xml │ │ ├── 00001-sbml-l2v1-sedml.xml │ │ ├── 00001-sbml-l2v1.xml │ │ ├── 00001-sbml-l2v2-sedml.xml │ │ ├── 00001-sbml-l2v2.xml │ │ ├── 00001-sbml-l2v3-sedml.xml │ │ ├── 00001-sbml-l2v3.xml │ │ ├── 00001-sbml-l2v4-sedml.xml │ │ ├── 00001-sbml-l2v4.xml │ │ ├── 00001-sbml-l3v1-sedml.xml │ │ ├── 00001-sbml-l3v1.xml │ │ └── 00001-settings.txt │ ├── 00002 │ │ ├── 00002-model.html │ │ ├── 00002-model.m │ │ ├── 00002-plot.jpg │ │ ├── 00002-plot.svg │ │ ├── 00002-results.csv │ │ ├── 00002-sbml-l1v2-sedml.xml │ │ ├── 00002-sbml-l1v2.xml │ │ ├── 00002-sbml-l1v2_sedml.xml │ │ ├── 00002-sbml-l2v1-sedml.xml │ │ ├── 00002-sbml-l2v1.xml │ │ ├── 00002-sbml-l2v2-sedml.xml │ │ ├── 00002-sbml-l2v2.xml │ │ ├── 00002-sbml-l2v3-sedml.xml │ │ ├── 00002-sbml-l2v3.xml │ │ ├── 00002-sbml-l2v4-sedml.xml │ │ ├── 00002-sbml-l2v4.xml │ │ ├── 00002-sbml-l3v1-sedml.xml │ │ ├── 00002-sbml-l3v1.xml │ │ └── 00002-settings.txt │ ├── BIOMD0000000012.xml │ ├── steadystate │ │ └── steadystate.xml │ └── stochastic │ │ ├── stochastic_00001.csv │ │ ├── stochastic_00002.csv │ │ ├── stochastic_00003.csv │ │ ├── stochastic_00004.csv │ │ ├── stochastic_00005.csv │ │ ├── stochastic_00006.csv │ │ ├── stochastic_00007.csv │ │ ├── stochastic_00008.csv │ │ ├── stochastic_00009.csv │ │ ├── stochastic_00012.csv │ │ ├── stochastic_00013.csv │ │ ├── stochastic_00014.csv │ │ ├── stochastic_00015.csv │ │ ├── stochastic_00016.csv │ │ ├── stochastic_00017.csv │ │ ├── stochastic_00018.csv │ │ ├── stochastic_00020.csv │ │ ├── stochastic_00021.csv │ │ ├── stochastic_00022.csv │ │ ├── stochastic_00023.csv │ │ ├── stochastic_00024.csv │ │ ├── stochastic_00025.csv │ │ ├── stochastic_00026.csv │ │ ├── stochastic_00027.csv │ │ ├── stochastic_00028.csv │ │ ├── stochastic_00029.csv │ │ ├── stochastic_00030.csv │ │ ├── stochastic_00031.csv │ │ ├── stochastic_00032.csv │ │ ├── stochastic_00033.csv │ │ ├── stochastic_00034.csv │ │ ├── stochastic_00035.csv │ │ ├── stochastic_00036.csv │ │ ├── stochastic_00037.csv │ │ ├── stochastic_00038.csv │ │ └── stochastic_00039.csv └── sedml │ ├── ClockSedML.xml │ ├── L1V1 │ └── leloup.xml │ ├── L1V2 │ ├── ikappab │ │ ├── ikappab.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ └── results │ │ │ ├── sedml_webtools │ │ │ └── plot1.pdf │ │ │ ├── simulation_core │ │ │ └── plot1.png │ │ │ └── tellurium │ │ │ └── plot1.pdf │ ├── leloup-sbml │ │ ├── leloup-sbml.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ └── results │ │ │ ├── sedml_webtools │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── plot3.pdf │ │ │ ├── simulation_core │ │ │ ├── plot1.png │ │ │ ├── plot2.png │ │ │ └── plot3.png │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── plot3.pdf │ ├── lorenz-sbml │ │ ├── lorenz-model.xml │ │ ├── lorenz.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ └── results │ │ │ ├── sedml_webtools │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── plot3.pdf │ │ │ ├── simulation_core │ │ │ ├── plot1.png │ │ │ ├── plot2.png │ │ │ └── plot3.png │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── plot3.pdf │ ├── oscli-nested-pulse │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── oscli-nested-pulse.xml │ │ ├── oscli.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ ├── plot1.pdf │ │ │ └── report1.xml │ │ │ ├── simulation_core │ │ │ └── plot1.png │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ └── report1.csv │ ├── parameter-scan-2d │ │ ├── BorisEJB.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── parameter-scan-2d.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ ├── plot1.pdf │ │ │ └── plot2.pdf │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── report1.csv │ ├── repeated-scan-oscli │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── oscli.xml │ │ ├── repeated-scan-oscli.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ └── plot1.pdf │ │ │ ├── simulation_core │ │ │ └── plot1.png │ │ │ └── tellurium │ │ │ └── plot1.pdf │ ├── repeated-steady-scan-oscli │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── oscli.xml │ │ ├── repeated-steady-scan-oscli.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ └── plot1.pdf │ │ │ ├── simulation_core │ │ │ └── plot1.png │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ └── report1.csv │ ├── repeated-stochastic-runs │ │ ├── BorisEJB.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── repeated-stochastic-runs.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ └── plot1.png │ │ │ ├── simulation_core │ │ │ └── plot1.png │ │ │ └── tellurium │ │ │ └── plot1.pdf │ └── repressilator │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── repressilator.xml │ │ └── results │ │ ├── sedml_webtools │ │ ├── postprocessing.pdf │ │ ├── preprocessing.pdf │ │ └── timecourse.pdf │ │ ├── simulation_core │ │ ├── postprocessing.png │ │ ├── preprocessing.png │ │ └── timecourse.png │ │ └── tellurium │ │ ├── postprocessing.pdf │ │ ├── preprocessing.pdf │ │ └── timecourse.pdf │ ├── L1V3 │ ├── ikappab │ │ ├── ikappab.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ └── results │ │ │ ├── sedml_webtools │ │ │ └── plot1.pdf │ │ │ └── tellurium │ │ │ └── plot1.pdf │ ├── leloup-sbml │ │ ├── leloup-sbml.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ └── results │ │ │ ├── sedml_webtools │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── plot3.pdf │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── plot3.pdf │ ├── lorenz-sbml │ │ ├── lorenz-model.xml │ │ ├── lorenz.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ └── results │ │ │ ├── sedml_webtools │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── plot3.pdf │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── plot3.pdf │ ├── oscli-nested-pulse │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── oscli-nested-pulse.xml │ │ ├── oscli.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ ├── plot1.pdf │ │ │ └── report1.xml │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ └── report1.csv │ ├── parameter-scan-2d │ │ ├── BorisEJB.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── parameter-scan-2d.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ ├── plot1.pdf │ │ │ └── plot2.pdf │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ ├── plot2.pdf │ │ │ └── report1.csv │ ├── repeated-scan-oscli │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── oscli.xml │ │ ├── repeated-scan-oscli.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ └── plot1.pdf │ │ │ └── tellurium │ │ │ └── plot1.pdf │ ├── repeated-steady-scan-oscli │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── oscli.xml │ │ ├── repeated-steady-scan-oscli.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ └── plot1.pdf │ │ │ └── tellurium │ │ │ ├── plot1.pdf │ │ │ └── report1.csv │ ├── repeated-stochastic-runs │ │ ├── BorisEJB.xml │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── repeated-stochastic-runs.xml │ │ └── results │ │ │ ├── sedml_webtools │ │ │ └── plot1.png │ │ │ └── tellurium │ │ │ └── plot1.pdf │ └── repressilator │ │ ├── manifest.json │ │ ├── metadata.rdf │ │ ├── repressilator.xml │ │ └── results │ │ ├── sedml_webtools │ │ ├── postprocessing.pdf │ │ ├── preprocessing.pdf │ │ └── timecourse.pdf │ │ └── tellurium │ │ ├── postprocessing.pdf │ │ ├── preprocessing.pdf │ │ └── timecourse.pdf │ ├── abc_1.xml │ └── sed1.xml └── scripts ├── CellDesigner4.0beta.sh ├── download_bigg_models.sh ├── download_biomodels.sh ├── download_sbml-test-suite.sh ├── sbml_test_suite_runner.sh ├── sbml_test_suite_runner_wrapper.sh ├── sbml_test_suite_runner_wrapper_lsoda.sh ├── start.bat ├── start.sh ├── start_cygwin.sh └── test.sh /.gitattributes: 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