MANIFEST.in
README.md
setup.py
libsignetsim/LibSigNetSimException.py
libsignetsim/__init__.py
libsignetsim/__main__.py
libsignetsim.egg-info/PKG-INFO
libsignetsim.egg-info/SOURCES.txt
libsignetsim.egg-info/dependency_links.txt
libsignetsim.egg-info/requires.txt
libsignetsim.egg-info/top_level.txt
libsignetsim/combine/CombineArchive.py
libsignetsim/combine/CombineException.py
libsignetsim/combine/File.py
libsignetsim/combine/ListOfFiles.py
libsignetsim/combine/Manifest.py
libsignetsim/combine/__init__.py
libsignetsim/combine/tests/TestCreateArchive.py
libsignetsim/combine/tests/TestNoManifest.py
libsignetsim/combine/tests/TestRunSedmls.py
libsignetsim/combine/tests/TestShowCase.py
libsignetsim/combine/tests/__init__.py
libsignetsim/combine/tests/files/00001-sbml-l3v1-sedml.xml
libsignetsim/combine/tests/files/00001-sbml-l3v1.xml
libsignetsim/combine/tests/files/00001.omex
libsignetsim/combine/tests/files/BIOMD0000000003.sedx
libsignetsim/combine/tests/files/CombineArchiveShowCase.omex
libsignetsim/combine/tests/files/experiment_0.xml
libsignetsim/continuation/EquilibriumPointCurve.py
libsignetsim/continuation/PyDSToolModel.py
libsignetsim/continuation/__init__.py
libsignetsim/cwriter/CMathWriter.py
libsignetsim/cwriter/CModelWriter.py
libsignetsim/cwriter/CWriterData.py
libsignetsim/cwriter/CWriterModelVsDataOptimization.py
libsignetsim/cwriter/CWriterModels.py
libsignetsim/cwriter/CWriterOptimization.py
libsignetsim/cwriter/__init__.py
libsignetsim/data/Experiment.py
libsignetsim/data/ExperimentalCondition.py
libsignetsim/data/ExperimentalData.py
libsignetsim/data/ListOfExperimentalData.py
libsignetsim/data/__init__.py
libsignetsim/data/tests/__init__.py
libsignetsim/data/tests/test_readwrite_data.py
libsignetsim/figure/SigNetSimFigure.py
libsignetsim/figure/__init__.py
libsignetsim/lib/scoreFunctions.c
libsignetsim/lib/scoreFunctions.h
libsignetsim/lib/integrate/Makefile
libsignetsim/lib/integrate/src/dae.c
libsignetsim/lib/integrate/src/dae.h
libsignetsim/lib/integrate/src/datas.h
libsignetsim/lib/integrate/src/events.c
libsignetsim/lib/integrate/src/events.h
libsignetsim/lib/integrate/src/integrate.c
libsignetsim/lib/integrate/src/integrate.h
libsignetsim/lib/integrate/src/models.h
libsignetsim/lib/integrate/src/ode.c
libsignetsim/lib/integrate/src/ode.h
libsignetsim/lib/integrate/src/realtype_math.c
libsignetsim/lib/integrate/src/realtype_math.h
libsignetsim/lib/integrate/src/shared.c
libsignetsim/lib/integrate/src/shared.h
libsignetsim/lib/integrate/src/types.h
libsignetsim/lib/templates/data_optimization/Makefile
libsignetsim/lib/templates/data_optimization/main.c
libsignetsim/lib/templates/simulation/Makefile
libsignetsim/lib/templates/simulation/main.c
libsignetsim/model/ListOfMathVariables.py
libsignetsim/model/ListOfSbmlVariables.py
libsignetsim/model/ListOfVariables.py
libsignetsim/model/Model.py
libsignetsim/model/ModelException.py
libsignetsim/model/ModelInstance.py
libsignetsim/model/SbmlDocument.py
libsignetsim/model/Variable.py
libsignetsim/model/__init__.py
libsignetsim/model/math/CFE.py
libsignetsim/model/math/ConservationLaw.py
libsignetsim/model/math/DAE.py
libsignetsim/model/math/MathAsymmetricModel.py
libsignetsim/model/math/MathDevelopper.py
libsignetsim/model/math/MathException.py
libsignetsim/model/math/MathFormula.py
libsignetsim/model/math/MathJacobianMatrix.py
libsignetsim/model/math/MathModel.py
libsignetsim/model/math/MathSlowModel.py
libsignetsim/model/math/MathStoichiometryMatrix.py
libsignetsim/model/math/MathSubmodel.py
libsignetsim/model/math/MathSymbol.py
libsignetsim/model/math/MathVariable.py
libsignetsim/model/math/ODE.py
libsignetsim/model/math/SbmlMathReader.py
libsignetsim/model/math/SbmlMathWriter.py
libsignetsim/model/math/__init__.py
libsignetsim/model/math/sympy_shortcuts.py
libsignetsim/model/math/container/ListOfCFEs.py
libsignetsim/model/math/container/ListOfConservationLaws.py
libsignetsim/model/math/container/ListOfDAEs.py
libsignetsim/model/math/container/ListOfODEs.py
libsignetsim/model/math/container/__init__.py
libsignetsim/model/math/tests/TestMath.py
libsignetsim/model/math/tests/__init__.py
libsignetsim/model/sbml/AlgebraicRule.py
libsignetsim/model/sbml/AssignmentRule.py
libsignetsim/model/sbml/CVTerm.py
libsignetsim/model/sbml/Compartment.py
libsignetsim/model/sbml/Constraint.py
libsignetsim/model/sbml/Deletion.py
libsignetsim/model/sbml/Event.py
libsignetsim/model/sbml/EventAssignedVariable.py
libsignetsim/model/sbml/EventAssignment.py
libsignetsim/model/sbml/EventDelay.py
libsignetsim/model/sbml/EventPriority.py
libsignetsim/model/sbml/EventTrigger.py
libsignetsim/model/sbml/ExternalModelDefinition.py
libsignetsim/model/sbml/FunctionDefinition.py
libsignetsim/model/sbml/HasConversionFactor.py
libsignetsim/model/sbml/HasId.py
libsignetsim/model/sbml/HasParentObj.py
libsignetsim/model/sbml/HasRef.py
libsignetsim/model/sbml/HasReplacedElements.py
libsignetsim/model/sbml/HasSBaseRef.py
libsignetsim/model/sbml/HasUnits.py
libsignetsim/model/sbml/InitialAssignment.py
libsignetsim/model/sbml/InitiallyAssignedVariable.py
libsignetsim/model/sbml/KineticLaw.py
libsignetsim/model/sbml/KineticLawIdentifier.py
libsignetsim/model/sbml/ModelDefinition.py
libsignetsim/model/sbml/ModelUnits.py
libsignetsim/model/sbml/Parameter.py
libsignetsim/model/sbml/Port.py
libsignetsim/model/sbml/RateRule.py
libsignetsim/model/sbml/Reaction.py
libsignetsim/model/sbml/ReplacedBy.py
libsignetsim/model/sbml/ReplacedElement.py
libsignetsim/model/sbml/Rule.py
libsignetsim/model/sbml/RuledVariable.py
libsignetsim/model/sbml/SbmlAnnotation.py
libsignetsim/model/sbml/SbmlModel.py
libsignetsim/model/sbml/SbmlModelAnnotation.py
libsignetsim/model/sbml/SbmlModelCreator.py
libsignetsim/model/sbml/SbmlModelHistory.py
libsignetsim/model/sbml/SbmlObject.py
libsignetsim/model/sbml/SbmlVariable.py
libsignetsim/model/sbml/SimpleSbmlObject.py
libsignetsim/model/sbml/Species.py
libsignetsim/model/sbml/SpeciesReference.py
libsignetsim/model/sbml/SubModel.py
libsignetsim/model/sbml/Unit.py
libsignetsim/model/sbml/UnitDefinition.py
libsignetsim/model/sbml/__init__.py
libsignetsim/model/sbml/container/HasIds.py
libsignetsim/model/sbml/container/HasMetaIds.py
libsignetsim/model/sbml/container/ListOf.py
libsignetsim/model/sbml/container/ListOfCompartments.py
libsignetsim/model/sbml/container/ListOfConstraints.py
libsignetsim/model/sbml/container/ListOfDeletions.py
libsignetsim/model/sbml/container/ListOfEvents.py
libsignetsim/model/sbml/container/ListOfExternalModelDefinitions.py
libsignetsim/model/sbml/container/ListOfFunctionDefinitions.py
libsignetsim/model/sbml/container/ListOfInitialAssignments.py
libsignetsim/model/sbml/container/ListOfModelDefinitions.py
libsignetsim/model/sbml/container/ListOfParameters.py
libsignetsim/model/sbml/container/ListOfPorts.py
libsignetsim/model/sbml/container/ListOfReactions.py
libsignetsim/model/sbml/container/ListOfReplacedElements.py
libsignetsim/model/sbml/container/ListOfRules.py
libsignetsim/model/sbml/container/ListOfSbmlObjects.py
libsignetsim/model/sbml/container/ListOfSpecies.py
libsignetsim/model/sbml/container/ListOfSpeciesReference.py
libsignetsim/model/sbml/container/ListOfSubmodels.py
libsignetsim/model/sbml/container/ListOfUnitDefinitions.py
libsignetsim/model/sbml/container/__init__.py
libsignetsim/model/tests/TestAnnotation.py
libsignetsim/model/tests/TestFindKineticLaws.py
libsignetsim/model/tests/TestLocalParameters.py
libsignetsim/model/tests/TestMetaIds.py
libsignetsim/model/tests/TestModelDefinition.py
libsignetsim/model/tests/TestReduceModel.py
libsignetsim/model/tests/TestRenameSbmlId.py
libsignetsim/model/tests/TestSubstitutions.py
libsignetsim/model/tests/TestUnits.py
libsignetsim/model/tests/TestXPaths.py
libsignetsim/model/tests/__init__.py
libsignetsim/model/tests/files/BIOMD0000000001.xml
libsignetsim/model/tests/files/modelqlzB7i.xml
libsignetsim/model/tests/files/comp_model/modelEHfev9.xml
libsignetsim/model/tests/files/comp_model/modelI1vrys.xml
libsignetsim/model/tests/files/comp_model/modelcEvRcX.xml
libsignetsim/model/tests/files/comp_model/modelz9xdww.xml
libsignetsim/numl/AtomicDescription.py
libsignetsim/numl/AtomicValue.py
libsignetsim/numl/CompositeDescription.py
libsignetsim/numl/CompositeValue.py
libsignetsim/numl/Dimension.py
libsignetsim/numl/DimensionDescription.py
libsignetsim/numl/NMBase.py
libsignetsim/numl/NuMLDocument.py
libsignetsim/numl/NuMLException.py
libsignetsim/numl/OntologyTerm.py
libsignetsim/numl/ResultComponent.py
libsignetsim/numl/TupleDescription.py
libsignetsim/numl/TupleValue.py
libsignetsim/numl/__init__.py
libsignetsim/numl/container/ListOf.py
libsignetsim/numl/container/ListOfOntologyTerms.py
libsignetsim/numl/container/ListOfResultComponents.py
libsignetsim/numl/container/__init__.py
libsignetsim/numl/tests/__init__.py
libsignetsim/numl/tests/test_example.py
libsignetsim/numl/tests/test_example_notes.py
libsignetsim/numl/tests/test_experiment.py
libsignetsim/numl/tests/files/example.xml
libsignetsim/numl/tests/files/experiment_0.xml
libsignetsim/optimization/ModelVsTimeseriesOptimization.py
libsignetsim/optimization/NoiseGenerator.py
libsignetsim/optimization/Optimization.py
libsignetsim/optimization/OptimizationException.py
libsignetsim/optimization/OptimizationExecution.py
libsignetsim/optimization/OptimizationMonitor.py
libsignetsim/optimization/OptimizationParameters.py
libsignetsim/optimization/__init__.py
libsignetsim/optimization/tests/TestOptimization.py
libsignetsim/optimization/tests/TestOptimizationComp.py
libsignetsim/optimization/tests/__init__.py
libsignetsim/optimization/tests/files/ras_data.xml
libsignetsim/optimization/tests/files/comp_model/modelEHfev9.xml
libsignetsim/optimization/tests/files/comp_model/modelI1vrys.xml
libsignetsim/optimization/tests/files/comp_model/modelcEvRcX.xml
libsignetsim/optimization/tests/files/comp_model/modelz9xdww.xml
libsignetsim/sedml/AbstractTask.py
libsignetsim/sedml/AddXML.py
libsignetsim/sedml/Algorithm.py
libsignetsim/sedml/AlgorithmParameter.py
libsignetsim/sedml/Change.py
libsignetsim/sedml/ChangeAttribute.py
libsignetsim/sedml/ComputeChange.py
libsignetsim/sedml/Curve.py
libsignetsim/sedml/DataGenerator.py
libsignetsim/sedml/DataSet.py
libsignetsim/sedml/FunctionalRange.py
libsignetsim/sedml/HasId.py
libsignetsim/sedml/Model.py
libsignetsim/sedml/NewXML.py
libsignetsim/sedml/OneStep.py
libsignetsim/sedml/Output.py
libsignetsim/sedml/Parameter.py
libsignetsim/sedml/Plot2D.py
libsignetsim/sedml/Range.py
libsignetsim/sedml/RepeatedTask.py
libsignetsim/sedml/Report.py
libsignetsim/sedml/SedBase.py
libsignetsim/sedml/SedmlDocument.py
libsignetsim/sedml/SedmlException.py
libsignetsim/sedml/SetValue.py
libsignetsim/sedml/Simulation.py
libsignetsim/sedml/Source.py
libsignetsim/sedml/SteadyState.py
libsignetsim/sedml/SubTask.py
libsignetsim/sedml/Task.py
libsignetsim/sedml/URI.py
libsignetsim/sedml/UniformRange.py
libsignetsim/sedml/UniformTimeCourse.py
libsignetsim/sedml/Variable.py
libsignetsim/sedml/VectorRange.py
libsignetsim/sedml/XPath.py
libsignetsim/sedml/__init__.py
libsignetsim/sedml/container/ListOf.py
libsignetsim/sedml/container/ListOfAlgorithmParameters.py
libsignetsim/sedml/container/ListOfChanges.py
libsignetsim/sedml/container/ListOfCurves.py
libsignetsim/sedml/container/ListOfDataGenerators.py
libsignetsim/sedml/container/ListOfDataSets.py
libsignetsim/sedml/container/ListOfIds.py
libsignetsim/sedml/container/ListOfModels.py
libsignetsim/sedml/container/ListOfOutputs.py
libsignetsim/sedml/container/ListOfParameters.py
libsignetsim/sedml/container/ListOfRanges.py
libsignetsim/sedml/container/ListOfSetValueChanges.py
libsignetsim/sedml/container/ListOfSimulations.py
libsignetsim/sedml/container/ListOfSubTasks.py
libsignetsim/sedml/container/ListOfTasks.py
libsignetsim/sedml/container/ListOfVariables.py
libsignetsim/sedml/container/__init__.py
libsignetsim/sedml/math/MathFormula.py
libsignetsim/sedml/math/SedmlMathReader.py
libsignetsim/sedml/math/SedmlMathWriter.py
libsignetsim/sedml/math/__init__.py
libsignetsim/sedml/math/sympy_shortcuts.py
libsignetsim/sedml/tests/TestBiomodelsURI.py
libsignetsim/sedml/tests/TestLogscaleTimeseries.py
libsignetsim/sedml/tests/TestMath.py
libsignetsim/sedml/tests/TestSpecificationL1V2.py
libsignetsim/sedml/tests/TestSteadyStatesScan.py
libsignetsim/sedml/tests/TestXMLChanges.py
libsignetsim/sedml/tests/__init__.py
libsignetsim/sedml/tests/files/BIOMD0000000001.xml
libsignetsim/sedml/tests/files/biomodels_uri.xml
libsignetsim/sedml/tests/files/specificationL1V2.sedml
libsignetsim/settings/Settings.py
libsignetsim/settings/__init__.py
libsignetsim/simulation/CWriterSimulation.py
libsignetsim/simulation/SigNetSimFigure.py
libsignetsim/simulation/Simulation.py
libsignetsim/simulation/SimulationException.py
libsignetsim/simulation/SteadyStatesSimulation.py
libsignetsim/simulation/TimeseriesSimulation.py
libsignetsim/simulation/__init__.py
libsignetsim/simulation/tests/TestSteadyStates.py
libsignetsim/simulation/tests/TestTimeseries.py
libsignetsim/simulation/tests/__init__.py
libsignetsim/simulation/tests/models/modelXZknew.xml
libsignetsim/tests/__init__.py
libsignetsim/tests/biomodels/BiomodelsTestCaseSimulation.py
libsignetsim/tests/biomodels/TestBiomodelsCompatibility.py
libsignetsim/tests/biomodels/__init__.py
libsignetsim/tests/sbmltestsuite/TestSuite.py
libsignetsim/tests/sbmltestsuite/TestSuiteCase.py
libsignetsim/tests/sbmltestsuite/TestSuite_l1v2.py
libsignetsim/tests/sbmltestsuite/TestSuite_l2v1.py
libsignetsim/tests/sbmltestsuite/TestSuite_l2v2.py
libsignetsim/tests/sbmltestsuite/TestSuite_l2v3.py
libsignetsim/tests/sbmltestsuite/TestSuite_l2v4.py
libsignetsim/tests/sbmltestsuite/TestSuite_l2v5.py
libsignetsim/tests/sbmltestsuite/TestSuite_l3v1.py
libsignetsim/tests/sbmltestsuite/__init__.py
libsignetsim/uris/GoResolver.py
libsignetsim/uris/MIRIAMRegistry.py
libsignetsim/uris/NCBITaxonomyResolver.py
libsignetsim/uris/PubmedResolver.py
libsignetsim/uris/SBOResolver.py
libsignetsim/uris/URI.py
libsignetsim/uris/__init__.py
libsignetsim/uris/tests/TestGOResolver.py
libsignetsim/uris/tests/__init__.py