Index

A

accumulateTimecourse() (tellurium.plotting.engine.PlottingEngine method) Accumulator (class in tellurium.utils.misc) add_child() (tellurium.sedml.tesedml.SEDMLCodeFactory.TaskNode method) addEntriesToCombineArchive() (in module tellurium.utils.omex) addFilesToCombineArchive() (in module tellurium.tellurium), [1] addFileToCombineArchive() (in module tellurium.tellurium), [1] addReaction() (tellurium.utils.misc.Accumulator method) addSbmlAsset() (tellurium.teconverters.convert_omex.Omex method) addSBOsToSBML() (tellurium.teconverters.antimony_sbo.antimonySBOParser method) addSedmlAsset() (tellurium.teconverters.convert_omex.Omex method) addXYDataset() (tellurium.plotting.engine.PlottingFigure method)

algorithmParameterToParameterKey() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) allowLog (tellurium.analysis.sensitivityanalysis.SensitivityAnalysis property) antimonyConverter (class in tellurium.teconverters.convert_antimony) antimonySBOConverter (class in tellurium.teconverters.antimony_sbo) antimonySBOParser (class in tellurium.teconverters.antimony_sbo) antimonyToCellML() (in module tellurium) (in module tellurium.tellurium), [1] antimonyToSBML() (in module tellurium) (in module tellurium.tellurium), [1] antimonyTosbml() (in module tellurium.tellurium) antimonyToSBML() (tellurium.teconverters.convert_antimony.antimonyConverter method) args (tellurium.analysis.sensitivityanalysis.SensitivityAnalysis property)

B

bifurcation() (in module tellurium.analysis.bifurcation) BioModHackRemoveDuplicates() (tellurium.teconverters.convert_omex.inlineOmexImporter method)

bounds (tellurium.analysis.sensitivityanalysis.SensitivityAnalysis property) bs() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method)

C

cellmlFileToAntimony() (tellurium.teconverters.convert_antimony.antimonyConverter method) cellmlToAntimony() (in module tellurium) (in module tellurium.tellurium), [1] cellmlToSBML() (in module tellurium) (in module tellurium.tellurium), [1] checkAntimonyReturnCode() (tellurium.teconverters.convert_antimony.antimonyConverter method) checkSEDMLDocument() (tellurium.sedml.tesedml.SEDMLTools class method) clearTiledFigure() (in module tellurium.plotting.api) collect_2DParameterScan_result() (tellurium.analysis.parameterscan.ParameterScan2D method) collect_plotArray_result() (tellurium.analysis.parameterscan.ParameterScan method) (tellurium.analysis.parameterscan.SteadyStateScan method) collect_plotGraduatedArray_result() (tellurium.analysis.parameterscan.ParameterScan method) collect_plotMultiArray_result() (tellurium.analysis.parameterscan.ParameterScan2D method) collect_plotPolyArray_result() (tellurium.analysis.parameterscan.ParameterScan method) collect_plotSurface_result() (tellurium.analysis.parameterscan.ParameterScan method) colorCycle() (in module tellurium.tellurium), [1] (tellurium.analysis.parameterscan.ParameterScan method)

combineArchiveFromDirectory() (in module tellurium.utils.omex) combineArchiveFromEntries() (in module tellurium.utils.omex) combineArchiveToPython() (in module tellurium.sedml.tesedml) conservedMoietyAnalysis (tellurium.analysis.sensitivityanalysis.SensitivityAnalysis property) containsSBMLOnly() (tellurium.teconverters.convert_omex.inlineOmexImporter method) convert() (tellurium.teconverters.antimony_sbo.antimonySBOConverter method) convertAndExecuteCombineArchive() (in module tellurium.tellurium), [1] convertCombineArchive() (in module tellurium) (in module tellurium.tellurium), [1] createColormap() (tellurium.analysis.parameterscan.ParameterScan class method) createColorPoints() (tellurium.analysis.parameterscan.ParameterScan method) createCombineArchive() (in module tellurium.tellurium), [1] createSBOTermStringForElt() (tellurium.teconverters.antimony_sbo.antimonySBOConverter method) createTaskTree() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) Creator (class in tellurium.utils.omex) custom_plot() (in module tellurium.tellurium) cycleMarker() (tellurium.plotting.engine.LowerTriFigure method) (tellurium.plotting.engine.TiledFigure method)

D

DataDescriptionParser (class in tellurium.sedml.data) dataDescriptionToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory method) dataGeneratorToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) deprecated() (in module tellurium.utils.misc) disablePlotting() (in module tellurium.tellurium) distributed_parameter_scanning() (in module tellurium.tellurium) distributed_sensitivity_analysis() (in module tellurium.tellurium)

distributed_stochastic_simulation() (in module tellurium.tellurium) draw() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) (tellurium.visualization.sbmldiagram.SBMLDiagram method) DumpJSONInfo() (in module tellurium.tellurium), [1] dv() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method)

E

elideSBOTerms() (tellurium.teconverters.antimony_sbo.antimonySBOParser method) Entry (class in tellurium.utils.omex) evaluableMathML() (in module tellurium.sedml.mathml) evaluateMathML() (in module tellurium.sedml.mathml) executeCombineArchive() (in module tellurium.sedml.tesedml) executeInlineOmex() (in module tellurium) (in module tellurium.tellurium), [1] executeInlineOmexFromFile() (in module tellurium.tellurium), [1] executeOmex() (tellurium.teconverters.convert_omex.Omex method) (tellurium.teconverters.inline_omex.inlineOmex method) executePython() (tellurium.sedml.tesedml.SEDMLCodeFactory method) executeSEDML() (in module tellurium.sedml.tesedml) exportInlineOmex() (in module tellurium) (in module tellurium.tellurium), [1]

exportToAntimony() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) exportToCellML() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) exportToCombine() (tellurium.teconverters.convert_omex.Omex method) (tellurium.teconverters.inline_omex.inlineOmex method) exportToMatlab() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) exportToSBML() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) ExtendedRoadRunner (class in tellurium.roadrunner.extended_roadrunner) (class in tellurium.tellurium), [1], [2], [3], [4] extractCombineArchive() (in module tellurium.utils.omex) extractFileFromCombineArchive() (in module tellurium) (in module tellurium.tellurium), [1]

F

figureFromTimecourse() (tellurium.plotting.engine.PlottingEngine method) figureFromXY() (tellurium.plotting.engine.PlottingEngine method) filename (tellurium.analysis.sensitivityanalysis.SensitivityAnalysis property) filterIfEmpty() (in module tellurium.teconverters.antimony_sbo) filterWithSelections() (in module tellurium.plotting.engine) fix_endpoints() (in module tellurium.sedml.tesedml) fixExt() (tellurium.teconverters.convert_omex.inlineOmexImporter method) fixModelRefs() (tellurium.teconverters.convert_phrasedml.phrasedmlImporter method) fixSep() (tellurium.teconverters.convert_omex.inlineOmexImporter method) fjac() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) FORMAT_CSV (tellurium.sedml.data.DataDescriptionParser attribute)

FORMAT_NUML (tellurium.sedml.data.DataDescriptionParser attribute) FORMAT_TSV (tellurium.sedml.data.DataDescriptionParser attribute) FORMAT_URN (tellurium.sedml.data.DataDescriptionParser attribute) formatPhrasedmlResource() (tellurium.teconverters.convert_omex.inlineOmexImporter method) formatResource() (tellurium.teconverters.convert_phrasedml.phrasedmlImporter method) from_time (tellurium.analysis.stochasticmodel.StochasticSimulationModel property) fromContent() (tellurium.teconverters.convert_phrasedml.phrasedmlImporter class method) fromFile() (tellurium.teconverters.convert_omex.inlineOmexImporter class method) fromSBMLFile() (tellurium.teconverters.antimony_sbo.antimonySBOConverter class method) fromSBMLString() (tellurium.teconverters.antimony_sbo.antimonySBOConverter class method) fromString() (tellurium.teconverters.inline_omex.inlineOmex class method) fs() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method)

G

get_computed_values() (tellurium.analysis.simulator.Simulator method) getAllSBOTerms() (tellurium.teconverters.antimony_sbo.antimonySBOConverter method) getAntimony() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getAppDir() (in module tellurium.tellurium) getArgsForDataset() (tellurium.plotting.engine_plotly.PlotlyFigure method) getBoundarySpeciesAmounts() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) getBoundarySpeciesConcentrationIds() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) getBoundarySpeciesConcentrations() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getBoundarySpeciesIds() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getCellML() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getCompartmentIds() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getCompartmentSBOTerms() (tellurium.teconverters.antimony_sbo.antimonySBOConverter method) getCompartmentVolumes() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getConservedMoietyValues() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getContent() (tellurium.teconverters.convert_omex.OmexAsset method) getCurrentAntimony() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getCurrentCellML() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getCurrentMatlab() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getDataGeneratorsForTask() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) getDatasets() (tellurium.plotting.engine.PlottingFigure method) getDefaultPlottingEngine() (in module tellurium.tellurium), [1] getEigenvalues() (in module tellurium) (in module tellurium.tellurium), [1] getEngines() (in module tellurium.plotting.factory) getEntries() (tellurium.teconverters.convert_omex.inlineOmexImporter method) getFileName() (tellurium.teconverters.convert_omex.OmexAsset method) getFloatingSpeciesAmounts() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) getFloatingSpeciesConcentrationIds() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) getFloatingSpeciesConcentrations() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getFloatingSpeciesIds() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getFormula() (tellurium.utils.misc.Accumulator method) getFunctionSBORegex() (in module tellurium.teconverters.antimony_regex) getFunctionStartRegex() (in module tellurium.teconverters.antimony_regex) getGlobalParameterIds() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getGlobalParameterValues() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getIntegratorNameForKisaoID() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) getKineticLaws() (tellurium.utils.misc.ODEExtractor method) getKisaoStringFromVal() (in module tellurium.sedml.tesedml) getKisaoValFromString() (in module tellurium.sedml.tesedml) getLastReport() (in module tellurium.tellurium), [1] getLocation() (tellurium.teconverters.convert_omex.OmexAsset method) getLocationsByFormat() (in module tellurium.utils.omex) getMaster() (tellurium.teconverters.convert_omex.OmexAsset method) getMatlab() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method)

getMergedTaggedDatasets() (tellurium.plotting.engine.PlottingFigure method) getModelEndRegex() (in module tellurium.teconverters.antimony_regex) getModelsFrom() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) getModelStartRegex() (in module tellurium.teconverters.antimony_regex) getModuleName() (tellurium.teconverters.convert_omex.SbmlAsset method) getNumBoundarySpecies() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getNumCompartments() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getNumConservedMoieties() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getNumEvents() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) getNumFloatingSpecies() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getNumGlobalParameters() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getNumRateRules() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) getNumReactions() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getODEsFromModel() (in module tellurium) (in module tellurium.utils.misc) getODEsFromSBMLFile() (in module tellurium) (in module tellurium.utils.misc) getODEsFromSBMLString() (in module tellurium) (in module tellurium.utils.misc) getOrderedSubtasks() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) getParameterSBOTerms() (tellurium.teconverters.antimony_sbo.antimonySBOConverter method) getPlottingEngine() (in module tellurium.tellurium) getPlottingEngineFactory() (in module tellurium.plotting.factory) (in module tellurium.tellurium) getRateOfChange() (tellurium.utils.misc.ODEExtractor method) getRatesOfChange() (tellurium.tellurium.ExtendedRoadRunner method) (tellurium.utils.misc.ODEExtractor method) getReactionIds() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getReactionRates() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getReactionSBOTerms() (tellurium.teconverters.antimony_sbo.antimonySBOConverter method) getRules() (tellurium.utils.misc.ODEExtractor method) getSbmlAssets() (tellurium.teconverters.convert_omex.Omex method) getSBMLFromBiomodelsURN() (in module tellurium.temiriam) getSBORegex() (in module tellurium.teconverters.antimony_regex) getSBOTermForElt() (tellurium.teconverters.antimony_sbo.antimonySBOConverter method) getScatterGOs() (tellurium.plotting.engine_plotly.PlotlyFigure method) getSedmlAssets() (tellurium.teconverters.convert_omex.Omex method) getSeed() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) getSpeciesSBOTerms() (tellurium.teconverters.antimony_sbo.antimonySBOConverter method) getSupportedTestCases() (in module tellurium.testcases) getTelluriumVersion() (in module tellurium) (in module tellurium.tellurium), [1] getTestModel() (in module tellurium) (in module tellurium.tellurium), [1] getVersionInfo() (in module tellurium) (in module tellurium.tellurium), [1] gillespie() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method)

H

hasSBOTerm() (tellurium.teconverters.antimony_sbo.antimonySBOConverter method)

I

info() (tellurium.sedml.tesedml.SEDMLCodeFactory.TaskNode method) inIPython() (in module tellurium.tellurium), [1] inlineOmex (class in tellurium.teconverters.inline_omex) inlineOmexImporter (class in tellurium.teconverters.convert_omex) INPUT_TYPE_FILE_COMBINE (tellurium.sedml.tesedml.SEDMLTools attribute) INPUT_TYPE_FILE_SEDML (tellurium.sedml.tesedml.SEDMLTools attribute) INPUT_TYPE_STR (tellurium.sedml.tesedml.SEDMLTools attribute) integrator (tellurium.analysis.stochasticmodel.StochasticSimulationModel property)

is_leaf() (tellurium.sedml.tesedml.SEDMLCodeFactory.TaskNode method) isEmpty() (tellurium.sedml.tesedml.SEDMLCodeFactory.Stack method) isExhausted() (tellurium.plotting.engine.TiledFigure method) isInRootDir() (tellurium.teconverters.convert_omex.inlineOmexImporter method) (tellurium.teconverters.convert_phrasedml.phrasedmlImporter method) isSBMLEntry() (tellurium.teconverters.convert_omex.OmexFormatDetector method) isSEDMLEntry() (tellurium.teconverters.convert_omex.OmexFormatDetector method) isSupportedAlgorithmForSimulationType() (tellurium.sedml.tesedml.SEDMLCodeFactory static method)

L

LatexExport (class in tellurium.teio.latex) listContents() (in module tellurium.utils.omex) listFiles() (in module tellurium.utils.misc) listTestModels() (in module tellurium) (in module tellurium.tellurium), [1] loada() (in module tellurium) (in module tellurium.tellurium), [1] loadAntimonyModel() (in module tellurium) (in module tellurium.tellurium), [1]

loadCellMLModel() (in module tellurium) (in module tellurium.tellurium), [1] loads() (in module tellurium.tellurium), [1] loadSBMLModel() (in module tellurium) (in module tellurium.tellurium), [1] loadTestModel() (in module tellurium) (in module tellurium.tellurium), [1] localParamsInModelChanges() (tellurium.sedml.tesedml.SEDMLCodeFactory method) LowerTriFigure (class in tellurium.plotting.engine)

M

makeFooter() (tellurium.teconverters.convert_omex.inlineOmexImporter method) makeHeader() (tellurium.teconverters.convert_omex.inlineOmexImporter method) makeLayout() (tellurium.plotting.engine_plotly.PlotlyFigure method) makeSBMLResourceMap() (tellurium.teconverters.convert_omex.inlineOmexImporter method) makeTitles() (tellurium.plotting.engine_null.PlotlyLowerTriFigure method) (tellurium.plotting.engine_plotly.PlotlyLowerTriFigure method) MatplotlibEngine (class in tellurium.plotting.engine_mpl) MatplotlibFigure (class in tellurium.plotting.engine_mpl) model (tellurium.analysis.sensitivityanalysis.SensitivityAnalysis property) (tellurium.analysis.stochasticmodel.StochasticSimulationModel property) model() (in module tellurium.tellurium), [1] modelChangeToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) modelToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory method) module tellurium tellurium.analysis tellurium.analysis.bifurcation tellurium.analysis.parameterestimation tellurium.analysis.parameterscan tellurium.analysis.sensitivityanalysis tellurium.analysis.simulator tellurium.analysis.stochasticmodel tellurium.analysis.test tellurium.plotting tellurium.plotting.api tellurium.plotting.engine tellurium.plotting.engine_mpl tellurium.plotting.engine_null tellurium.plotting.engine_plotly tellurium.plotting.factory tellurium.roadrunner tellurium.roadrunner.extended_roadrunner tellurium.sedml tellurium.sedml.data tellurium.sedml.mathml tellurium.sedml.templates tellurium.sedml.tesedml tellurium.sedml.utils tellurium.teconverters tellurium.teconverters.antimony_regex tellurium.teconverters.antimony_sbo tellurium.teconverters.convert_antimony tellurium.teconverters.convert_omex tellurium.teconverters.convert_phrasedml tellurium.teconverters.inline_omex tellurium.teio tellurium.teio.latex tellurium.tellurium, [1] tellurium.temiriam tellurium.testcases tellurium.utils tellurium.utils.matrix tellurium.utils.misc tellurium.utils.omex tellurium.visualization tellurium.visualization.sbmldiagram

N

newFigure() (tellurium.plotting.engine.PlottingEngine method) (tellurium.plotting.engine_mpl.MatplotlibEngine class method) (tellurium.plotting.engine_null.NullEngine method) (tellurium.plotting.engine_plotly.PlotlyEngine method) newLowerTriFigure() (in module tellurium.plotting.api) (tellurium.plotting.engine_null.NullEngine method) (tellurium.plotting.engine_plotly.PlotlyEngine method) newStackedFigure() (tellurium.plotting.engine_plotly.PlotlyEngine method) newTiledFigure() (in module tellurium.plotting.api) (tellurium.plotting.engine.PlottingEngine method) (tellurium.plotting.engine_null.NullEngine method) (tellurium.plotting.engine_plotly.PlotlyEngine method) nextFigure() (in module tellurium.plotting.api) (tellurium.plotting.engine.TiledFigure method) (tellurium.plotting.engine_null.PlotlyTiledFigure method) (tellurium.plotting.engine_plotly.PlotlyTiledFigure method)

normalizePath() (tellurium.teconverters.convert_omex.inlineOmexImporter method) noticesOff() (in module tellurium) (in module tellurium.tellurium), [1] noticesOn() (in module tellurium) (in module tellurium.tellurium), [1] NullEngine (class in tellurium.plotting.engine_null) NullFigure (class in tellurium.plotting.engine_null) nullspace() (in module tellurium) (in module tellurium.utils.matrix) numEntries() (tellurium.teconverters.convert_omex.inlineOmexImporter method) numSBMLEntries() (tellurium.teconverters.convert_omex.inlineOmexImporter method)

O

ODEExtractor (class in tellurium.utils.misc) Omex (class in tellurium.teconverters.convert_omex) OmexAsset (class in tellurium.teconverters.convert_omex) OmexFormatDetector (class in tellurium.teconverters.convert_omex)

outputPlot2DToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory method) outputPlot3DToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory method) outputPlotSettings() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) outputReportToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory method) outputToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory method)

P

ParameterEstimation (class in tellurium.analysis.parameterestimation) ParameterScan (class in tellurium.analysis.parameterscan) ParameterScan2D (class in tellurium.analysis.parameterscan) parse() (tellurium.sedml.data.DataDescriptionParser class method) parse_dimension_description() (tellurium.sedml.data.DataDescriptionParser class method) parseMagicArgs() (in module tellurium.teconverters.inline_omex) peek() (tellurium.sedml.tesedml.SEDMLCodeFactory.Stack method) perform_sampling() (in module tellurium.tellurium) phrasedmlImporter (class in tellurium.teconverters.convert_phrasedml) piecewise() (in module tellurium.sedml.mathml) plot() (in module tellurium) (in module tellurium.plotting.api) (tellurium.plotting.engine.PlottingEngine method) (tellurium.plotting.engine.PlottingFigure method) (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) plot2DParameterScan() (tellurium.analysis.parameterscan.ParameterScan2D method) plot_distributed_stochastic() (in module tellurium.tellurium) plot_stochastic_result() (in module tellurium.tellurium) plot_text() (in module tellurium.plotting.api) (tellurium.plotting.engine.PlottingEngine method) plotArray() (in module tellurium) (in module tellurium.tellurium), [1] (tellurium.analysis.parameterscan.ParameterScan method) (tellurium.analysis.parameterscan.SteadyStateScan method) plotArrayFunction() (tellurium.analysis.parameterscan.ParameterScan method) plotBifurcation() (in module tellurium.analysis.bifurcation) plotGraduatedArray() (tellurium.analysis.parameterscan.ParameterScan method) plotGraduatedArrayFunction() (tellurium.analysis.parameterscan.ParameterScan method)

plotImage() (in module tellurium.tellurium) PlotlyEngine (class in tellurium.plotting.engine_plotly) PlotlyFigure (class in tellurium.plotting.engine_plotly) PlotlyLowerTriFigure (class in tellurium.plotting.engine_null) (class in tellurium.plotting.engine_plotly) PlotlyStackedFigure (class in tellurium.plotting.engine_plotly) PlotlyTiledFigure (class in tellurium.plotting.engine_null) (class in tellurium.plotting.engine_plotly) plotMultiArray() (tellurium.analysis.parameterscan.ParameterScan2D method) plotPolyArray() (tellurium.analysis.parameterscan.ParameterScan method) plotPolyArrayFunction() (tellurium.analysis.parameterscan.ParameterScan method) plotSurface() (tellurium.analysis.parameterscan.ParameterScan method) plotTimecourse() (tellurium.plotting.engine.PlottingEngine method) PlottingEngine (class in tellurium.plotting.engine) PlottingEngineFactory (class in tellurium.plotting.factory) PlottingFigure (class in tellurium.plotting.engine) PlottingLayout (class in tellurium.plotting.engine) plotWithLegend() (in module tellurium.tellurium), [1] pop() (tellurium.sedml.tesedml.SEDMLCodeFactory.Stack method) pre_simulation() (tellurium.analysis.simulator.Simulator method) printContents() (in module tellurium.utils.omex) printVersionInfo() (in module tellurium) (in module tellurium.tellurium), [1] process_trace() (in module tellurium.sedml.tesedml) product() (in module tellurium.sedml.mathml) ps() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) push() (tellurium.analysis.simulator.Simulator method) (tellurium.sedml.tesedml.SEDMLCodeFactory.Stack method)

R

rank() (in module tellurium) (in module tellurium.utils.matrix) read_numl_document() (tellurium.sedml.data.DataDescriptionParser class method) readCreator() (in module tellurium.teconverters.convert_omex) readFromFile() (in module tellurium) (in module tellurium.utils.misc) readSEDMLDocument() (tellurium.sedml.tesedml.SEDMLTools class method) removeFileExt() (tellurium.teconverters.convert_phrasedml.phrasedmlImporter method) renameNPFuncs() (in module tellurium.sedml.mathml) render() (tellurium.plotting.engine.PlottingFigure method) (tellurium.plotting.engine_mpl.MatplotlibFigure method) (tellurium.plotting.engine_null.NullFigure method) (tellurium.plotting.engine_plotly.PlotlyFigure method) (tellurium.plotting.engine_plotly.PlotlyStackedFigure method) renderIfExhausted() (tellurium.plotting.engine_null.PlotlyLowerTriFigure method) (tellurium.plotting.engine_null.PlotlyTiledFigure method) (tellurium.plotting.engine_plotly.PlotlyLowerTriFigure method) (tellurium.plotting.engine_plotly.PlotlyTiledFigure method)

repeatedTaskToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) resolveModelChanges() (tellurium.sedml.tesedml.SEDMLTools static method) RoadRunner() (in module tellurium.tellurium) root() (in module tellurium.sedml.mathml) rref() (in module tellurium) (in module tellurium.utils.matrix) rs() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) run() (tellurium.analysis.parameterestimation.ParameterEstimation method) run_case() (in module tellurium.sedml.utils) runTool() (in module tellurium) (in module tellurium.utils.misc) rv() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method)

S

sample_plot() (in module tellurium.tellurium) save() (tellurium.plotting.engine.PlottingFigure method) (tellurium.plotting.engine_mpl.MatplotlibFigure method) (tellurium.plotting.engine_null.NullFigure method) (tellurium.plotting.engine_plotly.PlotlyFigure method) saveInlineOMEX() (in module tellurium.teconverters.inline_omex) saveToFile() (in module tellurium) (in module tellurium.utils.misc) (tellurium.teio.latex.LatexExport method) saveToOneFile() (tellurium.teio.latex.LatexExport method) sbml (tellurium.analysis.sensitivityanalysis.SensitivityAnalysis property) SbmlAsset (class in tellurium.teconverters.convert_omex) SBMLDiagram (class in tellurium.visualization.sbmldiagram) sbmlFileToAntimony() (tellurium.teconverters.convert_antimony.antimonyConverter method) sbmlToAntimony() (in module tellurium) (in module tellurium.tellurium), [1] (tellurium.teconverters.convert_antimony.antimonyConverter method) sbmlToCellML() (in module tellurium) (in module tellurium.tellurium), [1] SBOError SedmlAsset (class in tellurium.teconverters.convert_omex) SEDMLCodeFactory (class in tellurium.sedml.tesedml) SEDMLCodeFactory.Stack (class in tellurium.sedml.tesedml) SEDMLCodeFactory.TaskNode (class in tellurium.sedml.tesedml) sedmlString() (tellurium.sedml.tesedml.SEDMLCodeFactory method) SEDMLTools (class in tellurium.sedml.tesedml) sedmlToPython() (in module tellurium.sedml.tesedml) seed (tellurium.analysis.stochasticmodel.StochasticSimulationModel property) (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner property) selectionFromVariable() (tellurium.sedml.tesedml.SEDMLCodeFactory static method)

selectionsForTask() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) SensitivityAnalysis (class in tellurium.analysis.sensitivityanalysis) setDataFromFile() (tellurium.analysis.parameterestimation.ParameterEstimation method) setDefaultPlottingEngine() (in module tellurium.tellurium), [1] setLastReport() (in module tellurium.tellurium), [1] setSavePlotsToPDF() (in module tellurium.tellurium), [1] setSeed() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) setXLim() (tellurium.plotting.engine.PlottingFigure method) setYLim() (tellurium.plotting.engine.PlottingFigure method) show() (in module tellurium.plotting.api) (tellurium.plotting.engine.PlottingEngine method) (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) simpleTaskMainSim() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) simpleTaskParentInit() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) simpleTaskSetup() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) simpleTaskToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) simulate_sensitivity() (tellurium.analysis.simulator.Simulator method) simulation (tellurium.analysis.sensitivityanalysis.SensitivityAnalysis property) Simulator (class in tellurium.analysis.simulator) size() (tellurium.sedml.tesedml.SEDMLCodeFactory.Stack method) sm() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method) sqr() (in module tellurium.sedml.mathml) SteadyStateScan (class in tellurium.analysis.parameterscan) steadyStateSim() (tellurium.analysis.parameterscan.SteadyStateScan method) step_points (tellurium.analysis.stochasticmodel.StochasticSimulationModel property) StochasticSimulationModel (class in tellurium.analysis.stochasticmodel) SUPPORTED_FORMATS (tellurium.sedml.data.DataDescriptionParser attribute) sv() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method)

T

targetToExpr() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) targetToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) taskToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) taskTreeToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory static method) tellurium module tellurium.analysis module tellurium.analysis.bifurcation module tellurium.analysis.parameterestimation module tellurium.analysis.parameterscan module tellurium.analysis.sensitivityanalysis module tellurium.analysis.simulator module tellurium.analysis.stochasticmodel module tellurium.analysis.test module tellurium.plotting module tellurium.plotting.api module tellurium.plotting.engine module tellurium.plotting.engine_mpl module tellurium.plotting.engine_null module tellurium.plotting.engine_plotly module tellurium.plotting.factory module tellurium.roadrunner module tellurium.roadrunner.extended_roadrunner module tellurium.sedml module tellurium.sedml.data module tellurium.sedml.mathml module tellurium.sedml.templates module tellurium.sedml.tesedml module

tellurium.sedml.utils module tellurium.teconverters module tellurium.teconverters.antimony_regex module tellurium.teconverters.antimony_sbo module tellurium.teconverters.convert_antimony module tellurium.teconverters.convert_omex module tellurium.teconverters.convert_phrasedml module tellurium.teconverters.inline_omex module tellurium.teio module tellurium.teio.latex module tellurium.tellurium module, [1] tellurium.temiriam module tellurium.testcases module tellurium.utils module tellurium.utils.matrix module tellurium.utils.misc module tellurium.utils.omex module tellurium.visualization module tellurium.visualization.sbmldiagram module TEMPLATE_DIR (tellurium.sedml.tesedml.SEDMLCodeFactory attribute) terminate_trace() (in module tellurium.sedml.tesedml) TiledFigure (class in tellurium.plotting.engine) tiledFigure() (in module tellurium.plotting.api) to_time (tellurium.analysis.stochasticmodel.StochasticSimulationModel property) toInlineOmex() (tellurium.teconverters.convert_omex.inlineOmexImporter method) toPhrasedml() (tellurium.teconverters.convert_phrasedml.phrasedmlImporter method) toPython() (tellurium.sedml.tesedml.SEDMLCodeFactory method) toString() (tellurium.utils.misc.Accumulator method) (tellurium.utils.misc.ODEExtractor method) tryAddSBOTerms() (tellurium.teconverters.convert_antimony.antimonyConverter method)

U

uniformRangeToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory static method)

V

variable_step_size (tellurium.analysis.stochasticmodel.StochasticSimulationModel property) vectorRangeToPython() (tellurium.sedml.tesedml.SEDMLCodeFactory static method)

VersionDict() (in module tellurium.tellurium), [1] vs() (tellurium.roadrunner.extended_roadrunner.ExtendedRoadRunner method) (tellurium.tellurium.ExtendedRoadRunner method)

W

writeFiles() (tellurium.teconverters.convert_omex.Omex method)

X

xor() (in module tellurium.sedml.mathml)