Index

A

add_delay() (stochpy.implementations.DelayedDirectMethod.DelayedDirectMethod method) (stochpy.implementations.DelayedNRM.DelayedNRM method) addFormula() (stochpy.modules.PyscesMiniModel.Function method) ages (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) AnalyzeExtantCells() (stochpy.modules.StochPyCellDivision.CellDivision method) argsl (stochpy.modules.PyscesMiniModel.Function attribute) assignments (stochpy.modules.PyscesMiniModel.Event attribute)

Autocorrelation() (in module stochpy.modules.Analysis) Autocorrelations() (stochpy.modules.Analysis.DoPlotting method) AutoCov() (in module stochpy.modules.Analysis) AverageDistributions() (stochpy.modules.Analysis.DoPlotting method) AverageDistributionsCI() (stochpy.modules.Analysis.DoPlotting method) AverageTimeSeries() (stochpy.modules.Analysis.DoPlotting method)

B

Binning() (in module stochpy.modules.Analysis) BuildDependencyGraph() (stochpy.modules.PyscesMiniModel.PySCeS_Connector method) BuildInits() (stochpy.implementations.DelayedNRM.DelayedNRM method) BuildN() (stochpy.modules.PyscesMiniModel.PySCeS_Connector method) BuildN_react_prod() (stochpy.modules.PyscesMiniModel.PySCeS_Connector method) BuildPropensityCodes() (stochpy.modules.PyscesMiniModel.PySCeS_Connector method)

BuildReactionAffects() (stochpy.modules.PyscesMiniModel.PySCeS_Connector method) BuildReactions() (stochpy.modules.PyscesMiniModel.PySCeS_Connector method) BuildSpeciesDependsOn() (stochpy.modules.PyscesMiniModel.PySCeS_Connector method) BuildTaus() (stochpy.implementations.DelayedNRM.DelayedNRM method) BuildX() (stochpy.modules.PyscesMiniModel.PySCeS_Connector method)

C

CalculateSpecificGrowthRate() (stochpy.modules.StochPyCellDivision.CellDivision method) CellDivision (class in stochpy.modules.StochPyCellDivision) ChangeInitialSpeciesAmount() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) ChangeParameter() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) CheckReactantExhaustion() (stochpy.implementations.DelayedDirectMethod.DelayedDirectMethod method) (stochpy.implementations.DelayedNRM.DelayedNRM method)

code_string (stochpy.modules.PyscesMiniModel.Event attribute) (stochpy.modules.PyscesMiniModel.EventAssignment attribute) (stochpy.modules.PyscesMiniModel.Function attribute) CompleteReaction() (stochpy.implementations.DelayedDirectMethod.DelayedDirectMethod method) (stochpy.implementations.DelayedNRM.DelayedNRM method) Count() (in module stochpy.modules.Analysis) CrossCov() (in module stochpy.modules.Analysis)

D

delay (stochpy.modules.PyscesMiniModel.Event attribute) DelayedDirectMethod (class in stochpy.implementations.DelayedDirectMethod) DelayedNRM (class in stochpy.implementations.DelayedNRM) DeleteTempfiles() (stochpy.modules.StochSim.SSA method) Demo (class in stochpy.modules.StochPyDemo) Demo1() (stochpy.modules.StochPyDemo.Demo method) Demo10() (stochpy.modules.StochPyDemo.Demo method) Demo11() (stochpy.modules.StochPyDemo.Demo method) Demo2() (stochpy.modules.StochPyDemo.Demo method) Demo3() (stochpy.modules.StochPyDemo.Demo method) Demo4() (stochpy.modules.StochPyDemo.Demo method) Demo5() (stochpy.modules.StochPyDemo.Demo method) Demo6() (stochpy.modules.StochPyDemo.Demo method) Demo7() (stochpy.modules.StochPyDemo.Demo method) Demo8() (stochpy.modules.StochPyDemo.Demo method) Demo9() (stochpy.modules.StochPyDemo.Demo method) DetermineMethod() (stochpy.implementations.TauLeaping.OTL method) DirectMethod (class in stochpy.implementations.DirectMethod) Distributions() (stochpy.modules.Analysis.DoPlotting method)

division_times (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) DoCainStochSim() (stochpy.modules.StochSim.SSA method) DoCellDivisionStochSim() (stochpy.modules.StochPyCellDivision.CellDivision method) DoCompleteStochSim() (stochpy.modules.StochSim.SSA method) DoDelayedStochSim() (stochpy.modules.StochSim.SSA method) DoDemoSimulations() (stochpy.modules.StochPyDemo.Demo method) DoExample1() (stochpy.modules.StochPyUtils.Utils method) DoExample2() (stochpy.modules.StochPyUtils.Utils method) DoExample3() (stochpy.modules.StochPyUtils.Utils method) DoExample4() (stochpy.modules.StochPyUtils.Utils method) DoExample5() (stochpy.modules.StochPyUtils.Utils method) DoPlotting (class in stochpy.modules.Analysis) doSequentialSim() (in module stochpy.modules.StochPyUtils) DoSingleMoleculeStochSim() (stochpy.modules.StochSim.SSA method) DoStochKitStochSim() (stochpy.modules.StochSim.SSA method) DoStochSim() (stochpy.modules.StochSim.SSA method) DoTestsuite() (stochpy.modules.StochSim.SSA method) DumpTrajectoryData() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method)

E

Endtime() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) evaluateAssignment() (stochpy.modules.PyscesMiniModel.EventAssignment method) Event (class in stochpy.modules.PyscesMiniModel) EventAssignment (class in stochpy.modules.PyscesMiniModel)

Execute() (stochpy.implementations.DelayedDirectMethod.DelayedDirectMethod method) (stochpy.implementations.DelayedNRM.DelayedNRM method) (stochpy.implementations.DirectMethod.DirectMethod method) (stochpy.implementations.FirstReactionMethod.FirstReactionMethod method) (stochpy.implementations.NextReactionMethod.NextReactionMethod method) (stochpy.implementations.TauLeaping.OTL method) Execute_K_Reactions() (stochpy.implementations.TauLeaping.OTL method) Export2File() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) ExportExtant2File() (stochpy.modules.StochPyCellDivision.CellDivision method)

F

FFTconvolve() (in module stochpy.modules.Analysis) FillDataStochsim() (stochpy.modules.StochSim.SSA method) FillDataStochSimCellDivision() (stochpy.modules.StochPyCellDivision.CellDivision method) FirstReactionMethod (class in stochpy.implementations.FirstReactionMethod)

formula (stochpy.modules.PyscesMiniModel.Event attribute) (stochpy.modules.PyscesMiniModel.EventAssignment attribute) (stochpy.modules.PyscesMiniModel.Function attribute) Function (class in stochpy.modules.PyscesMiniModel) functions (stochpy.modules.PyscesMiniModel.Function attribute)

G

GenerateTau() (stochpy.implementations.DelayedDirectMethod.DelayedDirectMethod method) generation_timesteps (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) Generations() (stochpy.modules.StochPyCellDivision.CellDivision method) get() (stochpy.modules.PyscesMiniModel.NewCoreBase method) GetA0c() (stochpy.implementations.TauLeaping.OTL method) getAllSimData() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) GetAnalyticalPDF() (in module stochpy.modules.StochPyUtils) GetAnalyticalWaitingtimes() (in module stochpy.modules.StochPyUtils) GetAveragePropensitiesDistributions() (stochpy.modules.StochSim.SSA method) GetAverageResults() (in module stochpy.modules.Analysis) GetAverageSpeciesDistributions() (stochpy.modules.StochSim.SSA method) GetAverageSpeciesExtantDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) GetCriticalReactions() (stochpy.implementations.TauLeaping.OTL method) getDataAtTime() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) GetDataDistributions() (in module stochpy.modules.Analysis) getDataForTimeSimPlot() (in module stochpy.modules.Analysis) getDataInTimeInterval() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) getDaughterDataAtDivisionTime() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) GetG() (stochpy.implementations.TauLeaping.OTL method) GetK() (stochpy.implementations.TauLeaping.OTL method) getMotherDataAtDivisionTime() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) GetMuVar() (stochpy.implementations.TauLeaping.OTL method) getName() (stochpy.modules.PyscesMiniModel.NewCoreBase method) getPropensities() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) GetPropensitiesAutocorrelations() (stochpy.modules.StochSim.SSA method)

GetPropensitiesAutocovariances() (stochpy.modules.StochSim.SSA method) GetReactionOrders() (stochpy.modules.PyscesMiniModel.PySCeS_Connector method) GetRegularGrid() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) GetSample() (in module stochpy.implementations.TauLeaping) getSimData() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) getSpecies() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) GetSpeciesAutocorrelations() (stochpy.modules.StochSim.SSA method) GetSpeciesAutocovariances() (stochpy.modules.StochSim.SSA method) getSpeciesConcentrations() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) getSpeciesDaughter() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) getSpeciesMother() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) GetTauPrime() (stochpy.implementations.TauLeaping.OTL method) GetTauPrimePrime() (stochpy.implementations.TauLeaping.OTL method) GetTauReaction() (stochpy.implementations.DelayedNRM.DelayedNRM method) getTime() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) GetTrajectoryData() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) getValue() (stochpy.modules.PyscesMiniModel.NumberBase method) getVolume() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) getVolumeDaughter() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) getVolumeDeterministic() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) getVolumeMother() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) getWaitingtimes() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) GetWaitingtimes() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) getXData() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method)

H

HAS_AGES (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_AVERAGE_PROPENSITIES_DISTRIBUTIONS (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) HAS_AVERAGE_SPECIES_DISTRIBUTIONS (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) HAS_AVERAGE_SPECIES_EXTANT_DISTRIBUTIONS (stochpy.modules.StochPyCellDivision.RegularGridDataObj attribute) HAS_DETERMINISTIC (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_DT (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_GENERATION_TIMESTEPS (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_IDT (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_PROPENSITIES (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) HAS_PROPENSITIES_AUTOCORRELATIONS (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) HAS_PROPENSITIES_AUTOCOVARIANCES (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) HAS_SPECIES (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute)

HAS_SPECIES_AUTOCORRELATIONS (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) HAS_SPECIES_AUTOCOVARIANCES (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) HAS_SPECIES_CONCENTRATIONS (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) HAS_SPECIES_DAUGHTER (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_SPECIES_MOTHER (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_TIME (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_VOLUME (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) HAS_VOLUME_DAUGHTER (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_VOLUME_MOTHER (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) HAS_WAITINGTIMES (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) HAS_XDATA (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute)

I

Import2StochPy() (stochpy.modules.StochSim.SSA method) InitialiseEvents() (stochpy.modules.PyscesMiniModel.PyscesInputFileParser method) InitialiseInputFile() (stochpy.modules.PyscesMiniModel.PyscesInputFileParser method) InitialMonteCarloStep() (stochpy.implementations.NextReactionMethod.NextReactionMethod method) InitiateReaction() (stochpy.implementations.DelayedDirectMethod.DelayedDirectMethod method) (stochpy.implementations.DelayedNRM.DelayedNRM method)

IntegrationStochasticCellDivisionObj (class in stochpy.modules.StochPyCellDivision) IntegrationStochasticDataObj (class in stochpy.modules.PyscesMiniModel) interdivision_times (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) IS_VALID (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute)

L

LogBin() (in module stochpy.modules.Analysis)

M

Method() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) MinPositiveValue() (in module stochpy.implementations.TauLeaping) mod (stochpy.modules.PyscesMiniModel.Event attribute) (stochpy.modules.PyscesMiniModel.EventAssignment attribute) (stochpy.modules.PyscesMiniModel.Function attribute) Mode() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method)

Model() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) ModelDir (stochpy.modules.PyscesMiniModel.PyscesInputFileParser attribute) ModelFile (stochpy.modules.PyscesMiniModel.PyscesInputFileParser attribute) ModelOutput (stochpy.modules.PyscesMiniModel.PyscesInputFileParser attribute)

N

N (stochpy.modules.PyscesMiniModel.PyscesInputFileParser attribute) name (stochpy.modules.PyscesMiniModel.NewCoreBase attribute) NewCoreBase (class in stochpy.modules.PyscesMiniModel)

NextReactionMethod (class in stochpy.implementations.NextReactionMethod) NumberBase (class in stochpy.modules.PyscesMiniModel)

O

ObtainWaitingtimes() (in module stochpy.modules.Analysis)

OTL (class in stochpy.implementations.TauLeaping)

P

piecewises (stochpy.modules.PyscesMiniModel.Event attribute) (stochpy.modules.PyscesMiniModel.EventAssignment attribute) (stochpy.modules.PyscesMiniModel.Function attribute) PlotAveragePropensitiesAutocorrelations() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAveragePropensitiesAutocovariances() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAveragePropensitiesDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAveragePropensitiesDistributionsConfidenceIntervals() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAveragePropensitiesTimeSeries() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAverageSpeciesAutocorrelations() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAverageSpeciesAutocovariances() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAverageSpeciesDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAverageSpeciesDistributionsConfidenceIntervals() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAverageSpeciesExtantDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotAverageSpeciesTimeSeries() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotAverageSpeciesVolumeTimeSeries() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotAverageVolumeTimeSeries() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotCellAgeDistribution() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotExtantSpeciesDistribution() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotInterdivisionTimeDistribution() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotPropensitiesAutocorrelations() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotPropensitiesAutocovariances() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotPropensitiesDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotPropensitiesTimeSeries() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotSpeciesAutocorrelations() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotSpeciesAutocovariances() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotSpeciesDaughterDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotSpeciesDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotSpeciesExtantDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotSpeciesMotherDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotSpeciesTimeSeries() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PlotSpeciesVolumeTimeSeries() (stochpy.modules.StochPyCellDivision.CellDivision method)

PlotVolumeDaughterDistribution() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotVolumeMotherDistribution() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotVolumeTimeSeries() (stochpy.modules.StochPyCellDivision.CellDivision method) PlotWaitingtimesDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PrintAveragePropensitiesTimeSeries() (stochpy.modules.StochSim.SSA method) PrintAverageSpeciesTimeSeries() (stochpy.modules.StochSim.SSA method) PrintPropensitiesDistributions() (stochpy.modules.StochSim.SSA method) PrintPropensitiesMeans() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PrintPropensitiesStandardDeviations() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PrintPropensitiesTimeSeries() (stochpy.modules.StochSim.SSA method) PrintSpeciesDistributions() (stochpy.modules.StochSim.SSA method) PrintSpeciesExtantDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) PrintSpeciesExtantMeans() (stochpy.modules.StochPyCellDivision.CellDivision method) PrintSpeciesExtantStandardDeviations() (stochpy.modules.StochPyCellDivision.CellDivision method) PrintSpeciesMeans() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PrintSpeciesStandardDeviations() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) PrintSpeciesTimeSeries() (stochpy.modules.StochSim.SSA method) PrintWaitingtimesDistributions() (stochpy.modules.StochSim.SSA method) PrintWaitingtimesMeans() (stochpy.modules.StochSim.SSA method) PrintWaitingtimesStandardDeviations() (stochpy.modules.StochSim.SSA method) propensities (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) Propensities() (stochpy.implementations.DelayedNRM.DelayedNRM method) (stochpy.implementations.NextReactionMethod.NextReactionMethod method) propensities_distributions (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) propensities_labels (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) propensities_means (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) propensities_standard_deviations (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) PySCeS_Connector (class in stochpy.modules.PyscesMiniModel) PyscesInputFileParser (class in stochpy.modules.PyscesMiniModel)

R

RegularGridDataObj (class in stochpy.modules.PyscesMiniModel) (class in stochpy.modules.StochPyCellDivision) Reload() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) RemoveBias() (in module stochpy.modules.Analysis)

reset() (stochpy.modules.PyscesMiniModel.Event method) ResetPlotnum() (stochpy.modules.Analysis.DoPlotting method) RunExactTimestep() (stochpy.implementations.DelayedDirectMethod.DelayedDirectMethod method) (stochpy.implementations.DelayedNRM.DelayedNRM method) (stochpy.implementations.DirectMethod.DirectMethod method) (stochpy.implementations.FirstReactionMethod.FirstReactionMethod method) (stochpy.implementations.NextReactionMethod.NextReactionMethod method) (stochpy.implementations.TauLeaping.OTL method)

S

SBML2PSC (class in stochpy.modules.SBML2PSC) setAges() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setArg() (stochpy.modules.PyscesMiniModel.Function method) setAssignment() (stochpy.modules.PyscesMiniModel.Event method) SetDefaultParameters() (stochpy.modules.StochPyCellDivision.CellDivision method) SetDelayParameters() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) setDeterministicData() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) SetExactDividingSpecies() (stochpy.modules.StochPyCellDivision.CellDivision method) setFiredReactions() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) setFormula() (stochpy.modules.PyscesMiniModel.EventAssignment method) setGenerationTimesteps() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) SetGrowthFunction() (stochpy.modules.StochPyCellDivision.CellDivision method) SetInitialVolume() (stochpy.modules.StochPyCellDivision.CellDivision method) setInterdivisionTimes() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setLabels() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setName() (stochpy.modules.PyscesMiniModel.NewCoreBase method) SetNonDividingSpecies() (stochpy.modules.StochPyCellDivision.CellDivision method) setPropensities() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) setPropensitiesAutocorrelations() (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) setPropensitiesAutocovariances() (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) setPropensitiesDist() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) setPropensitiesDistributionAverage() (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) setPropensitiesLabels() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) SetPutativeReactionTimes() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) SetSeeding() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) setSimulationInfo() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setSpecies() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) setSpeciesAutocorrelations() (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) setSpeciesAutocovariances() (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) setSpeciesConcentrations() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) setSpeciesDaughter() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setSpeciesDaughterDist() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setSpeciesDist() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) setSpeciesDistributionAverage() (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) setSpeciesExtantDistributionAverage() (stochpy.modules.StochPyCellDivision.RegularGridDataObj method) setSpeciesExtantDistributions() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setSpeciesMother() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setSpeciesMotherDist() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setTime() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.PyscesMiniModel.RegularGridDataObj method) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setTrigger() (stochpy.modules.PyscesMiniModel.Event method) setValue() (stochpy.modules.PyscesMiniModel.NumberBase method) setVariable() (stochpy.modules.PyscesMiniModel.EventAssignment method) setVolume() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.PyscesMiniModel.RegularGridDataObj method)

setVolumeDaughter() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setVolumeDaughterDist() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) SetVolumeDependencies() (stochpy.modules.StochPyCellDivision.CellDivision method) SetVolumeDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) setVolumeMother() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setVolumeMotherDist() (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) setWaitingtimes() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) setWaitingtimesMeans() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) setWaitingtimesStandardDeviations() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) setXData() (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj method) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj method) ShowOverview() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) ShowSpecies() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) species (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) species_autocorrelations (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) species_autocorrelations_means (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) species_autocorrelations_standard_deviations (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) species_daughter (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) species_distributions (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) species_extant_distributions (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) species_labels (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) species_means (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) species_mother (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) species_standard_deviations (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) SSA (class in stochpy.modules.StochSim) SSASettings (class in stochpy.modules.StochSim) state (stochpy.modules.PyscesMiniModel.Event attribute) state0 (stochpy.modules.PyscesMiniModel.Event attribute) stochpy.implementations.DelayedDirectMethod (module) stochpy.implementations.DelayedNRM (module) stochpy.implementations.DirectMethod (module) stochpy.implementations.FirstReactionMethod (module) stochpy.implementations.NextReactionMethod (module) stochpy.implementations.TauLeaping (module) stochpy.modules.Analysis (module) stochpy.modules.PyscesMiniModel (module) stochpy.modules.PyscesParse (module) stochpy.modules.SBML2PSC (module) stochpy.modules.StochPyCellDivision (module) stochpy.modules.StochPyDemo (module) stochpy.modules.StochPyUtils (module) stochpy.modules.StochSim (module) SumExtantSpeciesDistributions() (stochpy.modules.StochPyCellDivision.CellDivision method) symbols (stochpy.modules.PyscesMiniModel.Event attribute) (stochpy.modules.PyscesMiniModel.EventAssignment attribute) (stochpy.modules.PyscesMiniModel.Function attribute)

T

time (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.PyscesMiniModel.RegularGridDataObj attribute) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) time_label (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) TimeSeries() (stochpy.modules.Analysis.DoPlotting method) Timesteps() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method)

Trajectories() (stochpy.modules.StochPyCellDivision.CellDivision method) (stochpy.modules.StochSim.SSA method) trigger (stochpy.modules.PyscesMiniModel.Event attribute) TYPE_INFO (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute)

U

UpdateHeap() (stochpy.implementations.NextReactionMethod.NextReactionMethod method) UpdateTP() (stochpy.implementations.DelayedNRM.DelayedNRM method)

Utils (class in stochpy.modules.StochPyUtils)

V

value (stochpy.modules.PyscesMiniModel.Function attribute) (stochpy.modules.PyscesMiniModel.NumberBase attribute) value_initial (stochpy.modules.PyscesMiniModel.NumberBase attribute) variable (stochpy.modules.PyscesMiniModel.EventAssignment attribute)

volume_daughter (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute) volume_mother (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute)

W

waiting_times (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) waiting_times_labels (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute)

WaitingtimesDistributions() (stochpy.modules.Analysis.DoPlotting method)

X

xcode (stochpy.modules.PyscesMiniModel.Event attribute) (stochpy.modules.PyscesMiniModel.EventAssignment attribute) (stochpy.modules.PyscesMiniModel.Function attribute) xdata (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute)

xdata_labels (stochpy.modules.PyscesMiniModel.IntegrationStochasticDataObj attribute) (stochpy.modules.StochPyCellDivision.IntegrationStochasticCellDivisionObj attribute)