Index

• ModelManager.mm_globals_ref
• ModelManager.ABCResult
• ModelManager.ABCSMC
• ModelManager.AbstractCalibrationMethod
• ModelManager.AbstractMonad
• ModelManager.AbstractSampling
• ModelManager.AbstractSimulator
• ModelManager.AbstractTrial
• ModelManager.AbstractVariation
• ModelManager.AddGridVariationsResult
• ModelManager.AddLHSVariationsResult
• ModelManager.AddRBDVariationsResult
• ModelManager.AddSobolVariationsResult
• ModelManager.AddVariationMethod
• ModelManager.AddVariationsResult
• ModelManager.Calibration
• ModelManager.CalibrationParameter
• ModelManager.CalibrationProblem
• ModelManager.CoVariation
• ModelManager.ComponentwiseKernel
• ModelManager.ConvergenceSummary
• ModelManager.DiscreteVariation
• ModelManager.DistributedVariation
• ModelManager.ElementaryVariation
• ModelManager.GSAMethod
• ModelManager.GSASampling
• ModelManager.GaussianKernel
• ModelManager.GenerationResult
• ModelManager.GridVariation
• ModelManager.HPCCompletionOptions
• ModelManager.InputFolder
• ModelManager.InputFolders
• ModelManager.LHSVariation
• ModelManager.LatentVariation
• ModelManager.LocalNNCovKernel
• ModelManager.LocalNNKernel
• ModelManager.MMOutput
• ModelManager.MOAT
• ModelManager.MOATSampling
• ModelManager.ModelManagerGlobals
• ModelManager.Monad
• ModelManager.ProjectLocations
• ModelManager.QoI
• ModelManager.RBD
• ModelManager.RBDSampling
• ModelManager.RBDVariation
• ModelManager.Sampling
• ModelManager.Simulation
• ModelManager.SimulationBank
• ModelManager.SimulationProcess
• ModelManager.SimulationSpec
• ModelManager.SobolMM
• ModelManager.SobolSampling
• ModelManager.SobolVariation
• ModelManager.Sobolʼ
• ModelManager.StudySpec
• ModelManager.Trial
• ModelManager.VariationID
• ModelManager.XMLPath
• PhysiCellModelManager.AverageSubstrateTimeSeries
• PhysiCellModelManager.ExtracellularSubstrateTimeSeries
• PhysiCellModelManager.MonadPopulationTimeSeries
• PhysiCellModelManager.PCMMException
• PhysiCellModelManager.PCMMMissingProject
• PhysiCellModelManager.PCMMPCFResult
• PhysiCellModelManager.PCMMStudioLaunchError
• PhysiCellModelManager.PhysiCellComponent
• PhysiCellModelManager.PhysiCellSimulator
• PhysiCellModelManager.PhysiCellSimulator
• PhysiCellModelManager.PruneOptions
• PhysiCellModelManager.SimulationPopulationTimeSeries
• PhysiCellOutput.PhysiCellSequence
• PhysiCellOutput.PhysiCellSnapshot
• Base.run
• Base.run
• Base.run
• Base.run
• Base.run
• ModelManager.NormalDistributedVariation
• ModelManager.UniformDistributedVariation
• ModelManager.addVariations
• ModelManager.appendTags!
• ModelManager.assertInitialized
• ModelManager.buildWhereClause
• ModelManager.calculateGSA!
• ModelManager.calibrationsSchema
• ModelManager.calibrationsTable
• ModelManager.centralDB
• ModelManager.centralDBFileName
• ModelManager.centralDBFileName
• ModelManager.clearSimulatorArtifacts
• ModelManager.columnName
• ModelManager.columnNameToXMLPath
• ModelManager.constituentIDs
• ModelManager.constructSelectQuery
• ModelManager.continueMilestoneUpgrade
• ModelManager.createMMTable
• ModelManager.createTrial
• ModelManager.createTrial
• ModelManager.createXMLFile
• ModelManager.currentSimulatorVersionID
• ModelManager.currentSimulatorVersionID
• ModelManager.dataDir
• ModelManager.databaseDiagnostics
• ModelManager.dbVersionTableName
• ModelManager.defaultJobOptions
• ModelManager.defaultLatentParameterNames
• ModelManager.deleteAllSimulations
• ModelManager.deleteCalibration
• ModelManager.deleteMonad
• ModelManager.deleteSampling
• ModelManager.deleteSimulation
• ModelManager.deleteSimulations
• ModelManager.deleteSimulationsByStatus
• ModelManager.deleteTrial
• ModelManager.elementIsTerminal
• ModelManager.findMonads
• ModelManager.findSimulationIDs
• ModelManager.findSimulations
• ModelManager.findTrials
• ModelManager.folderIsVaried
• ModelManager.getAllParameterValues
• ModelManager.getChildByAttribute
• ModelManager.getChildByChildContent
• ModelManager.getDBPackageVersion
• ModelManager.getInputFolderDescription
• ModelManager.getInstalledVersion
• ModelManager.getMonadIDDataFrame
• ModelManager.getParameterValue
• ModelManager.getParameterValue
• ModelManager.getSimpleContent
• ModelManager.gitState
• ModelManager.gsaLabels
• ModelManager.hasTag
• ModelManager.initializeDatabase
• ModelManager.initializeInputFolder
• ModelManager.initializeModelManager
• ModelManager.initializeModelManager
• ModelManager.inputsDict
• ModelManager.insertFolder
• ModelManager.isInitialized
• ModelManager.isRunningOnHPC
• ModelManager.locationFolder
• ModelManager.locationIDName
• ModelManager.locationIDNames
• ModelManager.locationPath
• ModelManager.locationPath
• ModelManager.locationPath
• ModelManager.locationTableName
• ModelManager.locationVariationIDName
• ModelManager.locationVariationIDNames
• ModelManager.locationVariationsDBName
• ModelManager.locationVariationsDatabase
• ModelManager.locationVariationsFolder
• ModelManager.locationVariationsTableName
• ModelManager.methodString
• ModelManager.mm_globals
• ModelManager.monadID
• ModelManager.monadIDs
• ModelManager.monadIDs
• ModelManager.monadIDs
• ModelManager.monadsTable
• ModelManager.monadsTableFromQuery
• ModelManager.mseDistance
• ModelManager.orphanedTagCounts
• ModelManager.parseProjectInputsConfigurationFile
• ModelManager.parseValueFromString
• ModelManager.pathToInputsConfig
• ModelManager.pathToOutputFolder
• ModelManager.pathToOutputFolder
• ModelManager.populateTableOnFeatureSubset
• ModelManager.postInitDisplay
• ModelManager.postInitDisplay
• ModelManager.postProcessingDBPath
• ModelManager.postProcessingTable
• ModelManager.postSimulationCleanup
• ModelManager.postSimulationProcessing
• ModelManager.postVariationXMLProcessing
• ModelManager.posterior
• ModelManager.prepareBaseFile
• ModelManager.prepareTrialHierarchy
• ModelManager.prepareVariedInputFolder
• ModelManager.prepareVariedInputFolder
• ModelManager.printCalibrationsTable
• ModelManager.printMonadsTable
• ModelManager.printPostProcessingTable
• ModelManager.printSimulationsTable
• ModelManager.printTagsTable
• ModelManager.projectLocations
• ModelManager.queryToDataFrame
• ModelManager.recognizedStatusCodes
• ModelManager.recommendedTagKeys
• ModelManager.reinitializeDatabase
• ModelManager.resetDatabase
• ModelManager.resetFolder
• ModelManager.resolvePackageVersion
• ModelManager.resolveSimulatorVersionID
• ModelManager.resumeABC
• ModelManager.resumeCalibration
• ModelManager.retrieveElement
• ModelManager.retrieveElementError
• ModelManager.rm_hpc_safe
• ModelManager.runABC
• ModelManager.runCalibration
• ModelManager.runSimulation
• ModelManager.setHPCCompletionOptions
• ModelManager.setJobOptions
• ModelManager.setNumberOfParallelSims
• ModelManager.setSimpleContent
• ModelManager.setTagHints!
• ModelManager.setupMonad
• ModelManager.setupSampling
• ModelManager.shellCommandExists
• ModelManager.shortLocationVariationID
• ModelManager.shortVariationName
• ModelManager.simulationCommand
• ModelManager.simulationID
• ModelManager.simulationIDs
• ModelManager.simulationIDs
• ModelManager.simulationIDs
• ModelManager.simulationsFromIDs
• ModelManager.simulationsTable
• ModelManager.simulationsTableFromQuery
• ModelManager.simulator
• ModelManager.simulatorDir
• ModelManager.simulatorInfo
• ModelManager.simulatorVersionIDName
• ModelManager.simulatorVersionIDName
• ModelManager.simulatorVersionSchema
• ModelManager.simulatorVersionTableName
• ModelManager.sqliteDataType
• ModelManager.stmtToDataFrame
• ModelManager.tableColumns
• ModelManager.tableExists
• ModelManager.tableIDName
• ModelManager.tag!
• ModelManager.tagKeys
• ModelManager.tagValues
• ModelManager.tags
• ModelManager.tagsTable
• ModelManager.trialFolder
• ModelManager.trialID
• ModelManager.trialType
• ModelManager.untag!
• ModelManager.upgradeMilestones
• ModelManager.upgradePackage
• ModelManager.upgradeToMilestone
• ModelManager.useHPC
• ModelManager.validateParsBytes
• ModelManager.variationName
• ModelManager.verifyStoredValues
• ModelManager.waitForDiagnostics
• ModelManager.wasSuccessful
• ModelManager.withTransaction
• PairCorrelationFunction.pcf
• PhysiCellModelManager.apoptosisPath
• PhysiCellModelManager.assembleIntracellular!
• PhysiCellModelManager.attackPath
• PhysiCellModelManager.attackRatePath
• PhysiCellModelManager.attackRatesPath
• PhysiCellModelManager.cellDefinitionPath
• PhysiCellModelManager.cellInteractionsPath
• PhysiCellModelManager.configPath
• PhysiCellModelManager.connectedComponents
• PhysiCellModelManager.createICCellXMLTemplate
• PhysiCellModelManager.createICECMXMLTemplate
• PhysiCellModelManager.createProject
• PhysiCellModelManager.customDataPath
• PhysiCellModelManager.cyclePath
• PhysiCellModelManager.deathPath
• PhysiCellModelManager.domainPath
• PhysiCellModelManager.domainVariations
• PhysiCellModelManager.endpointPopulationCountQoI
• PhysiCellModelManager.endpointPopulationCounts
• PhysiCellModelManager.endpointPopulationFractionQoI
• PhysiCellModelManager.endpointPopulationFractions
• PhysiCellModelManager.exportSimulation
• PhysiCellModelManager.finalPopulationCount
• PhysiCellModelManager.finalPopulationCount
• PhysiCellModelManager.fullSavePath
• PhysiCellModelManager.fusionPath
• PhysiCellModelManager.icCellsPath
• PhysiCellModelManager.icECMPath
• PhysiCellModelManager.importProject
• PhysiCellModelManager.initialParameterDistributionPath
• PhysiCellModelManager.integrityPath
• PhysiCellModelManager.makeMovie
• PhysiCellModelManager.meanPopulationTimeSeries
• PhysiCellModelManager.meanPopulationTimeSeriesQoI
• PhysiCellModelManager.mechanicsPath
• PhysiCellModelManager.motilityPath
• PhysiCellModelManager.motilityStatistics
• PhysiCellModelManager.necrosisPath
• PhysiCellModelManager.phagocytosisPath
• PhysiCellModelManager.phenotypePath
• PhysiCellModelManager.plotbycelltype
• PhysiCellModelManager.populationCount
• PhysiCellModelManager.populationCountQoI
• PhysiCellModelManager.populationTimeSeries
• PhysiCellModelManager.rulePath
• PhysiCellModelManager.runStudio
• PhysiCellModelManager.secretionPath
• PhysiCellModelManager.substratePath
• PhysiCellModelManager.svgSavePath
• PhysiCellModelManager.timePath
• PhysiCellModelManager.transformationPath
• PhysiCellModelManager.userParameterPath
• PhysiCellModelManager.userParametersPath
• PhysiCellModelManager.volumePath
• PhysiCellOutput.cellDataSequence