petab.C

This file contains constant definitions.

Module Attributes

`OBSERVABLE_ID`
`PREEQUILIBRATION_CONDITION_ID`
`SIMULATION_CONDITION_ID`
`MEASUREMENT`
`TIME`
`TIME_STEADY_STATE`	Time value that indicates steady-state measurements
`OBSERVABLE_PARAMETERS`
`NOISE_PARAMETERS`
`DATASET_ID`
`REPLICATE_ID`
`MEASUREMENT_DF_REQUIRED_COLS`	Mandatory columns of measurement table
`MEASUREMENT_DF_OPTIONAL_COLS`	Optional columns of measurement table
`MEASUREMENT_DF_COLS`	Measurement table columns
`PARAMETER_ID`
`PARAMETER_NAME`
`PARAMETER_SCALE`
`LOWER_BOUND`
`UPPER_BOUND`
`NOMINAL_VALUE`
`ESTIMATE`
`INITIALIZATION_PRIOR_TYPE`
`INITIALIZATION_PRIOR_PARAMETERS`
`OBJECTIVE_PRIOR_TYPE`
`OBJECTIVE_PRIOR_PARAMETERS`
`PARAMETER_DF_REQUIRED_COLS`	Mandatory columns of parameter table
`PARAMETER_DF_OPTIONAL_COLS`	Optional columns of parameter table
`PARAMETER_DF_COLS`	Parameter table columns
`INITIALIZATION`
`OBJECTIVE`
`CONDITION_ID`
`CONDITION_NAME`
`OBSERVABLE_NAME`
`OBSERVABLE_FORMULA`
`NOISE_FORMULA`
`OBSERVABLE_TRANSFORMATION`
`NOISE_DISTRIBUTION`
`OBSERVABLE_DF_REQUIRED_COLS`	Mandatory columns of observables table
`OBSERVABLE_DF_OPTIONAL_COLS`	Optional columns of observables table
`OBSERVABLE_DF_COLS`	Observables table columns
`LIN`
`LOG`
`LOG10`
`OBSERVABLE_TRANSFORMATIONS`	Supported observable transformations
`UNIFORM`
`PARAMETER_SCALE_UNIFORM`
`NORMAL`
`PARAMETER_SCALE_NORMAL`
`LAPLACE`
`PARAMETER_SCALE_LAPLACE`
`LOG_NORMAL`
`LOG_LAPLACE`
`PRIOR_TYPES`	Supported prior types
`NOISE_MODELS`	Supported noise distributions
`PLOT_ID`
`PLOT_NAME`
`PLOT_TYPE_SIMULATION`
`PLOT_TYPE_DATA`
`X_VALUES`
`X_OFFSET`
`X_LABEL`
`X_SCALE`
`Y_VALUES`
`Y_OFFSET`
`Y_LABEL`
`Y_SCALE`
`LEGEND_ENTRY`
`VISUALIZATION_DF_REQUIRED_COLS`	Mandatory columns of visualization table
`VISUALIZATION_DF_OPTIONAL_COLS`	Optional columns of visualization table
`VISUALIZATION_DF_COLS`	Visualization table columns
`VISUALIZATION_DF_SUBPLOT_LEVEL_COLS`	Visualization table columns that contain subplot specifications
`VISUALIZATION_DF_SINGLE_PLOT_LEVEL_COLS`	Visualization table columns that contain single plot specifications
`LINE_PLOT`
`BAR_PLOT`
`SCATTER_PLOT`
`PLOT_TYPES_SIMULATION`	Supported plot types
`X_SCALES`	Supported xScales
`Y_SCALES`	Supported yScales
`MEAN_AND_SD`
`MEAN_AND_SEM`
`REPLICATE`
`PROVIDED`
`PLOT_TYPES_DATA`	Supported settings for handling replicates
`FORMAT_VERSION`
`PARAMETER_FILE`
`PROBLEMS`
`SBML_FILES`
`MODEL_FILES`
`MODEL_LOCATION`
`MODEL_LANGUAGE`
`CONDITION_FILES`
`MEASUREMENT_FILES`
`OBSERVABLE_FILES`
`VISUALIZATION_FILES`
`MAPPING_FILES`
`EXTENSIONS`
`PETAB_ENTITY_ID`
`MODEL_ENTITY_ID`
`MAPPING_DF_REQUIRED_COLS`
`SIMULATION`
`RESIDUAL`
`NOISE_VALUE`

petab.C.BAR_PLOT = 'BarPlot'

petab.C.CONDITION_FILES = 'condition_files'

petab.C.CONDITION_ID = 'conditionId'

petab.C.CONDITION_NAME = 'conditionName'

petab.C.DATASET_ID = 'datasetId'

petab.C.ESTIMATE = 'estimate'

petab.C.EXTENSIONS = 'extensions'

petab.C.FORMAT_VERSION = 'format_version'

petab.C.INITIALIZATION = 'initialization'

petab.C.INITIALIZATION_PRIOR_PARAMETERS = 'initializationPriorParameters'

petab.C.INITIALIZATION_PRIOR_TYPE = 'initializationPriorType'

petab.C.LAPLACE = 'laplace'

petab.C.LEGEND_ENTRY = 'legendEntry'

petab.C.LIN = 'lin'

petab.C.LINE_PLOT = 'LinePlot'

petab.C.LOG = 'log'

petab.C.LOG10 = 'log10'

petab.C.LOG_LAPLACE = 'logLaplace'

petab.C.LOG_NORMAL = 'logNormal'

petab.C.LOWER_BOUND = 'lowerBound'

petab.C.MAPPING_DF_REQUIRED_COLS = ['petabEntityId', 'modelEntityId']

petab.C.MAPPING_FILES = 'mapping_files'

petab.C.MEAN_AND_SD = 'MeanAndSD'

petab.C.MEAN_AND_SEM = 'MeanAndSEM'

petab.C.MEASUREMENT = 'measurement'

petab.C.MEASUREMENT_DF_COLS = ['observableId', 'preequilibrationConditionId', 'simulationConditionId', 'measurement', 'time', 'observableParameters', 'noiseParameters', 'datasetId', 'replicateId']: Measurement table columns

petab.C.MEASUREMENT_DF_OPTIONAL_COLS = ['preequilibrationConditionId', 'observableParameters', 'noiseParameters', 'datasetId', 'replicateId']: Optional columns of measurement table

petab.C.MEASUREMENT_DF_REQUIRED_COLS = ['observableId', 'simulationConditionId', 'measurement', 'time']: Mandatory columns of measurement table

petab.C.MEASUREMENT_FILES = 'measurement_files'

petab.C.MODEL_ENTITY_ID = 'modelEntityId'

petab.C.MODEL_FILES = 'model_files'

petab.C.MODEL_LANGUAGE = 'language'

petab.C.MODEL_LOCATION = 'location'

petab.C.NOISE_DISTRIBUTION = 'noiseDistribution'

petab.C.NOISE_FORMULA = 'noiseFormula'

petab.C.NOISE_MODELS = ['normal', 'laplace']: Supported noise distributions

petab.C.NOISE_PARAMETERS = 'noiseParameters'

petab.C.NOISE_VALUE = 'noiseValue'

petab.C.NOMINAL_VALUE = 'nominalValue'

petab.C.NORMAL = 'normal'

petab.C.OBJECTIVE = 'objective'

petab.C.OBJECTIVE_PRIOR_PARAMETERS = 'objectivePriorParameters'

petab.C.OBJECTIVE_PRIOR_TYPE = 'objectivePriorType'

petab.C.OBSERVABLE_DF_COLS = ['observableId', 'observableFormula', 'noiseFormula', 'observableName', 'observableTransformation', 'noiseDistribution']: Observables table columns

petab.C.OBSERVABLE_DF_OPTIONAL_COLS = ['observableName', 'observableTransformation', 'noiseDistribution']: Optional columns of observables table

petab.C.OBSERVABLE_DF_REQUIRED_COLS = ['observableId', 'observableFormula', 'noiseFormula']: Mandatory columns of observables table

petab.C.OBSERVABLE_FILES = 'observable_files'

petab.C.OBSERVABLE_FORMULA = 'observableFormula'

petab.C.OBSERVABLE_ID = 'observableId'

petab.C.OBSERVABLE_NAME = 'observableName'

petab.C.OBSERVABLE_PARAMETERS = 'observableParameters'

petab.C.OBSERVABLE_TRANSFORMATION = 'observableTransformation'

petab.C.OBSERVABLE_TRANSFORMATIONS = ['lin', 'log', 'log10']: Supported observable transformations

petab.C.PARAMETER_DF_COLS = ['parameterId', 'parameterName', 'parameterScale', 'lowerBound', 'upperBound', 'estimate', 'nominalValue', 'initializationPriorType', 'initializationPriorParameters', 'objectivePriorType', 'objectivePriorParameters']: Parameter table columns

petab.C.PARAMETER_DF_OPTIONAL_COLS = ['parameterName', 'nominalValue', 'initializationPriorType', 'initializationPriorParameters', 'objectivePriorType', 'objectivePriorParameters']: Optional columns of parameter table

petab.C.PARAMETER_DF_REQUIRED_COLS = ['parameterId', 'parameterScale', 'lowerBound', 'upperBound', 'estimate']: Mandatory columns of parameter table

petab.C.PARAMETER_FILE = 'parameter_file'

petab.C.PARAMETER_ID = 'parameterId'

petab.C.PARAMETER_NAME = 'parameterName'

petab.C.PARAMETER_SCALE = 'parameterScale'

petab.C.PARAMETER_SCALE_LAPLACE = 'parameterScaleLaplace'

petab.C.PARAMETER_SCALE_NORMAL = 'parameterScaleNormal'

petab.C.PARAMETER_SCALE_UNIFORM = 'parameterScaleUniform'

petab.C.PETAB_ENTITY_ID = 'petabEntityId'

petab.C.PLOT_ID = 'plotId'

petab.C.PLOT_NAME = 'plotName'

petab.C.PLOT_TYPES_DATA = ['MeanAndSD', 'MeanAndSEM', 'replicate', 'provided']: Supported settings for handling replicates

petab.C.PLOT_TYPES_SIMULATION = ['LinePlot', 'BarPlot', 'ScatterPlot']: Supported plot types

petab.C.PLOT_TYPE_DATA = 'plotTypeData'

petab.C.PLOT_TYPE_SIMULATION = 'plotTypeSimulation'

petab.C.PREEQUILIBRATION_CONDITION_ID = 'preequilibrationConditionId'

petab.C.PRIOR_TYPES = ['uniform', 'normal', 'laplace', 'logNormal', 'logLaplace', 'parameterScaleUniform', 'parameterScaleNormal', 'parameterScaleLaplace']: Supported prior types

petab.C.PROBLEMS = 'problems'

petab.C.PROVIDED = 'provided'

petab.C.REPLICATE = 'replicate'

petab.C.REPLICATE_ID = 'replicateId'

petab.C.RESIDUAL = 'residual'

petab.C.SBML_FILES = 'sbml_files'

petab.C.SCATTER_PLOT = 'ScatterPlot'

petab.C.SIMULATION = 'simulation'

petab.C.SIMULATION_CONDITION_ID = 'simulationConditionId'

petab.C.TIME = 'time'

petab.C.TIME_STEADY_STATE = inf: Time value that indicates steady-state measurements

petab.C.UNIFORM = 'uniform'

petab.C.UPPER_BOUND = 'upperBound'

petab.C.VISUALIZATION_DF_COLS = ['plotId', 'plotName', 'plotTypeSimulation', 'plotTypeData', 'xValues', 'xOffset', 'xLabel', 'xScale', 'yValues', 'yOffset', 'yLabel', 'yScale', 'legendEntry', 'datasetId']: Visualization table columns

petab.C.VISUALIZATION_DF_OPTIONAL_COLS = ['plotName', 'plotTypeSimulation', 'plotTypeData', 'xValues', 'xOffset', 'xLabel', 'xScale', 'yValues', 'yOffset', 'yLabel', 'yScale', 'legendEntry', 'datasetId']: Optional columns of visualization table

petab.C.VISUALIZATION_DF_REQUIRED_COLS = ['plotId']: Mandatory columns of visualization table

petab.C.VISUALIZATION_DF_SINGLE_PLOT_LEVEL_COLS = ['xValues', 'xOffset', 'yValues', 'yOffset', 'legendEntry', 'datasetId']: Visualization table columns that contain single plot specifications

petab.C.VISUALIZATION_DF_SUBPLOT_LEVEL_COLS = ['plotId', 'plotName', 'plotTypeSimulation', 'plotTypeData', 'xLabel', 'xScale', 'yLabel', 'yScale']: Visualization table columns that contain subplot specifications

petab.C.VISUALIZATION_FILES = 'visualization_files'

petab.C.X_LABEL = 'xLabel'

petab.C.X_OFFSET = 'xOffset'

petab.C.X_SCALE = 'xScale'

petab.C.X_SCALES = ['lin', 'log', 'log10']: Supported xScales

petab.C.X_VALUES = 'xValues'

petab.C.Y_LABEL = 'yLabel'

petab.C.Y_OFFSET = 'yOffset'

petab.C.Y_SCALE = 'yScale'

petab.C.Y_SCALES = ['lin', 'log', 'log10']: Supported yScales

petab.C.Y_VALUES = 'yValues'