petab.v2.C

This file contains constant definitions.

Module Attributes

OBSERVABLE_ID	Observable ID column in the observable and measurement tables
PREEQUILIBRATION_CONDITION_ID	Preequilibration condition ID column in the measurement table
SIMULATION_CONDITION_ID	Simulation condition ID column in the measurement table
MEASUREMENT	Measurement value column in the measurement table
TIME	Time column in the measurement table
TIME_STEADY_STATE	Time value that indicates steady-state measurements
OBSERVABLE_PARAMETERS	Observable parameters column in the measurement table
NOISE_PARAMETERS	Noise parameters column in the measurement table
DATASET_ID	Dataset ID column in the measurement table
REPLICATE_ID	Replicate ID column in the measurement table
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 ID column in the parameter table
PARAMETER_NAME	Parameter name column in the parameter table
PARAMETER_SCALE	Parameter scale column in the parameter table
LOWER_BOUND	Lower bound column in the parameter table
UPPER_BOUND	Upper bound column in the parameter table
NOMINAL_VALUE	Nominal value column in the parameter table
ESTIMATE	Estimate column in the parameter table
INITIALIZATION_PRIOR_TYPE	Initialization prior type column in the parameter table
INITIALIZATION_PRIOR_PARAMETERS	Initialization prior parameters column in the parameter table
OBJECTIVE_PRIOR_TYPE	Objective prior type column in the parameter table
OBJECTIVE_PRIOR_PARAMETERS	Objective prior parameters column in the parameter table
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	Initialization-type prior
OBJECTIVE	Objective-type prior
CONDITION_ID	Condition ID column in the condition table
CONDITION_NAME	Condition name column in the condition table
OBSERVABLE_NAME	Observable name column in the observables table
OBSERVABLE_FORMULA	Observable formula column in the observables table
NOISE_FORMULA	Noise formula column in the observables table
OBSERVABLE_TRANSFORMATION	Observable transformation column in the observables table
NOISE_DISTRIBUTION	Noise distribution column in the observables table
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	Linear transformation
LOG	Logarithmic transformation
LOG10	Logarithmic base 10 transformation
OBSERVABLE_TRANSFORMATIONS	Supported observable transformations
UNIFORM	Uniform distribution
PARAMETER_SCALE_UNIFORM	Uniform distribution on the parameter scale
NORMAL	Normal distribution
PARAMETER_SCALE_NORMAL	Normal distribution on the parameter scale
LAPLACE	Laplace distribution
PARAMETER_SCALE_LAPLACE	Laplace distribution on the parameter scale
LOG_NORMAL	Log-normal distribution
LOG_LAPLACE	Log-Laplace distribution
PRIOR_TYPES	Supported prior types
NOISE_MODELS	Supported noise distributions
PLOT_ID	Plot ID column in the visualization table
PLOT_NAME	Plot name column in the visualization table
PLOT_TYPE_SIMULATION	Value for plot type 'simulation' in the visualization table
PLOT_TYPE_DATA	Value for plot type 'data' in the visualization table
X_VALUES	X values column in the visualization table
X_OFFSET	X offset column in the visualization table
X_LABEL	X label column in the visualization table
X_SCALE	X scale column in the visualization table
Y_VALUES	Y values column in the visualization table
Y_OFFSET	Y offset column in the visualization table
Y_LABEL	Y label column in the visualization table
Y_SCALE	Y scale column in the visualization table
LEGEND_ENTRY	Legend entry column in the visualization table
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	Plot type value in the visualization table for line plot
BAR_PLOT	Plot type value in the visualization table for bar plot
SCATTER_PLOT	Plot type value in the visualization table for scatter plot
PLOT_TYPES_SIMULATION	Supported plot types
X_SCALES	Supported xScales
Y_SCALES	Supported yScales
REPLICATE	Plot type "data" value in the visualization table for replicates
PROVIDED	Plot type "data" value in the visualization table for provided noise values
PLOT_TYPES_DATA	Supported settings for handling replicates
FORMAT_VERSION	PEtab version key in the YAML file
PARAMETER_FILE	Parameter file key in the YAML file
PROBLEMS	Problems key in the YAML file
MODEL_FILES	Model files key in the YAML file
MODEL_LOCATION	Model location key in the YAML file
MODEL_LANGUAGE	Model language key in the YAML file
CONDITION_FILES	Condition files key in the YAML file
MEASUREMENT_FILES	Measurement files key in the YAML file
OBSERVABLE_FILES	Observable files key in the YAML file
VISUALIZATION_FILES	Visualization files key in the YAML file
MAPPING_FILES	Mapping files key in the YAML file
EXTENSIONS	Extensions key in the YAML file
PETAB_ENTITY_ID	PEtab entity ID column in the mapping table
MODEL_ENTITY_ID	Model entity ID column in the mapping table
MAPPING_DF_REQUIRED_COLS	Required columns of the mapping table
SIMULATION	Simulated value column in the simulation table
RESIDUAL	Residual value column in the residuals table
NOISE_VALUE
PARAMETER_SEPARATOR	separator for multiple parameter values (bounds, observableParameters, ...)

petab.v2.C.BAR_PLOT = 'BarPlot'

Plot type value in the visualization table for bar plot

petab.v2.C.CONDITION_FILES = 'condition_files'

Condition files key in the YAML file

petab.v2.C.CONDITION_ID = 'conditionId'

Condition ID column in the condition table

petab.v2.C.CONDITION_NAME = 'conditionName'

Condition name column in the condition table

petab.v2.C.DATASET_ID = 'datasetId'

Dataset ID column in the measurement table

petab.v2.C.ESTIMATE = 'estimate'

Estimate column in the parameter table

petab.v2.C.EXTENSIONS = 'extensions'

Extensions key in the YAML file

petab.v2.C.FORMAT_VERSION = 'format_version'

PEtab version key in the YAML file

petab.v2.C.INITIALIZATION = 'initialization'

Initialization-type prior

petab.v2.C.INITIALIZATION_PRIOR_PARAMETERS = 'initializationPriorParameters'

Initialization prior parameters column in the parameter table

petab.v2.C.INITIALIZATION_PRIOR_TYPE = 'initializationPriorType'

Initialization prior type column in the parameter table

petab.v2.C.LAPLACE = 'laplace'

Laplace distribution

petab.v2.C.LEGEND_ENTRY = 'legendEntry'

Legend entry column in the visualization table

petab.v2.C.LIN = 'lin'

Linear transformation

petab.v2.C.LINE_PLOT = 'LinePlot'

Plot type value in the visualization table for line plot

petab.v2.C.LOG = 'log'

Logarithmic transformation

petab.v2.C.LOG10 = 'log10'

Logarithmic base 10 transformation

petab.v2.C.LOG_LAPLACE = 'logLaplace'

Log-Laplace distribution

petab.v2.C.LOG_NORMAL = 'logNormal'

Log-normal distribution

petab.v2.C.LOWER_BOUND = 'lowerBound'

Lower bound column in the parameter table

petab.v2.C.MAPPING_DF_REQUIRED_COLS = ['petabEntityId', 'modelEntityId']

Required columns of the mapping table

petab.v2.C.MAPPING_FILES = 'mapping_files'

Mapping files key in the YAML file

petab.v2.C.MEASUREMENT = 'measurement'

Measurement value column in the measurement table

petab.v2.C.MEASUREMENT_DF_COLS = ['observableId', 'preequilibrationConditionId', 'simulationConditionId', 'measurement', 'time', 'observableParameters', 'noiseParameters', 'datasetId', 'replicateId']

Measurement table columns

petab.v2.C.MEASUREMENT_DF_OPTIONAL_COLS = ['preequilibrationConditionId', 'observableParameters', 'noiseParameters', 'datasetId', 'replicateId']

Optional columns of measurement table

petab.v2.C.MEASUREMENT_DF_REQUIRED_COLS = ['observableId', 'simulationConditionId', 'measurement', 'time']

Mandatory columns of measurement table

petab.v2.C.MEASUREMENT_FILES = 'measurement_files'

Measurement files key in the YAML file

petab.v2.C.MODEL_ENTITY_ID = 'modelEntityId'

Model entity ID column in the mapping table

petab.v2.C.MODEL_FILES = 'model_files'

Model files key in the YAML file

petab.v2.C.MODEL_LANGUAGE = 'language'

Model language key in the YAML file

petab.v2.C.MODEL_LOCATION = 'location'

Model location key in the YAML file

petab.v2.C.NOISE_DISTRIBUTION = 'noiseDistribution'

Noise distribution column in the observables table

petab.v2.C.NOISE_FORMULA = 'noiseFormula'

Noise formula column in the observables table

petab.v2.C.NOISE_MODELS = ['normal', 'laplace']

Supported noise distributions

petab.v2.C.NOISE_PARAMETERS = 'noiseParameters'

Noise parameters column in the measurement table

petab.v2.C.NOISE_VALUE = 'noiseValue'

???

petab.v2.C.NOMINAL_VALUE = 'nominalValue'

Nominal value column in the parameter table

petab.v2.C.NORMAL = 'normal'

Normal distribution

petab.v2.C.OBJECTIVE = 'objective'

Objective-type prior

petab.v2.C.OBJECTIVE_PRIOR_PARAMETERS = 'objectivePriorParameters'

Objective prior parameters column in the parameter table

petab.v2.C.OBJECTIVE_PRIOR_TYPE = 'objectivePriorType'

Objective prior type column in the parameter table

petab.v2.C.OBSERVABLE_DF_COLS = ['observableId', 'observableFormula', 'noiseFormula', 'observableName', 'observableTransformation', 'noiseDistribution']

Observables table columns

petab.v2.C.OBSERVABLE_DF_OPTIONAL_COLS = ['observableName', 'observableTransformation', 'noiseDistribution']

Optional columns of observables table

petab.v2.C.OBSERVABLE_DF_REQUIRED_COLS = ['observableId', 'observableFormula', 'noiseFormula']

Mandatory columns of observables table

petab.v2.C.OBSERVABLE_FILES = 'observable_files'

Observable files key in the YAML file

petab.v2.C.OBSERVABLE_FORMULA = 'observableFormula'

Observable formula column in the observables table

petab.v2.C.OBSERVABLE_ID = 'observableId'

Observable ID column in the observable and measurement tables

petab.v2.C.OBSERVABLE_NAME = 'observableName'

Observable name column in the observables table

petab.v2.C.OBSERVABLE_PARAMETERS = 'observableParameters'

Observable parameters column in the measurement table

petab.v2.C.OBSERVABLE_TRANSFORMATION = 'observableTransformation'

Observable transformation column in the observables table

petab.v2.C.OBSERVABLE_TRANSFORMATIONS = ['lin', 'log', 'log10']

Supported observable transformations

petab.v2.C.PARAMETER_DF_COLS = ['parameterId', 'parameterName', 'parameterScale', 'lowerBound', 'upperBound', 'estimate', 'nominalValue', 'initializationPriorType', 'initializationPriorParameters', 'objectivePriorType', 'objectivePriorParameters']

Parameter table columns

petab.v2.C.PARAMETER_DF_OPTIONAL_COLS = ['parameterName', 'nominalValue', 'initializationPriorType', 'initializationPriorParameters', 'objectivePriorType', 'objectivePriorParameters']

Optional columns of parameter table

petab.v2.C.PARAMETER_DF_REQUIRED_COLS = ['parameterId', 'parameterScale', 'lowerBound', 'upperBound', 'estimate']

Mandatory columns of parameter table

petab.v2.C.PARAMETER_FILE = 'parameter_file'

Parameter file key in the YAML file

petab.v2.C.PARAMETER_ID = 'parameterId'

Parameter ID column in the parameter table

petab.v2.C.PARAMETER_NAME = 'parameterName'

Parameter name column in the parameter table

petab.v2.C.PARAMETER_SCALE = 'parameterScale'

Parameter scale column in the parameter table

petab.v2.C.PARAMETER_SCALE_LAPLACE = 'parameterScaleLaplace'

Laplace distribution on the parameter scale

petab.v2.C.PARAMETER_SCALE_NORMAL = 'parameterScaleNormal'

Normal distribution on the parameter scale

petab.v2.C.PARAMETER_SCALE_UNIFORM = 'parameterScaleUniform'

Uniform distribution on the parameter scale

petab.v2.C.PARAMETER_SEPARATOR = ';'

separator for multiple parameter values (bounds, observableParameters, …)

petab.v2.C.PETAB_ENTITY_ID = 'petabEntityId'

PEtab entity ID column in the mapping table

petab.v2.C.PLOT_ID = 'plotId'

Plot ID column in the visualization table

petab.v2.C.PLOT_NAME = 'plotName'

Plot name column in the visualization table

petab.v2.C.PLOT_TYPES_DATA = ['MeanAndSD', 'MeanAndSEM', 'replicate', 'provided']

Supported settings for handling replicates

petab.v2.C.PLOT_TYPES_SIMULATION = ['LinePlot', 'BarPlot', 'ScatterPlot']

Supported plot types

petab.v2.C.PLOT_TYPE_DATA = 'plotTypeData'

Value for plot type ‘data’ in the visualization table

petab.v2.C.PLOT_TYPE_SIMULATION = 'plotTypeSimulation'

Value for plot type ‘simulation’ in the visualization table

petab.v2.C.PREEQUILIBRATION_CONDITION_ID = 'preequilibrationConditionId'

Preequilibration condition ID column in the measurement table

petab.v2.C.PRIOR_TYPES = ['uniform', 'normal', 'laplace', 'logNormal', 'logLaplace', 'parameterScaleUniform', 'parameterScaleNormal', 'parameterScaleLaplace']

Supported prior types

petab.v2.C.PROBLEMS = 'problems'

Problems key in the YAML file

petab.v2.C.PROVIDED = 'provided'

Plot type “data” value in the visualization table for provided noise values

petab.v2.C.REPLICATE = 'replicate'

Plot type “data” value in the visualization table for replicates

petab.v2.C.REPLICATE_ID = 'replicateId'

Replicate ID column in the measurement table

petab.v2.C.RESIDUAL = 'residual'

Residual value column in the residuals table

petab.v2.C.SCATTER_PLOT = 'ScatterPlot'

Plot type value in the visualization table for scatter plot

petab.v2.C.SIMULATION = 'simulation'

Simulated value column in the simulation table

petab.v2.C.SIMULATION_CONDITION_ID = 'simulationConditionId'

Simulation condition ID column in the measurement table

petab.v2.C.TIME = 'time'

Time column in the measurement table

petab.v2.C.TIME_STEADY_STATE = inf

Time value that indicates steady-state measurements

petab.v2.C.UNIFORM = 'uniform'

Uniform distribution

petab.v2.C.UPPER_BOUND = 'upperBound'

Upper bound column in the parameter table

petab.v2.C.VISUALIZATION_DF_COLS = ['plotId', 'plotName', 'plotTypeSimulation', 'plotTypeData', 'xValues', 'xOffset', 'xLabel', 'xScale', 'yValues', 'yOffset', 'yLabel', 'yScale', 'legendEntry', 'datasetId']

Visualization table columns

petab.v2.C.VISUALIZATION_DF_OPTIONAL_COLS = ['plotName', 'plotTypeSimulation', 'plotTypeData', 'xValues', 'xOffset', 'xLabel', 'xScale', 'yValues', 'yOffset', 'yLabel', 'yScale', 'legendEntry', 'datasetId']

Optional columns of visualization table

petab.v2.C.VISUALIZATION_DF_REQUIRED_COLS = ['plotId']

Mandatory columns of visualization table

petab.v2.C.VISUALIZATION_DF_SINGLE_PLOT_LEVEL_COLS = ['xValues', 'xOffset', 'yValues', 'yOffset', 'legendEntry', 'datasetId']

Visualization table columns that contain single plot specifications

petab.v2.C.VISUALIZATION_DF_SUBPLOT_LEVEL_COLS = ['plotId', 'plotName', 'plotTypeSimulation', 'plotTypeData', 'xLabel', 'xScale', 'yLabel', 'yScale']

Visualization table columns that contain subplot specifications

petab.v2.C.VISUALIZATION_FILES = 'visualization_files'

Visualization files key in the YAML file

petab.v2.C.X_LABEL = 'xLabel'

X label column in the visualization table

petab.v2.C.X_OFFSET = 'xOffset'

X offset column in the visualization table

petab.v2.C.X_SCALE = 'xScale'

X scale column in the visualization table

petab.v2.C.X_SCALES = ['lin', 'log', 'log10']

Supported xScales

petab.v2.C.X_VALUES = 'xValues'

X values column in the visualization table

petab.v2.C.Y_LABEL = 'yLabel'

Y label column in the visualization table

petab.v2.C.Y_OFFSET = 'yOffset'

Y offset column in the visualization table

petab.v2.C.Y_SCALE = 'yScale'

Y scale column in the visualization table

petab.v2.C.Y_SCALES = ['lin', 'log', 'log10']

Supported yScales

petab.v2.C.Y_VALUES = 'yValues'

Y values column in the visualization table