petab.v2.C

This file contains constant definitions.

Module Attributes

OBSERVABLE_ID	Observable ID column in the observable and measurement tables
EXPERIMENT_ID	Experiment 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
TIME_PREEQUILIBRATION	Time value that indicates pre-equilibration in the experiments table
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
MODEL_ID	The model 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
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
PRIOR_DISTRIBUTION	Prior distribution type column in the parameter table
PRIOR_PARAMETERS	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
TARGET_ID	Column in the condition table with the ID of an entity that is changed
TARGET_VALUE	Column in the condition table with the new value of the target entity
OBSERVABLE_NAME	Observable name column in the observable table
OBSERVABLE_FORMULA	Observable formula column in the observable table
OBSERVABLE_PLACEHOLDERS	Observable placeholders column in the observable table
NOISE_FORMULA	Noise formula column in the observable table
NOISE_DISTRIBUTION	Noise distribution column in the observable table
NOISE_PLACEHOLDERS	Noise placeholders column in the observable table
OBSERVABLE_DF_REQUIRED_COLS	Mandatory columns of observable table
OBSERVABLE_DF_OPTIONAL_COLS	Optional columns of observable table
OBSERVABLE_DF_COLS	Observables table columns
LIN	Linear transformation
LOG	Logarithmic transformation
LOG10	Logarithmic base 10 transformation
CAUCHY	Cauchy distribution.
EXPONENTIAL	Exponential distribution.
GAMMA	Gamma distribution.
LAPLACE	Laplace distribution
LOG_LAPLACE	Log-Laplace distribution
LOG_NORMAL	Log-normal distribution
LOG_UNIFORM	Log-uniform distribution.
NORMAL	Normal distribution
RAYLEIGH	Rayleigh distribution.
UNIFORM	Uniform distribution
PRIOR_DISTRIBUTIONS	Supported prior distribution types
NOISE_DISTRIBUTIONS	Supported noise distributions
FORMAT_VERSION	PEtab version key in the YAML file
PARAMETER_FILES	Parameter files 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
EXPERIMENT_FILES	Experiment 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
NAME	Arbitrary name
MAPPING_DF_REQUIRED_COLS	Required columns of the mapping table
SIMULATION	Simulated value column in the simulation table
RESIDUAL	Residual value column in the residual table
PARAMETER_SEPARATOR	separator for multiple parameter values (bounds, observableParameters, ...)
TIME_SYMBOL	The time symbol for use in any PEtab-specific mathematical expressions

petab.v2.C.CAUCHY = 'cauchy'

Cauchy distribution.

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.DATASET_ID = 'datasetId'

Dataset ID column in the measurement table

petab.v2.C.ESTIMATE = 'estimate'

Estimate column in the parameter table

petab.v2.C.EXPERIMENT_FILES = 'experiment_files'

Experiment files key in the YAML file

petab.v2.C.EXPERIMENT_ID = 'experimentId'

Experiment ID column in the measurement table

petab.v2.C.EXPONENTIAL = 'exponential'

Exponential distribution.

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.GAMMA = 'gamma'

Gamma distribution.

petab.v2.C.INITIALIZATION = 'initialization'

Initialization-type prior

petab.v2.C.LAPLACE = 'laplace'

Laplace distribution

petab.v2.C.LIN = 'lin'

Linear transformation

petab.v2.C.LOG = 'log'

Logarithmic transformation

petab.v2.C.LOG10 = 'log10'

Logarithmic base 10 transformation

petab.v2.C.LOG_LAPLACE = 'log-laplace'

Log-Laplace distribution

petab.v2.C.LOG_NORMAL = 'log-normal'

Log-normal distribution

petab.v2.C.LOG_UNIFORM = 'log-uniform'

Log-uniform 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', 'observableParameters', 'experimentId', 'measurement', 'time', 'noiseParameters', 'datasetId', 'replicateId', 'modelId']

Measurement table columns

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

Optional columns of measurement table

petab.v2.C.MEASUREMENT_DF_REQUIRED_COLS = ['observableId', 'experimentId', '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_ID = 'modelId'

The model ID column in the measurement table

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.NAME = 'name'

Arbitrary name

petab.v2.C.NOISE_DISTRIBUTION = 'noiseDistribution'

Noise distribution column in the observable table

petab.v2.C.NOISE_DISTRIBUTIONS = ['normal', 'laplace', 'log-normal', 'log-laplace']

Supported noise distributions

petab.v2.C.NOISE_FORMULA = 'noiseFormula'

Noise formula column in the observable table

petab.v2.C.NOISE_PARAMETERS = 'noiseParameters'

Noise parameters column in the measurement table

petab.v2.C.NOISE_PLACEHOLDERS = 'noisePlaceholders'

Noise placeholders column in the observable table

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.OBSERVABLE_DF_COLS = ['observableId', 'observableFormula', 'noiseFormula', 'observableName', 'noiseDistribution']

Observables table columns

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

Optional columns of observable table

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

Mandatory columns of observable 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 observable 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 observable table

petab.v2.C.OBSERVABLE_PARAMETERS = 'observableParameters'

Observable parameters column in the measurement table

petab.v2.C.OBSERVABLE_PLACEHOLDERS = 'observablePlaceholders'

Observable placeholders column in the observable table

petab.v2.C.PARAMETER_DF_COLS = ['parameterId', 'parameterName', 'lowerBound', 'upperBound', 'estimate', 'nominalValue', 'priorDistribution', 'priorParameters']

Parameter table columns

petab.v2.C.PARAMETER_DF_OPTIONAL_COLS = ['parameterName', 'nominalValue', 'priorDistribution', 'priorParameters']

Optional columns of parameter table

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

Mandatory columns of parameter table

petab.v2.C.PARAMETER_FILES = 'parameter_files'

Parameter files 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_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.PRIOR_DISTRIBUTION = 'priorDistribution'

Prior distribution type column in the parameter table

petab.v2.C.PRIOR_DISTRIBUTIONS = ['cauchy', 'chisquare', 'exponential', 'gamma', 'laplace', 'log-laplace', 'log-normal', 'log-uniform', 'normal', 'rayleigh', 'uniform']

Supported prior distribution types

petab.v2.C.PRIOR_PARAMETERS = 'priorParameters'

Prior parameters column in the parameter table

petab.v2.C.PROBLEMS = 'problems'

Problems key in the YAML file

petab.v2.C.RAYLEIGH = 'rayleigh'

Rayleigh distribution.

petab.v2.C.REPLICATE_ID = 'replicateId'

Replicate ID column in the measurement table

petab.v2.C.RESIDUAL = 'residual'

Residual value column in the residual table

petab.v2.C.SIMULATION = 'simulation'

Simulated value column in the simulation table

petab.v2.C.TARGET_ID = 'targetId'

Column in the condition table with the ID of an entity that is changed

petab.v2.C.TARGET_VALUE = 'targetValue'

Column in the condition table with the new value of the target entity

petab.v2.C.TIME = 'time'

Time column in the measurement table

petab.v2.C.TIME_PREEQUILIBRATION = -inf

Time value that indicates pre-equilibration in the experiments table

petab.v2.C.TIME_STEADY_STATE = inf

Time value that indicates steady-state measurements

petab.v2.C.TIME_SYMBOL = 'time'

The time symbol for use in any PEtab-specific mathematical expressions

petab.v2.C.UNIFORM = 'uniform'

Uniform distribution

petab.v2.C.UPPER_BOUND = 'upperBound'

Upper bound column in the parameter table

petab.v2.C.VISUALIZATION_FILES = 'visualization_files'

Visualization files key in the YAML file