petab.C
This file contains constant definitions.
Module Attributes
Time value that indicates steady-state measurements |
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Mandatory columns of measurement table |
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Optional columns of measurement table |
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Measurement table columns |
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Mandatory columns of parameter table |
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Optional columns of parameter table |
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Parameter table columns |
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Mandatory columns of observables table |
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Optional columns of observables table |
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Observables table columns |
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Supported observable transformations |
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Supported prior types |
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Supported noise distributions |
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Mandatory columns of visualization table |
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Optional columns of visualization table |
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Visualization table columns |
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Visualization table columns that contain subplot specifications |
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Visualization table columns that contain single plot specifications |
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Supported plot types |
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Supported settings for handling replicates |
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- 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.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.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.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_VALUES = 'xValues'
- petab.C.Y_LABEL = 'yLabel'
- petab.C.Y_OFFSET = 'yOffset'
- petab.C.Y_SCALE = 'yScale'
- petab.C.Y_VALUES = 'yValues'