petab - a Python package for handling PEtab files
PEtab is a data format for specifying
parameter estimation problems in systems biology. This repository provides
the petab Python package for reading, writing and validating PEtab files.
Documentation
Documentation of the petab Python package is available at
https://libpetab-python.readthedocs.io/en/latest/.
Documentation of the PEtab format in general is available at
https://petab.readthedocs.io/en/latest/.
Installation
The PEtab library is available on pypi and the easiest way to install it is running
pip3 install petab
It will require Python>=3.10 to run. (We are following the numpy Python support policy).
Development versions of the PEtab library can be installed using
pip3 install https://github.com/PEtab-dev/libpetab-python/archive/develop.zip
(replace develop by the branch or commit you would like to install).
When setting up a new parameter estimation problem, the most useful tools will be:
The PEtab validator, which is automatically installed using Python entrypoints to be available as a shell command from anywhere, called
petablintpetab.create_parameter_df to create the parameter table, once you have set up the model, condition table, observable table and measurement table
petab.create_combine_archive to create a COMBINE Archive from PEtab files
Examples
Examples for PEtab Python library usage:
Getting help
If you have any questions or problems with this package, feel free to post them at our GitHub issue tracker.
Contributing
Contributions and feedback to this package are very welcome, see our contribution guide.
Python package
- API Reference
- petab
- petab.v1
CompositeProblemParMappingDictParMappingDictQuadrupleParMappingDictTupleProblemScaleMappingDictScaleMappingDictTupleSimulatorassert_all_parameters_present_in_parameter_df()assert_measured_observables_defined()assert_measurement_conditions_present_in_condition_table()assert_measurements_not_null()assert_measurements_numeric()assert_model_parameters_in_condition_or_parameter_table()assert_no_leading_trailing_whitespace()assert_noise_distributions_valid()assert_overrides_match_parameter_count()assert_parameter_bounds_are_numeric()assert_parameter_estimate_is_boolean()assert_parameter_id_is_string()assert_parameter_prior_parameters_are_valid()assert_parameter_prior_type_is_valid()assert_parameter_scale_is_valid()assert_single_condition_and_sbml_file()assert_unique_observable_ids()assert_unique_parameter_ids()calculate_chi2()calculate_chi2_for_table_from_residuals()calculate_llh()calculate_llh_for_table()calculate_residuals()calculate_residuals_for_table()calculate_single_llh()check_condition_df()check_ids()check_mapping_df()check_measurement_df()check_observable_df()check_parameter_bounds()check_parameter_df()concat_tables()condition_table_is_parameter_free()create_combine_archive()create_condition_df()create_measurement_df()create_observable_df()create_parameter_df()create_problem_yaml()evaluate_noise_formula()flatten_timepoint_specific_output_overrides()get_condition_df()get_formula_placeholders()get_mapping_df()get_measurement_df()get_measurement_parameter_ids()get_model_for_condition()get_model_parameters()get_notnull_columns()get_observable_df()get_optimization_parameter_scaling()get_optimization_parameters()get_optimization_to_simulation_parameter_mapping()get_output_parameters()get_parameter_df()get_parameter_mapping_for_condition()get_parametric_overrides()get_path_prefix()get_placeholders()get_priors_from_df()get_rows_for_condition()get_sbml_model()get_simulation_conditions()get_simulation_df()get_symbolic_noise_formulas()get_valid_parameters_for_parameter_table()get_visualization_df()globalize_parameters()handle_missing_overrides()is_composite_problem()is_empty()is_sbml_consistent()is_scalar_float()is_valid_identifier()lint_problem()load_sbml_from_file()load_sbml_from_string()load_yaml()log_sbml_errors()map_scale()map_unscale()measurement_is_at_steady_state()measurement_table_has_observable_parameter_numeric_overrides()measurement_table_has_timepoint_specific_mappings()measurements_have_replicates()merge_preeq_and_sim_pars()merge_preeq_and_sim_pars_condition()normalize_parameter_df()observable_table_has_nontrivial_noise_formula()resolve_mapping()sample_from_prior()sample_noise()sample_parameter_startpoints()scale()split_parameter_replacement_list()to_float_if_float()unflatten_simulation_df()unique_preserve_order()unscale()validate()validate_yaml_semantics()validate_yaml_syntax()write_condition_df()write_mapping_df()write_measurement_df()write_observable_df()write_parameter_df()write_sbml()write_simulation_df()write_visualization_df()write_yaml()- petab.v1.C
- petab.v1.calculate
- petab.v1.composite_problem
- petab.v1.conditions
- petab.v1.core
- petab.v1.format_version
- petab.v1.lint
- petab.v1.mapping
- petab.v1.math
- petab.v1.measurements
- petab.v1.models
- petab.v1.observables
- petab.v1.parameter_mapping
- petab.v1.parameters
- petab.v1.problem
- petab.v1.sampling
- petab.v1.sbml
- petab.v1.simplify
- petab.v1.simulate
- petab.v1.visualize
- petab.v1.yaml
- petab.v1.C
BAR_PLOTCONDITION_FILESCONDITION_IDCONDITION_NAMEDATASET_IDESTIMATEFORMAT_VERSIONINITIALIZATIONINITIALIZATION_PRIOR_PARAMETERSINITIALIZATION_PRIOR_TYPELAPLACELEGEND_ENTRYLINLINE_PLOTLOGLOG10LOG_LAPLACELOG_NORMALLOWER_BOUNDMEASUREMENTMEASUREMENT_DF_COLSMEASUREMENT_DF_OPTIONAL_COLSMEASUREMENT_DF_REQUIRED_COLSMEASUREMENT_FILESNOISE_DISTRIBUTIONNOISE_FORMULANOISE_MODELSNOISE_PARAMETERSNOISE_VALUENOMINAL_VALUENORMALOBJECTIVEOBJECTIVE_PRIOR_PARAMETERSOBJECTIVE_PRIOR_TYPEOBSERVABLE_DF_COLSOBSERVABLE_DF_OPTIONAL_COLSOBSERVABLE_DF_REQUIRED_COLSOBSERVABLE_FILESOBSERVABLE_FORMULAOBSERVABLE_IDOBSERVABLE_NAMEOBSERVABLE_PARAMETERSOBSERVABLE_TRANSFORMATIONOBSERVABLE_TRANSFORMATIONSPARAMETER_DF_COLSPARAMETER_DF_OPTIONAL_COLSPARAMETER_DF_REQUIRED_COLSPARAMETER_FILEPARAMETER_IDPARAMETER_NAMEPARAMETER_SCALEPARAMETER_SCALE_LAPLACEPARAMETER_SCALE_NORMALPARAMETER_SCALE_UNIFORMPARAMETER_SEPARATORPLOT_IDPLOT_NAMEPLOT_TYPES_DATAPLOT_TYPES_SIMULATIONPLOT_TYPE_DATAPLOT_TYPE_SIMULATIONPREEQUILIBRATION_CONDITION_IDPRIOR_TYPESPROBLEMSPROVIDEDREPLICATEREPLICATE_IDRESIDUALSBML_FILESSCATTER_PLOTSIMULATIONSIMULATION_CONDITION_IDTIMETIME_STEADY_STATEUNIFORMUPPER_BOUNDVISUALIZATION_DF_COLSVISUALIZATION_DF_OPTIONAL_COLSVISUALIZATION_DF_REQUIRED_COLSVISUALIZATION_DF_SINGLE_PLOT_LEVEL_COLSVISUALIZATION_DF_SUBPLOT_LEVEL_COLSVISUALIZATION_FILESX_LABELX_OFFSETX_SCALEX_SCALESX_VALUESY_LABELY_OFFSETY_SCALEY_SCALESY_VALUES
- petab.v1.calculate
- petab.v1.composite_problem
- petab.v1.conditions
- petab.v1.core
- petab.v1.lint
assert_all_parameters_present_in_parameter_df()assert_measured_observables_defined()assert_measurement_conditions_present_in_condition_table()assert_measurements_not_null()assert_measurements_numeric()assert_model_parameters_in_condition_or_parameter_table()assert_no_leading_trailing_whitespace()assert_noise_distributions_valid()assert_parameter_bounds_are_numeric()assert_parameter_estimate_is_boolean()assert_parameter_id_is_string()assert_parameter_prior_parameters_are_valid()assert_parameter_prior_type_is_valid()assert_parameter_scale_is_valid()assert_unique_observable_ids()assert_unique_parameter_ids()check_condition_df()check_ids()check_measurement_df()check_observable_df()check_parameter_bounds()check_parameter_df()condition_table_is_parameter_free()is_scalar_float()is_valid_identifier()lint_problem()measurement_table_has_observable_parameter_numeric_overrides()measurement_table_has_timepoint_specific_mappings()observable_table_has_nontrivial_noise_formula()
- petab.v1.measurements
- petab.v1.models
- petab.v1.observables
- petab.v1.parameter_mapping
- petab.v1.parameters
- petab.v1.problem
- petab.v1.sampling
- petab.v1.sbml
- petab.v1.simulate
- petab.v1.simplify
- petab.v1.visualize
- Visualize
DataProviderFigureMPLPlotterplot_goodness_of_fit()plot_problem()plot_residuals_vs_simulation()plot_with_vis_spec()plot_without_vis_spec()- petab.v1.visualize.cli
- petab.v1.visualize.data_overview
- petab.v1.visualize.helper_functions
- petab.v1.visualize.lint
- petab.v1.visualize.plot_data_and_simulation
- petab.v1.visualize.plot_residuals
- petab.v1.visualize.plotter
- petab.v1.visualize.plotting
- petab.v1.yaml
- petab.v2
CompositeProblemParMappingDictParMappingDictQuadrupleParMappingDictTupleProblemScaleMappingDictScaleMappingDictTupleSimulatorassert_all_parameters_present_in_parameter_df()assert_measured_observables_defined()assert_measurement_conditions_present_in_condition_table()assert_measurements_not_null()assert_measurements_numeric()assert_model_parameters_in_condition_or_parameter_table()assert_no_leading_trailing_whitespace()assert_noise_distributions_valid()assert_overrides_match_parameter_count()assert_parameter_bounds_are_numeric()assert_parameter_estimate_is_boolean()assert_parameter_id_is_string()assert_parameter_prior_parameters_are_valid()assert_parameter_prior_type_is_valid()assert_parameter_scale_is_valid()assert_single_condition_and_sbml_file()assert_unique_observable_ids()assert_unique_parameter_ids()calculate_chi2()calculate_chi2_for_table_from_residuals()calculate_llh()calculate_llh_for_table()calculate_residuals()calculate_residuals_for_table()calculate_single_llh()check_condition_df()check_ids()check_mapping_df()check_measurement_df()check_observable_df()check_parameter_bounds()check_parameter_df()concat_tables()condition_table_is_parameter_free()create_combine_archive()create_condition_df()create_measurement_df()create_observable_df()create_parameter_df()create_problem_yaml()evaluate_noise_formula()flatten_timepoint_specific_output_overrides()get_condition_df()get_formula_placeholders()get_mapping_df()get_measurement_df()get_measurement_parameter_ids()get_model_for_condition()get_model_parameters()get_notnull_columns()get_observable_df()get_optimization_parameter_scaling()get_optimization_parameters()get_optimization_to_simulation_parameter_mapping()get_output_parameters()get_parameter_df()get_parameter_mapping_for_condition()get_parametric_overrides()get_path_prefix()get_placeholders()get_priors_from_df()get_rows_for_condition()get_sbml_model()get_simulation_conditions()get_simulation_df()get_symbolic_noise_formulas()get_valid_parameters_for_parameter_table()get_visualization_df()globalize_parameters()handle_missing_overrides()is_composite_problem()is_empty()is_sbml_consistent()is_scalar_float()is_valid_identifier()lint_problem()load_sbml_from_file()load_sbml_from_string()load_yaml()log_sbml_errors()map_scale()map_unscale()measurement_is_at_steady_state()measurement_table_has_observable_parameter_numeric_overrides()measurement_table_has_timepoint_specific_mappings()measurements_have_replicates()merge_preeq_and_sim_pars()merge_preeq_and_sim_pars_condition()normalize_parameter_df()observable_table_has_nontrivial_noise_formula()resolve_mapping()sample_from_prior()sample_noise()sample_parameter_startpoints()scale()split_parameter_replacement_list()to_float_if_float()unflatten_simulation_df()unique_preserve_order()unscale()validate()validate_yaml_semantics()validate_yaml_syntax()warn()write_condition_df()write_mapping_df()write_measurement_df()write_observable_df()write_parameter_df()write_sbml()write_simulation_df()write_visualization_df()write_yaml()- petab.v2.C
- petab.v2.lint
- petab.v2.petab1to2
- petab.v2.problem
- petab.v2.C
BAR_PLOTCONDITION_FILESCONDITION_IDCONDITION_NAMEDATASET_IDESTIMATEEXTENSIONSFORMAT_VERSIONINITIALIZATIONINITIALIZATION_PRIOR_PARAMETERSINITIALIZATION_PRIOR_TYPELAPLACELEGEND_ENTRYLINLINE_PLOTLOGLOG10LOG_LAPLACELOG_NORMALLOWER_BOUNDMAPPING_DF_REQUIRED_COLSMAPPING_FILESMEASUREMENTMEASUREMENT_DF_COLSMEASUREMENT_DF_OPTIONAL_COLSMEASUREMENT_DF_REQUIRED_COLSMEASUREMENT_FILESMODEL_ENTITY_IDMODEL_FILESMODEL_LANGUAGEMODEL_LOCATIONNOISE_DISTRIBUTIONNOISE_FORMULANOISE_MODELSNOISE_PARAMETERSNOISE_VALUENOMINAL_VALUENORMALOBJECTIVEOBJECTIVE_PRIOR_PARAMETERSOBJECTIVE_PRIOR_TYPEOBSERVABLE_DF_COLSOBSERVABLE_DF_OPTIONAL_COLSOBSERVABLE_DF_REQUIRED_COLSOBSERVABLE_FILESOBSERVABLE_FORMULAOBSERVABLE_IDOBSERVABLE_NAMEOBSERVABLE_PARAMETERSOBSERVABLE_TRANSFORMATIONOBSERVABLE_TRANSFORMATIONSPARAMETER_DF_COLSPARAMETER_DF_OPTIONAL_COLSPARAMETER_DF_REQUIRED_COLSPARAMETER_FILEPARAMETER_IDPARAMETER_NAMEPARAMETER_SCALEPARAMETER_SCALE_LAPLACEPARAMETER_SCALE_NORMALPARAMETER_SCALE_UNIFORMPARAMETER_SEPARATORPETAB_ENTITY_IDPLOT_IDPLOT_NAMEPLOT_TYPES_DATAPLOT_TYPES_SIMULATIONPLOT_TYPE_DATAPLOT_TYPE_SIMULATIONPREEQUILIBRATION_CONDITION_IDPRIOR_TYPESPROBLEMSPROVIDEDREPLICATEREPLICATE_IDRESIDUALSCATTER_PLOTSIMULATIONSIMULATION_CONDITION_IDTIMETIME_STEADY_STATEUNIFORMUPPER_BOUNDVISUALIZATION_DF_COLSVISUALIZATION_DF_OPTIONAL_COLSVISUALIZATION_DF_REQUIRED_COLSVISUALIZATION_DF_SINGLE_PLOT_LEVEL_COLSVISUALIZATION_DF_SUBPLOT_LEVEL_COLSVISUALIZATION_FILESX_LABELX_OFFSETX_SCALEX_SCALESX_VALUESY_LABELY_OFFSETY_SCALEY_SCALESY_VALUES
- petab.v2.lint
CheckAllParametersPresentInParameterTableCheckConditionTableCheckMeasurementTableCheckModelCheckObservableTableCheckParameterTableCheckTableExistsCheckValidParameterInConditionOrParameterTableCheckVisualizationTableValidationErrorValidationIssueValidationIssueSeverityValidationResultListValidationTaskdefault_validation_taskslint_problem()
- petab.v2.problem
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