petab.problem

PEtab Problem class

Functions

get_default_condition_file_name(model_name, …) Get file name according to proposed convention
get_default_measurement_file_name(…) Get file name according to proposed convention
get_default_parameter_file_name(model_name, …) Get file name according to proposed convention
get_default_sbml_file_name(model_name, folder) Get file name according to proposed convention

Classes

Problem(sbml_model, sbml_reader, …) PEtab parameter estimation problem as defined by
class petab.problem.Problem(sbml_model: libsbml.Model = None, sbml_reader: libsbml.SBMLReader = None, sbml_document: libsbml.SBMLDocument = None, condition_df: pandas.core.frame.DataFrame = None, measurement_df: pandas.core.frame.DataFrame = None, parameter_df: pandas.core.frame.DataFrame = None, visualization_df: pandas.core.frame.DataFrame = None, observable_df: pandas.core.frame.DataFrame = None)

Bases: object

PEtab parameter estimation problem as defined by

  • SBML model
  • condition table
  • measurement table
  • parameter table
  • observables table

Optionally it may contain visualization tables.

condition_df

PEtab condition table

measurement_df

PEtab measurement table

parameter_df

PEtab parameter table

observable_df

PEtab observable table

visualization_df

PEtab visualization table

sbml_reader

Stored to keep object alive.

sbml_document

Stored to keep object alive.

sbml_model

PEtab SBML model

create_parameter_df(*args, **kwargs)

Create a new PEtab parameter table

See create_parameter_df

static from_files(sbml_file: str = None, condition_file: str = None, measurement_file: Union[str, Iterable[str]] = None, parameter_file: str = None, visualization_files: Union[str, Iterable[str]] = None, observable_files: Union[str, Iterable[str]] = None) → petab.problem.Problem

Factory method to load model and tables from files.

Parameters:
  • sbml_file – PEtab SBML model
  • condition_file – PEtab condition table
  • measurement_file – PEtab measurement table
  • parameter_file – PEtab parameter table
  • visualization_files – PEtab visualization tables
  • observable_files – PEtab observables tables
static from_folder(folder: str, model_name: str = None) → petab.problem.Problem

Factory method to use the standard folder structure and file names, i.e.

${model_name}/
  +-- experimentalCondition_${model_name}.tsv
  +-- measurementData_${model_name}.tsv
  +-- model_${model_name}.xml
  +-- parameters_${model_name}.tsv
Parameters:
  • folder – Path to the directory in which the files are located.
  • model_name – If specified, overrides the model component in the file names. Defaults to the last component of folder.
static from_yaml(yaml_config: Union[Dict[KT, VT], str]) → petab.problem.Problem

Factory method to load model and tables as specified by YAML file.

Parameters:yaml_config – PEtab configuration as dictionary or YAML file name
get_dynamic_simulation_parameters()

See get_model_parameters

get_noise_distributions()

See get_noise_distributions.

get_observables(remove: bool = False)

Returns dictionary of observables definitions See assignment_rules_to_dict for details.

get_optimization_parameters()

Return list of optimization parameter IDs.

See get_optimization_parameters.

get_optimization_to_simulation_parameter_mapping(warn_unmapped: bool = True)

See get_simulation_to_optimization_parameter_mapping.

get_sigmas(remove: bool = False)

Return dictionary of observableId => sigma as defined in the SBML model. This does not include parameter mappings defined in the measurement table.

get_simulation_conditions_from_measurement_df()

See petab.get_simulation_conditions

lb

Parameter table lower bounds

lb_scaled

Parameter table lower bounds with applied parameter scaling

sample_parameter_startpoints(n_starts: int = 100)

Create starting points for optimization

See sample_parameter_startpoints

to_files(sbml_file: Optional[str] = None, condition_file: Optional[str] = None, measurement_file: Optional[str] = None, parameter_file: Optional[str] = None, visualization_file: Optional[str] = None, observable_file: Optional[str] = None) → None

Write PEtab tables to files for this problem

Writes PEtab files for those entities for which a destination was passed.

NOTE: If this instance was created from multiple measurement or visualization tables, they will be merged and written to a single file.

Parameters:
  • sbml_file – SBML model destination
  • condition_file – Condition table destination
  • measurement_file – Measurement table destination
  • parameter_file – Parameter table destination
  • visualization_file – Visualization table destination
  • observable_file – Observables table destination
Raises:
  • ValueError – If a destination was provided for a non-existing
  • entity.
ub

Parameter table upper bounds

ub_scaled

Parameter table upper bounds with applied parameter scaling

x_fixed_indices

Parameter table non-estimated parameter indices

x_fixed_vals

Nominal values for parameter table non-estimated parameters

x_ids

Parameter table parameter IDs

x_nominal

Parameter table nominal values

x_nominal_scaled

Parameter table nominal values with applied parameter scaling

petab.problem.get_default_condition_file_name(model_name: str, folder: str = '')

Get file name according to proposed convention

petab.problem.get_default_measurement_file_name(model_name: str, folder: str = '')

Get file name according to proposed convention

petab.problem.get_default_parameter_file_name(model_name: str, folder: str = '')

Get file name according to proposed convention

petab.problem.get_default_sbml_file_name(model_name: str, folder: str = '')

Get file name according to proposed convention