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 |
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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)¶ Bases:
object
PEtab parameter estimation problem as defined by
- SBML model
- condition table
- measurement table
- parameter table
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condition_df
¶ PEtab condition table
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measurement_df
¶ PEtab measurement table
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parameter_df
¶ PEtab parameter table
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sbml_reader
¶ Stored to keep object alive.
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sbml_document
¶ Stored to keep object alive.
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sbml_model
¶ PEtab SBML model
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create_parameter_df
(*args, **kwargs)¶ Create a new PEtab parameter table
See create_parameter_df
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static
from_files
(sbml_file: str = None, condition_file: str = None, measurement_file: str = None, parameter_file: 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
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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
.
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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
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get_dynamic_simulation_parameters
()¶ See get_model_parameters
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get_noise_distributions
()¶ See get_noise_distributions.
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get_observables
(remove: bool = False)¶ Returns dictionary of observables definitions See assignment_rules_to_dict for details.
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get_optimization_parameters
()¶ Return list of optimization parameter IDs.
See get_optimization_parameters.
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get_optimization_to_simulation_parameter_mapping
(warn_unmapped: bool = True)¶ See get_simulation_to_optimization_parameter_mapping.
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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.
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get_simulation_conditions_from_measurement_df
()¶ See petab.get_simulation_conditions
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lb
¶ Parameter table lower bounds
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lb_scaled
¶ Parameter table lower bounds with applied parameter scaling
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sample_parameter_startpoints
(n_starts: int = 100)¶ Create starting points for optimization
See sample_parameter_startpoints
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ub
¶ Parameter table upper bounds
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ub_scaled
¶ Parameter table upper bounds with applied parameter scaling
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x_fixed_indices
¶ Parameter table non-estimated parameter indices
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x_fixed_vals
¶ Nominal values for parameter table non-estimated parameters
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x_ids
¶ Parameter table parameter IDs
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x_nominal
¶ Parameter table nominal values
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x_nominal_scaled
¶ Parameter table nominal values with applied parameter scaling
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petab.problem.
get_default_condition_file_name
(model_name: str, folder: str = '')¶ Get file name according to proposed convention
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petab.problem.
get_default_measurement_file_name
(model_name: str, folder: str = '')¶ Get file name according to proposed convention
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petab.problem.
get_default_parameter_file_name
(model_name: str, folder: str = '')¶ Get file name according to proposed convention
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petab.problem.
get_default_sbml_file_name
(model_name: str, folder: str = '')¶ Get file name according to proposed convention