amici.petab_import_pysb.PysbPetabProblem¶
-
class
amici.petab_import_pysb.
PysbPetabProblem
(pysb_model=None, *args, **kwargs)[source]¶ Representation of a PySB-model-based PEtab problem
This class extends
petab.Problem
with a PySB model. The model is augmented with the observation model based on the PEtab observable table. For now, a dummy SBML model is created which allows used the existing SBML-PEtab API.- Variables
pysb_model – PySB model instance from of this PEtab problem.
-
__init__
(pysb_model=None, *args, **kwargs)[source] Constructor
- Parameters
pysb_model (
typing.Optional
[pysb.core.Model
]) – PySB model instance for this PEtab problemargs – See
petab.Problem.__init__()
kwargs – See
petab.Problem.__init__()
Methods Summary
__init__
([pysb_model])Constructor
create_parameter_df
(*args, **kwargs)Create a new PEtab parameter table
from_combine
(filename)Read PEtab COMBINE archive (http://co.mbine.org/documents/archive).
from_files
([condition_file, …])Factory method to load model and tables from files.
from_folder
(folder[, model_name])Factory method to use the standard folder structure and file names, i.e.
from_yaml
(yaml_config)Factory method to load model and tables as specified by YAML file.
get_lb
([free, fixed, scaled])Generic function to get lower parameter bounds.
See petab.sbml.get_model_parameters
See get_noise_distributions.
Returns dictionary of observable ids.
get_observables
([remove])Returns dictionary of observables definitions.
Return list of optimization parameter scaling strings.
Return list of optimization parameter IDs.
See get_simulation_to_optimization_parameter_mapping.
get_sigmas
([remove])Return dictionary of observableId => sigma as defined in the SBML model.
See petab.get_simulation_conditions
get_ub
([free, fixed, scaled])Generic function to get upper parameter bounds.
get_x_ids
([free, fixed])Generic function to get parameter ids.
get_x_nominal
([free, fixed, scaled])Generic function to get parameter nominal values.
sample_parameter_startpoints
([n_starts])Create starting points for optimization
to_files
([sbml_file, condition_file, …])Write PEtab tables to files for this problem
Attributes
lb
Parameter table lower bounds.
lb_scaled
Parameter table lower bounds with applied parameter scaling
ub
Parameter table upper bounds
ub_scaled
Parameter table upper bounds with applied parameter scaling
x_fixed_ids
Parameter table parameter IDs, for fixed parameters.
x_fixed_indices
Parameter table non-estimated parameter indices.
x_free_ids
Parameter table parameter IDs, for free parameters.
x_free_indices
Parameter table estimated parameter indices.
x_ids
Parameter table parameter IDs
x_nominal
Parameter table nominal values
x_nominal_fixed
Parameter table nominal values, for fixed parameters.
x_nominal_fixed_scaled
Parameter table nominal values with applied parameter scaling, for fixed parameters.
x_nominal_free
Parameter table nominal values, for free parameters.
x_nominal_free_scaled
Parameter table nominal values with applied parameter scaling, for free parameters.
x_nominal_scaled
Parameter table nominal values with applied parameter scaling
Methods
-
__init__
(pysb_model=None, *args, **kwargs)[source]¶ Constructor
- Parameters
pysb_model (
typing.Optional
[pysb.core.Model
]) – PySB model instance for this PEtab problemargs – See
petab.Problem.__init__()
kwargs – See
petab.Problem.__init__()
-
create_parameter_df
(*args, **kwargs)¶ Create a new PEtab parameter table
See create_parameter_df
-
static
from_combine
(filename)¶ Read PEtab COMBINE archive (http://co.mbine.org/documents/archive).
See also
create_combine_archive
.- Parameters
filename (
str
) – Path to the PEtab-COMBINE archive- Return type
- Returns
A
petab.Problem
instance.
-
static
from_files
(condition_file=None, measurement_file=None, parameter_file=None, visualization_files=None, observable_files=None, pysb_model_file=None)[source]¶ Factory method to load model and tables from files.
- Parameters
condition_file (
typing.Optional
[str
]) – PEtab condition tablemeasurement_file (
typing.Union
[str
,typing.Iterable
[str
],None
]) – PEtab measurement tableparameter_file (
typing.Union
[str
,typing.List
[str
],None
]) – PEtab parameter tablevisualization_files (
typing.Union
[str
,typing.Iterable
[str
],None
]) – PEtab visualization tablesobservable_files (
typing.Union
[str
,typing.Iterable
[str
],None
]) – PEtab observables tablespysb_model_file (
typing.Optional
[str
]) – PySB model file
- Return type
-
static
from_folder
(folder, model_name=None)¶ 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 (
str
) – Path to the directory in which the files are located.model_name (
typing.Optional
[str
]) – If specified, overrides the model component in the file names. Defaults to the last component offolder
.
- Return type
-
static
from_yaml
(yaml_config)[source]¶ Factory method to load model and tables as specified by YAML file.
NOTE: The PySB model is currently expected in the YAML file under
sbml_files
.- Parameters
yaml_config (
typing.Union
[typing.Dict
,str
]) – PEtab configuration as dictionary or YAML file name- Return type
-
get_lb
(free=True, fixed=True, scaled=False)¶ Generic function to get lower parameter bounds.
- Parameters
- Returns
The lower parameter bounds.
- Return type
v
-
get_model_parameters
()¶ See petab.sbml.get_model_parameters
-
get_noise_distributions
()¶ See get_noise_distributions.
-
get_observable_ids
()¶ Returns dictionary of observable ids.
-
get_observables
(remove=False)¶ Returns dictionary of observables definitions. See assignment_rules_to_dict for details.
-
get_optimization_parameter_scales
()¶ Return list of optimization parameter scaling strings.
See
petab.parameters.get_optimization_parameters
.
-
get_optimization_parameters
()¶ Return list of optimization parameter IDs.
See
petab.parameters.get_optimization_parameters
.
-
get_optimization_to_simulation_parameter_mapping
(warn_unmapped=True, scaled_parameters=False)¶ See get_simulation_to_optimization_parameter_mapping.
-
get_sigmas
(remove=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
-
get_ub
(free=True, fixed=True, scaled=False)¶ Generic function to get upper parameter bounds.
- Parameters
- Returns
The upper parameter bounds.
- Return type
v
-
get_x_ids
(free=True, fixed=True)¶ Generic function to get parameter ids.
-
get_x_nominal
(free=True, fixed=True, scaled=False)¶ Generic function to get parameter nominal values.
- Parameters
- Returns
The parameter nominal values.
- Return type
v
-
sample_parameter_startpoints
(n_starts=100)¶ Create starting points for optimization
See sample_parameter_startpoints
-
to_files
(sbml_file=None, condition_file=None, measurement_file=None, parameter_file=None, visualization_file=None, observable_file=None, yaml_file=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 (
typing.Optional
[str
]) – SBML model destinationcondition_file (
typing.Optional
[str
]) – Condition table destinationmeasurement_file (
typing.Optional
[str
]) – Measurement table destinationparameter_file (
typing.Optional
[str
]) – Parameter table destinationvisualization_file (
typing.Optional
[str
]) – Visualization table destinationobservable_file (
typing.Optional
[str
]) – Observables table destinationyaml_file (
typing.Optional
[str
]) – YAML file destination
- Raises
ValueError – If a destination was provided for a non-existing
entity. –
- Return type