BioMASS model object (biomass.model_object)

class biomass.model_object.ModelObject(path, biomass_model)

The BioMASS model object.

Examples

>>> from biomass import create_model
>>> from biomass.models import mapk_cascade
>>> model = create_model(mapk_cascade.__package__)
>>> type(model)
<class 'biomass.model_object.ModelObject'>
>>> print('Parameters:', len(model.parameters))
Parameters: 22
>>> print('Species:', len(model.species))
Species: 8
>>> print('Observables:', len(model.observables))
Observables: 2
gene2val(indiv_gene)

Convert gene to actual value. Mainly used in parameter estimation.

Parameters:

indiv_gene (numpy.ndarray) – Individual gene.

Returns:

indiv_values – Corresponding values.

Return type:

numpy.ndarray

get_executable()

Get executable parameter sets from optimization results.

Return type:

List[int]

get_individual(paramset_id)

Get estimated parameter values from optimization results.

Parameters:

paramset_id (int) – Index of parameter set.

Returns:

best_individual – Estimated parameter values.

Return type:

numpy.ndarray

get_obj_val(indiv_gene)

An objective function to minimize in parameter estimation.

Parameters:

indiv_gene (numpy.ndarray) – Genes, not parameter values.

Returns:

obj_val – Objective function value.

Return type:

float

load_param(paramset)

Load a parameter set from optimization results.

Parameters:

paramset (int) – Index of parameter set.

Returns:

optimized_values – Optimized parameter/initial values.

Return type:

biomass.model_object.OptimizedValues