vivarium.parameters.parameters module

class vivarium.parameters.parameters.TestConvienceKinetics(config=None)

Bases: vivarium.core.process.Generator

defaults = {'boundary_path': ('boundary',), 'config': {'process': {'initial_state': {'fluxes': {'reaction1': 0.0}, 'internal': {'A': 100.0, 'B': 100.0, 'C': 100.0, 'E': 100.0}}, 'kinetic_parameters': {'reaction1': {('internal', 'E'): {'kcat_f': 10.0, ('internal', 'A'): 0.1, ('internal', 'B'): 0.1}}}, 'ports': {'external': [], 'internal': ['A', 'B', 'C', 'E']}, 'reactions': {'reaction1': {'catalyzed by': [('internal', 'E')], 'is reversible': False, 'stoichiometry': {('internal', 'A'): -1, ('internal', 'B'): -1, ('internal', 'C'): 2}}}}}}

generate_processes(config)

generate_topology(config)

vivarium.parameters.parameters.check_path_exists(path, dict)

vivarium.parameters.parameters.get_nested(dict, keys)

vivarium.parameters.parameters.get_parameters_logspace(min, max, number)

get list of n parameters logarithmically spaced between min and max

vivarium.parameters.parameters.organize_param_scan_results(data)

vivarium.parameters.parameters.parameter_scan(config)

Pass in a config (dict) with:

• compartment (object) – a compartment class, for configuration by the parameters

• scan_parameters (dict) – each parameter location (tuple) mapped to a list of values

• metrics (list) – a list of output values (tuple) with the (port, key)

• conditions (list) – a list of state values (dict) with {port: {variable: value}}

  for the default state the condition is and empty dict, [{}]

• settings (dict) – simulation settings for the experiments

Returns a list of all parameter combinations, and a dictionary with output values for those parameters

vivarium.parameters.parameters.plot_scan_results(results, out_dir='out', filename='parameter_scan')

vivarium.parameters.parameters.run_compartment_get_output(compartment, parameters, condition, metrics, settings)

vivarium.parameters.parameters.scan_test()

vivarium.parameters.parameters.set_nested(dict, keys, value, create_missing=True)