vivarium.compartments.transport_metabolism module

class vivarium.compartments.transport_metabolism.TransportMetabolism(config=None)

Bases: vivarium.core.process.Generator

Transport/Metabolism Compartment, with ODE expression

defaults = {'agents_path': ('agents',), 'boundary_path': ('boundary',), 'daughter_path': (), 'dimensions_path': ('dimensions',), 'divide': True, 'division': {}, 'expression': {'degradation_rates': {'LacY': 3e-05, 'lacy_RNA': 0.003}, 'initial_state': {'external': {'glc__D_e': 8.0, 'lcts_e': 8.0}, 'internal': {'LacY': 0.0, 'lacy_RNA': 0.0}}, 'protein_map': {'LacY': 'lacy_RNA'}, 'regulation': {'lacy_RNA': 'if (external, glc__D_e) > 0.005 and (internal, lcts_p) < 0.05'}, 'regulators': [('external', 'glc__D_e'), ('internal', 'lcts_p')], 'time_step': 5, 'transcription_leak': {'magnitude': 1e-06, 'rate': 7e-05}, 'transcription_rates': {'lacy_RNA': 1e-07}, 'translation_rates': {'LacY': 0.005}}, 'fields_path': ('fields',), 'metabolism': {'initial_mass': 1339.0, 'model_path': 'models/iAF1260b.json', 'time_step': 5, 'tolerance': {'EX_glc__D_e': [1.05, 1.0], 'EX_lcts_e': [1.05, 1.0]}}, 'transport': {'initial_state': {'external': {'glc__D_e': 10.0, 'lcts_e': 10.0}, 'internal': {'EIIglc': 0.0018, 'LacY': 0, 'g6p_c': 0.0, 'lcts_p': 0.0, 'pep_c': 0.18, 'pyr_c': 0.0}}, 'kinetic_parameters': {'EX_glc__D_e': {('internal', 'EIIglc'): {('external', 'glc__D_e'): 0.2, ('internal', 'pep_c'): None, 'kcat_f': 60.0}}, 'EX_lcts_e': {('internal', 'LacY'): {('external', 'lcts_e'): 0.1, 'kcat_f': 60.0}}}, 'ports': {'external': ['glc__D_e', 'lcts_e'], 'internal': ['g6p_c', 'pep_c', 'pyr_c', 'EIIglc', 'LacY', 'lcts_p']}, 'reactions': {'EX_glc__D_e': {'catalyzed by': [('internal', 'EIIglc')], 'is reversible': False, 'stoichiometry': {('external', 'glc__D_e'): -1.0, ('internal', 'g6p_c'): 1.0, ('internal', 'pep_c'): -1.0, ('internal', 'pyr_c'): 1.0}}, 'EX_lcts_e': {'catalyzed by': [('internal', 'LacY')], 'is reversible': False, 'stoichiometry': {('external', 'lcts_e'): -1.0, ('internal', 'lcts_p'): 1.0}}}, 'time_step': 5}}

generate_processes(config)

generate_topology(config)

name = 'transport_metabolism'

vivarium.compartments.transport_metabolism.analyze_transport_metabolism(timeseries, config={}, out_dir='out')

vivarium.compartments.transport_metabolism.default_expression_config()

vivarium.compartments.transport_metabolism.default_metabolism_config()

vivarium.compartments.transport_metabolism.default_transport_config()

vivarium.compartments.transport_metabolism.get_metabolism_initial_state(scale_concentration=1, override={})

vivarium.compartments.transport_metabolism.scan_transport_metabolism()

vivarium.compartments.transport_metabolism.simulate_transport_metabolism(config={})

vivarium.compartments.transport_metabolism.test_txp_mtb_ge()