vivarium.compartments.antibiotics module

class vivarium.compartments.antibiotics.Antibiotics(config)

Bases: vivarium.core.process.Generator

defaults = {'antibiotic_transport': {'initial_external_antibiotic': 1, 'initial_internal_antibiotic': 0.5, 'initial_pump': 0.0, 'pump_kcat': 0.0005}, 'death': {'detectors': {'antibiotic': {'antibiotic_threshold': 0.95}}, 'targets': ['antibiotic_transport', 'growth', 'expression', 'death', 'division']}, 'diffusion': {'default_state': {'external': {'antibiotic': 1}, 'internal': {'antibiotic': 0.5}, 'membrane': {'porin': 1e-20}}, 'molecules_to_diffuse': ['antibiotic'], 'permeability_per_porin': {'porin': 0.005}}, 'dimensions_path': ('dimensions',), 'division': {}, 'fields_path': ('fields',), 'growth': {'growth_rate': 0.00028881132523331054}, 'ode_expression': {'degradation_rates': {'AcrAB-TolC': 0.001, 'AcrAB-TolC_RNA': 1.0}, 'protein_map': {'AcrAB-TolC': 'AcrAB-TolC_RNA'}, 'transcription_rates': {'AcrAB-TolC_RNA': 0.001}, 'translation_rates': {'AcrAB-TolC': 1.0}}}

generate_processes(config)

generate_topology(config)

name = 'antibiotics_compartment'

vivarium.compartments.antibiotics.main()

vivarium.compartments.antibiotics.run_antibiotics_composite()

vivarium.compartments.antibiotics.test_antibiotics_composite_similar_to_reference()