ecoli.experiments.metabolism_redux_sim
Metabolism using user-friendly FBA
- ecoli.experiments.metabolism_redux_sim.run_colony(filename='metabolism_redux_classic', total_time=1400, divide=True, progress_bar=True, log_updates=False, emitter='timeseries', name='metabolism-redux-classic-rich', raw_output=False, save=True, save_times=[1, 200, 400, 1300], condition='with_aa', fixed_media='minimal_plus_amino_acids')[source]
- ecoli.experiments.metabolism_redux_sim.run_ecoli_with_default_metabolism(filename='default', total_time=10, divide=False, progress_bar=True, log_updates=False, emitter='timeseries')[source]
- ecoli.experiments.metabolism_redux_sim.run_ecoli_with_metabolism_redux(filename='metabolism_redux', total_time=5000, divide=True, initial_state_file='wcecoli_t0', progress_bar=True, log_updates=False, emitter='timeseries', name='metabolism-redux', raw_output=False, save=False)[source]
- ecoli.experiments.metabolism_redux_sim.run_ecoli_with_metabolism_redux_classic(filename='metabolism_redux_classic', total_time=10, divide=True, progress_bar=True, log_updates=False, emitter='timeseries', name='convex_kinetics_minimal', raw_output=False, save=True, save_times=[1, 10], condition='basal', fixed_media='minimal')[source]