Simulation Runs

bio-compose has a run_simulation method that can be used to run either: a Smoldyn simulation OR a SBML simulation.

Running a Smoldyn simulation:

from bio_compose import run_simulation

filepath = '/path/to/a/valid/smoldyn/configuration/txt/file.txt'
duration = 10
dt = 0.02
result = run_simulation(filepath, duration, dt)

Running a SBML simulation:

from bio_compose import run_simulation

filepath = '/path/to/a/valid/sbml/file.xml'
simulator = 'copasi'
start_time = 0
duration = 100
n_steps = 1000
result = run_simulation(filepath, start_time, duration, n_steps, simulator)