Verification

Running a verification with bio-compose can be achieved in a few simple steps.

Running OMEX verifications:

from bio_compose import verify

filepath = '/path/to/a/valid/omex/file.omex'
simulators = ['amici', 'copasi', 'tellurium']

verification = verify(filepath, simulators)

Running SBML verifications:

from bio_compose import verify

filepath = '/path/to/a/valid/sbml/file.xml'
simulators = ['amici', 'copasi', 'tellurium']
start_time = 0
duration = 100
n_steps = 1000

verification = verify(filepath, start_time, duration, n_steps, simulators)

Visualizing verifications:

verification.observables()  # visualize observables
verification.rmse(save_dest='/my/save/path/for/observables')  # visualize root-mean-square error scores for all simulators involved in the verification.