Getting Started

Installation

The easiest way to install BioCompose is using pip:

pip install bio-compose

Verification

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

Running OMEX verifications:

import bio_compose as bc

filepath = '/path/to/a/valid/omex/file.omex'

verification = bc.verify(filepath)

Running SBML verifications:

import bio_compose as bc

filepath = '/path/to/a/valid/sbml/file.xml'
start_time = 0
duration = 100
n_steps = 1000

verification = bc.verify(filepath, start_time, duration, n_steps)

Visualizing verifications:

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

Verifications for OMEX or SBML files can also be executed using the command-line interface which is installed with the package:

verify /path/to/a/valid/omex/file.omex