biosimulators-utils 0.1.59

Command-line program and library for reading, writing, validating and executing modeling projects (COMBINE/OMEX archives with SED-ML files).

BioSimulators utils

Command-line application and high-level utilities for reading, writing, validating, and executing COMBINE/OMEX format files that contain descriptions of simulations in Simulation Experiment Description Markup Language (SED-ML) format with models in formats such as the BioNetGen Language (BNGL) and the Systems Biology Markup Language (SBML).

Installation

Requirements

• Python >= 3.7

• pip

Optional requirements

• Docker: required to execute containerized simulation tools

Install latest release from PyPI

pip install biosimulators-utils

Install latest revision from GitHub

pip install git+https://github.com/biosimulators/Biosimulators_utils.git#biosimulators_utils

Installation optional features

To use BioSimulators utils to validate SBML models, install BioSimulators utils with the sbml option:

pip install biosimulators-utils[sbml]

To use BioSimulators utils to execute containerized simulation tools, install BioSimulators utils with the containers option:

pip install biosimulators-utils[containers]

To use BioSimulators utils to log the standard output and error produced by simulation tools, install BioSimulators utils with the logging option:

pip install biosimulators-utils[logging]

API documentation

API documentation is available here.

License

This package is released under the MIT license.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York and the Center for Reproducible Biomedical Modeling.

Contributing to BioSimulators utils

We enthusiastically welcome contributions to BioSimulators utils! Please see the guide to contributing and the developer’s code of conduct.

Acknowledgements

This work was supported by National Institutes of Health award P41EB023912.

Questions and comments

Please contact the BioSimulators Team with any questions or comments.