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