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biosimulators / Biosimulators_utils

Utilities for building standardized command-line interfaces for biosimulation software packages
https://docs.biosimulators.org/Biosimulators_utils
MIT License
4 stars 6 forks source link
biosimulators combine computational-biology kisao mathematical-modeling omex python sed-ml simulation systems-biology

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Latest release PyPI CI status Test coverage Binder All Contributors

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

Optional requirements

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 BNGL models, install BioSimulators utils with the bgnl option:

pip install biosimulators-utils[bgnl]

To use BioSimulators utils to validate CellML models, install BioSimulators utils with the cellml option:

pip install biosimulators-utils[cellml]

To use BioSimulators utils to validate LEMS models, install Java and then install BioSimulators utils with the lems option:

pip install biosimulators-utils[lems]

To use BioSimulators utils to validate NeuroML models, install BioSimulators utils with the neuroml option:

pip install biosimulators-utils[neuroml]

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 validate SBML models, install BioSimulators utils with the smoldyn option:

pip install biosimulators-utils[smoldyn]

To use BioSimulators utils to convert Escher metabolic maps to Vega flux data visualizations, install BioSimulators utils with the escher option:

pip install biosimulators-utils[escher]

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]

Dockerfile and Docker image

This package is available in the ghcr.io/biosimulators/biosimulators Docker image. This image includes all of the optional dependencies and installation options.

To install and run this image, run the following commands:

docker pull ghcr.io/biosimulators/biosimulators
docker run -it --rm ghcr.io/biosimulators/biosimulators

This image includes this package, as well as standardized Python APIs for the simulation tools validated by BioSimulators. Because this image aims to incorporate as many simulation tools as possible within a single Python environment, this image may sometimes lag behind the latest version of this package.

The Dockerfile for this image is available here.

Tutorials

Command-line interface

A tutorial for the command-line interface is available here.

Python API

Interactive tutorials for using BioSimulators-utils and Python APIs for simulation tools to execute simulations are available online from Binder here. The Jupyter notebooks for these tutorials are also available here.

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 with assistance from the contributors listed here.

Contributing to BioSimulators utils

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

Funding

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

Questions and comments

Please contact the BioSimulators Team with any questions or comments.