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returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biochemical-networks","biosimulators","combine-archive","computational-biology","copasi","docker","dynamical-modeling","omex-metadata","python","sbml","sed-ml","simulation","systems-biology"],"created_at":"2026-01-14T08:01:07.973Z","updated_at":"2026-01-14T08:01:09.240Z","avatar_url":"https://github.com/biosimulators.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Latest release](https://img.shields.io/github/v/tag/biosimulators/Biosimulators_COPASI)](https://github.com/biosimulations/Biosimulators_COPASI/releases)\n[![PyPI](https://img.shields.io/pypi/v/biosimulators_copasi)](https://pypi.org/project/biosimulators_copasi/)\n[![CI status](https://github.com/biosimulators/Biosimulators_COPASI/workflows/Continuous%20integration/badge.svg)](https://github.com/biosimulators/Biosimulators_COPASI/actions?query=workflow%3A%22Continuous+integration%22)\n[![Test coverage](https://codecov.io/gh/biosimulators/Biosimulators_COPASI/branch/dev/graph/badge.svg)](https://codecov.io/gh/biosimulators/Biosimulators_COPASI)\n[![All Contributors](https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_COPASI/HEAD)](#contributors-)\n\n\n# BioSimulators-COPASI\nBioSimulators-compliant command-line interface and Docker image for the [COPASI](http://copasi.org/) simulation program.\n\nThis command-line interface and Docker image enable users to use COPASI to execute [COMBINE/OMEX archives](https://combinearchive.org/) that describe one or more simulation experiments (in [SED-ML format](https://sed-ml.org)) of one or more models (in [SBML format](http://sbml.org])).\n\nA list of the algorithms and algorithm parameters supported by COPASI is available at [BioSimulators](https://biosimulators.org/simulators/copasi).\n\nA simple web application and web service for using COPASI to execute COMBINE/OMEX archives is also available at [runBioSimulations](https://run.biosimulations.org).\n\n## Installation\n\n### Install Python package\n```\npip install biosimulators-copasi\n```\n\n### Install Docker image\n```\ndocker pull ghcr.io/biosimulators/copasi\n```\n\n## Usage\n\n### Local usage\n```\nusage: biosimulators-copasi [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]\n\nBioSimulators-compliant command-line interface to the COPASI simulation program \u003chttp://copasi.org\u003e.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -d, --debug           full application debug mode\n  -q, --quiet           suppress all console output\n  -i ARCHIVE, --archive ARCHIVE\n                        Path to OMEX file which contains one or more SED-ML-\n                        encoded simulation experiments\n  -o OUT_DIR, --out-dir OUT_DIR\n                        Directory to save outputs\n  -v, --version         show program's version number and exit\n```\n\n### Usage through Docker container\nThe entrypoint to the Docker image supports the same command-line interface described above.\n\nFor example, the following command could be used to use the Docker image to execute the COMBINE/OMEX archive `./modeling-study.omex` and save its outputs to `./`.\n\n```\ndocker run \\\n  --tty \\\n  --rm \\\n  --mount type=bind,source=\"$(pwd)\",target=/root/in,readonly \\\n  --mount type=bind,source=\"$(pwd)\",target=/root/out \\\n  ghcr.io/biosimulators/copasi:latest \\\n    -i /root/in/modeling-study.omex \\\n    -o /root/out\n```\n\n## Documentation\nDocumentation is available at https://docs.biosimulators.org/Biosimulators_COPASI/.\n\n## License\nThis package is released under the [MIT license](LICENSE). COPASI is released under the [Artistic 2.0 License](http://copasi.org/Download/License/).\n\n## Development team\nThis package was developed by the [Center for Reproducible Biomedical Modeling](http://reproduciblebiomodels.org). COPASI was developed by a [team](http://copasi.org/About/Team/) at the University of Connecticut, the University of Heidelberg, and the University of Virginia with assistance from the contributors listed [here](CONTRIBUTORS.md).\n\n## Questions and comments\nPlease contact the [BioSimulators Team](mailto:info@biosimulators.org) with any questions or comments.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosimulators%2Fbiosimulators_copasi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiosimulators%2Fbiosimulators_copasi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosimulators%2Fbiosimulators_copasi/lists"}