https://github.com/biosimulators/biosimulators_copasi

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
https://github.com/biosimulators/biosimulators_copasi

biochemical-networks biosimulators combine-archive computational-biology copasi docker dynamical-modeling omex-metadata python sbml sed-ml simulation systems-biology

Last synced: 12 days ago
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COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

• Host: GitHub
• URL: https://github.com/biosimulators/biosimulators_copasi
• Owner: biosimulators
• License: mit
• Created: 2019-12-04T14:50:35.000Z (about 6 years ago)
• Default Branch: dev
• Last Pushed: 2025-12-06T02:48:52.000Z (about 2 months ago)
• Last Synced: 2026-01-03T15:20:34.110Z (23 days ago)
• Topics: biochemical-networks, biosimulators, combine-archive, computational-biology, copasi, docker, dynamical-modeling, omex-metadata, python, sbml, sed-ml, simulation, systems-biology
• Language: Python
• Homepage: https://docs.biosimulators.org/Biosimulators_COPASI
• Size: 10.9 MB
• Stars: 2
• Watchers: 5
• Forks: 3
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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# BioSimulators-COPASI

BioSimulators-compliant command-line interface and Docker image for the [COPASI](http://copasi.org/) simulation program.

This 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])).

A list of the algorithms and algorithm parameters supported by COPASI is available at [BioSimulators](https://biosimulators.org/simulators/copasi).

A simple web application and web service for using COPASI to execute COMBINE/OMEX archives is also available at [runBioSimulations](https://run.biosimulations.org).

## Installation

### Install Python package

```

pip install biosimulators-copasi

```

### Install Docker image

```

docker pull ghcr.io/biosimulators/copasi

```

## Usage

### Local usage

```

usage: biosimulators-copasi [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the COPASI simulation program .

optional arguments:

  -h, --help            show this help message and exit

  -d, --debug           full application debug mode

  -q, --quiet           suppress all console output

  -i ARCHIVE, --archive ARCHIVE

                        Path to OMEX file which contains one or more SED-ML-

                        encoded simulation experiments

  -o OUT_DIR, --out-dir OUT_DIR

                        Directory to save outputs

  -v, --version         show program's version number and exit

```

### Usage through Docker container

The entrypoint to the Docker image supports the same command-line interface described above.

For 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 `./`.

```

docker run \

  --tty \

  --rm \

  --mount type=bind,source="$(pwd)",target=/root/in,readonly \

  --mount type=bind,source="$(pwd)",target=/root/out \

  ghcr.io/biosimulators/copasi:latest \

    -i /root/in/modeling-study.omex \

    -o /root/out

```

## Documentation

Documentation is available at https://docs.biosimulators.org/Biosimulators_COPASI/.

## License

This package is released under the [MIT license](LICENSE). COPASI is released under the [Artistic 2.0 License](http://copasi.org/Download/License/).

## Development team

This 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).

## Questions and comments

Please contact the [BioSimulators Team](mailto:info@biosimulators.org) with any questions or comments.