biosimulators-amici 0.1.30
BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.com/AMICI-dev/amici>.
Requires Python: >=3.11
Keywords: BioSimulators, systems biology, computational biology, mathematical model, kinetic model, simulation, SBML, SED-ML, COMBINE, OMEX

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# BioSimulators-AMICI
BioSimulators-compliant command-line interface to the [AMICI](https://github.com/AMICI-dev/AMICI) simulation program.

This command-line interface and Docker image enable users to use AMICI 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 AMICI is available at [BioSimulators](https://biosimulators.org/simulators/amici).

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

## Installation

### Dependencies

* Python >= 3.11
* pip
* g++

### Install Python package
```
pip install biosimulators-amici
```

### Install Docker image
```
docker pull ghcr.io/biosimulators/amici
```

## Usage

### Local usage
```
usage: biosimulators-amici [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.com/AMICI-dev/AMICI>.

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/amici:latest \
    -i /root/in/modeling-study.omex \
    -o /root/out
```

## Documentation
Documentation is available at https://docs.biosimulators.org/Biosimulators_AMICI/.

## License
This package is released under the [MIT license](LICENSE).

## Development team
This package was developed by the [Center for Reproducible Biomedical Modeling](http://reproduciblebiomodels.org) and the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York 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.