BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.com/AMICI-dev/amici>.
BioSimulators-compliant command-line interface to the AMICI simulation program.
This command-line interface and Docker image enable users to use AMICI to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in SBML format).
A list of the algorithms and algorithm parameters supported by AMICI is available at BioSimulators.
A simple web application and web service for using AMICI to execute COMBINE/OMEX archives is also available at runBioSimulations.
Python >= 3.7
Install Python package
pip install biosimulators-amici
Install Docker image
docker pull ghcr.io/biosimulators/amici
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 is available at https://docs.biosimulators.org/Biosimulators_AMICI/.
This package is released under the MIT license.
This package was developed by the Center for Reproducible Biomedical Modeling and the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York with assistance from the contributors listed here.
Questions and comments
Please contact the BioSimulators Team with any questions or comments.
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