biosimulators-amici

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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 >= 3.7
-  pip
-  libatlas
-  g++
-  swig

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:[e-mail]>__ with any questions or comments.

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