|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors|
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:info@biosimulators.org>`__ with any questions or comments.
.. |Latest release| image:: https://img.shields.io/github/v/tag/biosimulators/Biosimulators_AMICI
:target: https://github.com/biosimulations/Biosimulators_AMICI/releases
.. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_amici
:target: https://pypi.org/project/biosimulators_amici/
.. |CI status| image:: https://github.com/biosimulators/Biosimulators_AMICI/workflows/Continuous%20integration/badge.svg
:target: https://github.com/biosimulators/Biosimulators_AMICI/actions?query=workflow%3A%22Continuous+integration%22
.. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_AMICI/branch/dev/graph/badge.svg
:target: https://codecov.io/gh/biosimulators/Biosimulators_AMICI
.. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_AMICI/HEAD
:target: #contributors-
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