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biosimulators-gillespy2-0.1.9
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BioSimulators-compliant command-line interface to the GillesPy2 simulation program.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | biosimulators-gillespy2-0.1.9 |
| نام | biosimulators-gillespy2 |
| نسخه کتابخانه | 0.1.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | BioSimulators Team |
| ایمیل نویسنده | info@biosimulators.org |
| آدرس صفحه اصلی | https://github.com/biosimulators/Biosimulators_GillesPy2 |
| آدرس اینترنتی | https://pypi.org/project/biosimulators-gillespy2/ |
| مجوز | MIT |
|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors|
BioSimulators-GillesPy2
=======================
BioSimulators-compliant command-line interface and Docker image for the
`GillesPy2 <https://stochss.github.io/GillesPy2>`__ simulation program.
This command-line interface and Docker image enable users to use
GillesPy2 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 GillesPy2
is available at
`BioSimulators <https://biosimulators.org/simulators/gillespy2>`__.
A simple web application and web service for using GillesPy2 to execute
COMBINE/OMEX archives is also available at
`runBioSimulations <https://run.biosimulations.org>`__.
Installation
------------
Dependencies
~~~~~~~~~~~~
- Python >= 3.7
- pip
- build-essential
Install Python package
~~~~~~~~~~~~~~~~~~~~~~
::
pip install biosimulators-gillespy2
Install Docker image
~~~~~~~~~~~~~~~~~~~~
::
docker pull ghcr.io/biosimulators/gillespy2
Usage
-----
Local usage
~~~~~~~~~~~
::
usage: biosimulators-gillespy2 [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulators-compliant command-line interface to the GillesPy2 <https://stochss.github.io/GillesPy2> 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/gillespy2:latest \
-i /root/in/modeling-study.omex \
-o /root/out
Documentation
-------------
Documentation is available at
https://docs.biosimulators.org/Biosimulators_GillesPy2/.
License
-------
This package is released under the `MIT <LICENSE>`__.
Development team
----------------
This package was developed by the `Karr Lab <https://www.karrlab.org>`__
at the Icahn School of Medicine at Mount Sinai and the `Center for
Reproducible Biomedical Modeling <https://reproduciblebiomodels.org/>`__
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_GillesPy2
:target: https://github.com/biosimulations/Biosimulators_GillesPy2/releases
.. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_gillespy2
:target: https://pypi.org/project/biosimulators_gillespy2/
.. |CI status| image:: https://github.com/biosimulators/Biosimulators_GillesPy2/workflows/Continuous%20integration/badge.svg
:target: https://github.com/biosimulators/Biosimulators_GillesPy2/actions?query=workflow%3A%22Continuous+integration%22
.. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_GillesPy2/branch/dev/graph/badge.svg
:target: https://codecov.io/gh/biosimulators/Biosimulators_GillesPy2
.. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_GillesP2/HEAD
:target: #contributors-
نیازمندی
| مقدار | نام |
|---|---|
| >=0.1.151 | biosimulators-utils[logging] |
| <=1.6.6,>=1.6.0 | gillespy2 |
| - | kisao |
| - | lxml |
| - | numpy |
| - | python-libsbml |
| - | biosimulators-utils[containers] |
| - | python-dateutil |
| - | biosimulators-utils[containers] |
| - | python-dateutil |
نحوه نصب
نصب پکیج whl biosimulators-gillespy2-0.1.9:
pip install biosimulators-gillespy2-0.1.9.whl
نصب پکیج tar.gz biosimulators-gillespy2-0.1.9:
pip install biosimulators-gillespy2-0.1.9.tar.gz