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biosimulators-bionetgen-0.1.9
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مشاهده بیشترتوضیحات
BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | biosimulators-bionetgen-0.1.9 |
| نام | biosimulators-bionetgen |
| نسخه کتابخانه | 0.1.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | BioSimulators Team |
| ایمیل نویسنده | info@biosimulators.org |
| آدرس صفحه اصلی | https://github.com/biosimulators/Biosimulators_BioNetGen |
| آدرس اینترنتی | https://pypi.org/project/biosimulators-bionetgen/ |
| مجوز | MIT |
|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors|
BioSimulators-BioNetGen
=======================
BioSimulators-compliant command-line interface and Docker image for the
`BioNetGen <https://bionetgen.org/>`__ simulation program.
This command-line interface and Docker image enable users to use
BioNetGen 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 `BNGL format <https://bionetgen.org]>`__).
A list of the algorithms and algorithm parameters supported by BioNetGen
is available at
`BioSimulators <https://biosimulators.org/simulators/bionetgen>`__.
A simple web application and web service for using BioNetGen to execute
COMBINE/OMEX archives is also available at
`runBioSimulations <https://run.biosimulations.org>`__.
Installation
------------
Install Python package
~~~~~~~~~~~~~~~~~~~~~~
After installing BioNetGen, use pip to install this package as
illustrated below.
::
pip install biosimulators-bionetgen
Install Docker image
~~~~~~~~~~~~~~~~~~~~
::
docker pull ghcr.io/biosimulators/bionetgen
Usage
-----
Local usage
~~~~~~~~~~~
::
usage: bionetgen [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.
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/bionetgen:latest \
-i /root/in/modeling-study.omex \
-o /root/out
Documentation
-------------
Documentation is available at
https://docs.biosimulators.org/Biosimulators_BioNetGen/.
License
-------
This package is released under the `MIT license <LICENSE>`__.
Development team
----------------
This package was developed by the `Karr Lab <https://www.karrlab.org>`__
at the Icahn School of Medicine at Mount Sinai, `Ali Sinan
Saglam <https://scholar.google.com/citations?user=7TM0eekAAAAJ&hl=en>`__
in the Faeder Lab at the University of Pittsburgh, and the `Center for
Reproducible Biomedical Modeling <http://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
about the command-line program or Docker image. Please contact `Ali
Sinan Saglam <mailto:als251@pitt.edu>`__ with any questions or comments
about BioNetGen.
.. |Latest release| image:: https://img.shields.io/github/v/tag/biosimulators/Biosimulators_BioNetGen
:target: https://github.com/biosimulations/Biosimulators_BioNetGen/releases
.. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_bionetgen
:target: https://pypi.org/project/biosimulators_bionetgen/
.. |CI status| image:: https://github.com/biosimulators/Biosimulators_BioNetGen/workflows/Continuous%20integration/badge.svg
:target: https://github.com/biosimulators/Biosimulators_BioNetGen/actions?query=workflow%3A%22Continuous+integration%22
.. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_BioNetGen/branch/dev/graph/badge.svg
:target: https://codecov.io/gh/biosimulators/Biosimulators_BioNetGen
.. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_BioNetGen/HEAD
:target: #contributors-
نیازمندی
| مقدار | نام |
|---|---|
| >=0.1.124 | biosimulators-utils[bngl,logging] |
| >=2.29 | kisao |
| - | pandas |
| - | biosimulators-utils[containers] |
| - | numpy |
| - | pytest |
| - | python-dateutil |
| - | biosimulators-utils[containers] |
| - | numpy |
| - | pytest |
| - | python-dateutil |
نحوه نصب
نصب پکیج whl biosimulators-bionetgen-0.1.9:
pip install biosimulators-bionetgen-0.1.9.whl
نصب پکیج tar.gz biosimulators-bionetgen-0.1.9:
pip install biosimulators-bionetgen-0.1.9.tar.gz