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توضیحات

BioSimulators-compliant command-line interface to the GINsim simulation program.

ویژگی	مقدار
سیستم عامل	-
نام فایل	biosimulators-ginsim-0.0.9
نام	biosimulators-ginsim
نسخه کتابخانه	0.0.9
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	BioSimulators Team
ایمیل نویسنده	info@biosimulators.org
آدرس صفحه اصلی	https://github.com/biosimulators/Biosimulators_GINsim
آدرس اینترنتی	https://pypi.org/project/biosimulators-ginsim/
مجوز	MIT

|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors| BioSimulators-GINsim ==================== BioSimulators-compliant command-line interface to the `GINsim <http://ginsim.org/>`__ simulation program. This command-line interface and Docker image enable users to use GINsim 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 logical models (in `SBML-qual <http://sbml.org]>`__ or GINsim's formats). A list of the algorithms and algorithm parameters supported by GINsim is available at `BioSimulators <https://biosimulators.org/simulators/ginsim>`__. A simple web application and web service for using GINsim to execute COMBINE/OMEX archives is also available at `runBioSimulations <https://run.biosimulations.org>`__. Installation ------------ Install Python package ~~~~~~~~~~~~~~~~~~~~~~ 1. Install Java, Python, and pip 2. Install the `GINsim Python package <https://github.com/GINsim/GINsim-python>`__ 3. Install this package :: pip install biosimulators-ginsim Install Docker image ~~~~~~~~~~~~~~~~~~~~ :: docker pull ghcr.io/biosimulators/ginsim Usage ----- Local usage ~~~~~~~~~~~ :: usage: biosimulators-ginsim [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v] BioSimulators-compliant command-line interface to the GINsim simulation program <http://ginsim.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/ginsim:latest \ -i /root/in/modeling-study.omex \ -o /root/out Documentation ------------- Documentation is available at https://docs.biosimulators.org/Biosimulators_GINsim/. 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_GINsim :target: https://github.com/biosimulations/Biosimulators_GINsim/releases .. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_ginsim :target: https://pypi.org/project/biosimulators_ginsim/ .. |CI status| image:: https://github.com/biosimulators/Biosimulators_GINsim/workflows/Continuous%20integration/badge.svg :target: https://github.com/biosimulators/Biosimulators_GINsim/actions?query=workflow%3A%22Continuous+integration%22 .. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_GINsim/branch/dev/graph/badge.svg :target: https://codecov.io/gh/biosimulators/Biosimulators_GINsim .. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_GINsim/HEAD :target: #contributors-

نیازمندی

مقدار	نام
>=0.1.122	biosimulators-utils[logging,sbml]
>=0.4.4	ginsim
>=2.28	kisao
-	lxml
-	numpy
-	biosimulators-utils[containers]
-	python-dateutil
-	pyyaml
-	biosimulators-utils[containers]
-	python-dateutil
-	pyyaml

نحوه نصب

نصب پکیج whl biosimulators-ginsim-0.0.9:

pip install biosimulators-ginsim-0.0.9.whl

نصب پکیج tar.gz biosimulators-ginsim-0.0.9:

pip install biosimulators-ginsim-0.0.9.tar.gz