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توضیحات

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

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

|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors| BioSimulators-OpenCOR ===================== BioSimulators-compliant command-line interface and Docker image for the `OpenCOR <https://opencor.ws/>`__ simulation program. This command-line interface and Docker image enable users to use OpenCOR 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 `CellML format <https://cellml.org]>`__). A list of the algorithms and algorithm parameters supported by OpenCOR is available at `BioSimulators <https://biosimulators.org/simulators/opencor>`__. A simple web application and web service for using OpenCOR to execute COMBINE/OMEX archives is also available at `runBioSimulations <https://run.biosimulations.org>`__. Installation ------------ Install Python package and command-line application ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1. Install the requirements for OpenCOR: .. code:: sh apt-get install -y \ curl \ libpulse-mainloop-glib0 \ libx11-6 \ libxext6 \ libxslt1.1 \ sqlite3 2. Install `OpenCOR <https://opencor.ws/downloads/index.html>`__: .. code:: sh url=https://opencor.ws/downloads/snapshots/2021-05-19/OpenCOR-2021-05-19-Linux.tar.gz curl $url | tar -xz --directory=/opt/ 3. Add OpenCOR to your system path: .. code:: sh export PATH=/opt/OpenCOR-2021-05-19-Linux:$PATH 4. Install pip for this version of Python: .. code:: sh curl https://bootstrap.pypa.io/get-pip.py | OpenCOR -c PythonShell 5. Use pip to install this package: .. code:: sh /opt/OpenCOR-2021-05-19-Linux/python/bin/python -m pip install biosimulators-opencor Install Docker image ~~~~~~~~~~~~~~~~~~~~ :: docker pull ghcr.io/biosimulators/opencor Usage ----- Local usage ~~~~~~~~~~~ :: usage: opencor [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v] BioSimulators-compliant command-line interface to the OpenCOR <https://opencor.ws> 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/opencor:latest \ -i /root/in/modeling-study.omex \ -o /root/out Documentation ------------- Documentation is available at https://docs.biosimulators.org/Biosimulators_OpenCOR/. 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_OpenCOR :target: https://github.com/biosimulations/Biosimulators_OpenCOR/releases .. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_opencor :target: https://pypi.org/project/biosimulators_opencor/ .. |CI status| image:: https://github.com/biosimulators/Biosimulators_OpenCOR/workflows/Continuous%20integration/badge.svg :target: https://github.com/biosimulators/Biosimulators_OpenCOR/actions?query=workflow%3A%22Continuous+integration%22 .. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_OpenCOR/branch/dev/graph/badge.svg :target: https://codecov.io/gh/biosimulators/Biosimulators_OpenCOR .. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_OpenCOR/HEAD :target: #contributors-

نیازمندی

مقدار	نام
>=0.1.155	biosimulators-utils[cellml,logging]
>=2.28	kisao
-	lxml
-	numpy
-	python-dateutil
-	python-dateutil

نحوه نصب

نصب پکیج whl biosimulators-opencor-0.0.9:

pip install biosimulators-opencor-0.0.9.whl

نصب پکیج tar.gz biosimulators-opencor-0.0.9:

pip install biosimulators-opencor-0.0.9.tar.gz