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biosimulators-rbapy-0.0.4

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0.0.4
0.0.3
0.0.2
0.0.1
0.0.4
0.0.3
0.0.2
0.0.1

توضیحات

BioSimulators-compliant command-line interface to the RBApy simulation program.
ویژگی مقدار
سیستم عامل -
نام فایل biosimulators-rbapy-0.0.4
نام biosimulators-rbapy
نسخه کتابخانه 0.0.4
نگهدارنده []
ایمیل نگهدارنده []
نویسنده BioSimulators Team
ایمیل نویسنده info@biosimulators.org
آدرس صفحه اصلی https://github.com/biosimulators/Biosimulators_RBApy
آدرس اینترنتی https://pypi.org/project/biosimulators-rbapy/
مجوز MIT
|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors| BioSimulators-RBApy =================== BioSimulators-compliant command-line interface to the `RBApy <https://sysbioinra.github.io/RBApy/>`__ simulation program for Resource Balance Analysis (RBA) models. This command-line interface and Docker image enable users to use RBApy 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 RBA models in the `RBApy format <https://sysbioinra.github.io/RBApy/usage.html>`__. A list of the algorithms and algorithm parameters supported by RBApy is available at `BioSimulators <https://biosimulators.org/simulators/rbapy>`__. A simple web application and web service for using RBApy to execute COMBINE/OMEX archives is also available at `runBioSimulations <https://run.biosimulations.org>`__. Installation ------------ BioSimulators-RBApy requires one of the linear programming solvers `IBM CPLEX <https://www.ibm.com/analytics/cplex-optimizer>`__, `GLPK <https://www.gnu.org/software/glpk/>`__, or `Gurobi <https://www.gurobi.com/products/gurobi-optimizer/>`__. Note, GLPK is slower than CPLEX and Gurobi. IBM and Gurobi both provide free licenses for academic research. Install Python package ~~~~~~~~~~~~~~~~~~~~~~ 1. Install requirements - `Python <https://python.org>`__ - `Pip <https://pip.pypa.io/>`__ - Optionally, install CPLEX 2. Install this package :: pip install biosimulators-rbapy To use BioSimulators-RBApy with CPLEX, install BioSimulators-RBApy with the ``cplex`` option. Note, this requires CPLEX and a CPLEX license: :: pip install rbapy[cplex] To use BioSimulators-RBApy with GLPK, install BioSimulators-RBApy with the ``glpk`` option. Note, this requires ``libglpk-dev``: :: pip install rbapy[glpk] To use BioSimulators-RBApy with Gurobi, install BioSimulators-RBApy with the ``gurobi`` option. Note, this requires a Gurobi license: :: pip install rbapy[gurobi] Install Docker image ~~~~~~~~~~~~~~~~~~~~ :: docker pull ghcr.io/biosimulators/rbapy Usage ----- Local usage ~~~~~~~~~~~ :: usage: biosimulators-rbapy [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v] BioSimulators-compliant command-line interface to the RBApy simulation program <https://sysbioinra.github.io/RBApy/>. 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/rbapy:latest \ -i /root/in/modeling-study.omex \ -o /root/out Using BioSimulators-RBApy with a Gurobi license ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gurobi licenses can be used either by setting environment variables prefixed with ``GRB_`` or by saving your license to your home directory (``~/gurobi.lic``) or the appropriate location for your OS (e.g., ``/opt/gurobi/gurobi.lic`` for Linux). Documentation ------------- Documentation is available at https://docs.biosimulators.org/Biosimulators_RBApy/. 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_RBApy :target: https://github.com/biosimulations/Biosimulators_RBApy/releases .. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_rbapy :target: https://pypi.org/project/biosimulators_rbapy/ .. |CI status| image:: https://github.com/biosimulators/Biosimulators_RBApy/workflows/Continuous%20integration/badge.svg :target: https://github.com/biosimulators/Biosimulators_RBApy/actions?query=workflow%3A%22Continuous+integration%22 .. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_RBApy/branch/dev/graph/badge.svg :target: https://codecov.io/gh/biosimulators/Biosimulators_RBApy .. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_RBApy/HEAD :target: #contributors-


نیازمندی

مقدار نام
>=0.1.117 biosimulators-utils[logging]
>=2.28 kisao
- numpy
- biosimulators-utils[containers]
- python-dateutil
- pyyaml
- rbapy[cplex]
- rbapy[glpk]
- rbapy[gurobi]
- rbapy[cplex]
- rbapy[glpk]
- rbapy[gurobi]
- biosimulators-utils[containers]
- python-dateutil
- pyyaml


نحوه نصب


نصب پکیج whl biosimulators-rbapy-0.0.4:

    pip install biosimulators-rbapy-0.0.4.whl


نصب پکیج tar.gz biosimulators-rbapy-0.0.4:

    pip install biosimulators-rbapy-0.0.4.tar.gz