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biosimulators-cobrapy-0.1.9
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BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | biosimulators-cobrapy-0.1.9 |
| نام | biosimulators-cobrapy |
| نسخه کتابخانه | 0.1.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Center for Reproducible Biomedical Modeling |
| ایمیل نویسنده | info@biosimulators.org |
| آدرس صفحه اصلی | https://github.com/biosimulators/biosimulators_cobrapy |
| آدرس اینترنتی | https://pypi.org/project/biosimulators-cobrapy/ |
| مجوز | MIT |
|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors|
BioSimulators-COBRApy
=====================
BioSimulators-compliant command-line interface and Docker image for the
`COBRApy <https://opencobra.github.io/cobrapy/>`__ simulation program.
This command-line interface and Docker image enable users to use COBRApy
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 COBRApy
is available at
`BioSimulators <https://biosimulators.org/simulators/cobrapy>`__.
A simple web application and web service for using COBRApy to execute
COMBINE/OMEX archives is also available at
`runBioSimulations <https://run.biosimulations.org>`__.
Installation
------------
Install Python package
~~~~~~~~~~~~~~~~~~~~~~
::
pip install biosimulators-cobrapy
Install Docker image
~~~~~~~~~~~~~~~~~~~~
::
docker pull ghcr.io/biosimulators/cobrapy
Usage
-----
SED-ML targets for simulation predictions
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BioSimulators-COBRApy recognizes the following targets for simulation
predictions:
- FBA (``KISAO_0000437``), parsimonious FBA (``KISAO_0000528``),
geometric FBA (``KISAO_0000527``):
- Objective: ``fbc:objective/@value``
- Reaction flux: ``sbml:reaction/@flux``
- Reaction reduced cost: ``sbml:reaction/@reducedCost``
- Species shadow price: ``sbml:species/@shadowPrice``
- FVA (``KISAO_0000526``):
- Minimum reaction flux: ``sbml:reaction/@minFlux``
- Maximum reaction flux: ``sbml:reaction/@maxFlux``
Please see https://docs.biosimulations.org for more information.
Local usage
~~~~~~~~~~~
::
usage: biosimulators-cobrapy [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.
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/cobrapy:latest \
-i /root/in/modeling-study.omex \
-o /root/out
Documentation
-------------
Documentation is available at
https://docs.biosimulators.org/Biosimulators_COBRApy/.
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 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_COBRApy
:target: https://github.com/biosimulations/Biosimulators_COBRApy/releases
.. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_cobrapy
:target: https://pypi.org/project/biosimulators_cobrapy/
.. |CI status| image:: https://github.com/biosimulators/Biosimulators_COBRApy/workflows/Continuous%20integration/badge.svg
:target: https://github.com/biosimulators/Biosimulators_COBRApy/actions?query=workflow%3A%22Continuous+integration%22
.. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_COBRApy/branch/dev/graph/badge.svg
:target: https://codecov.io/gh/biosimulators/Biosimulators_COBRApy
.. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_COBRApy/HEAD
:target: #contributors-
نیازمندی
| مقدار | نام |
|---|---|
| >=0.1.162 | biosimulators-utils[logging] |
| - | cobra |
| - | kisao |
| - | lxml |
| - | numpy |
| - | python-libsbml |
| - | attrdict |
| - | biosimulators-utils[containers] |
| - | gurobipy |
| - | python-dateutil |
| - | gurobipy |
| - | attrdict |
| - | biosimulators-utils[containers] |
| - | python-dateutil |
نحوه نصب
نصب پکیج whl biosimulators-cobrapy-0.1.9:
pip install biosimulators-cobrapy-0.1.9.whl
نصب پکیج tar.gz biosimulators-cobrapy-0.1.9:
pip install biosimulators-cobrapy-0.1.9.tar.gz