commscores


Namecommscores JSON
Version 0.0.10 PyPI version JSON
download
home_pagehttps://github.com/freiburgermsu/CommScores
SummaryA Python package for quantifying microbial interactions
upload_time2023-08-23 05:52:46
maintainer
docs_urlNone
authorAndrew Freiburger
requires_python
licenseMIT License Copyright (c) 2023 CommScores Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
keywords microbiology community scores interaction syntrophy competition
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls. 
            Quantifying microbial interactions within microbial communities
________________________________________________________________________

|PyPI version| |Downloads| |docs| |License|

.. |Supported Python Versions| image:: https://img.shields.io/pypi/pyversions/commscores
   :target: https://pypi.org/project/commscores/
   :alt: Python versions

.. |PyPI version| image:: https://img.shields.io/pypi/v/modelseedpy.svg?logo=PyPI&logoColor=brightgreen
   :target: https://pypi.org/project/commscores/
   :alt: PyPI version

.. |Actions Status| image:: https://github.com/freiburgermsu/modelseedpy/workflows/Test%20modelseedpy/badge.svg
   :target: https://github.com/freiburgermsu/commscores/actions
   :alt: Actions Status

.. |License| image:: https://img.shields.io/badge/License-MIT-blue.svg
   :target: https://opensource.org/licenses/MIT
   :alt: License

.. |Downloads| image:: https://pepy.tech/badge/commscores
   :target: https://pepy.tech/project/commscores
   :alt: Downloads   

.. |docs| image:: https://readthedocs.org/projects/commscores/badge/?version=latest
   :target: https://commscores.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

Microbial communities predicate most biological systems on Earth, yet the interaction dynamics between community members remains opaque. Quantitative metrics offer a means of isolating these complex, multi-dimensional, interactions into single biological dimensions; although, several ostensibly important biological dimensions evade existing metrics and extant metrics have moreover not be consolidated into a single operable package. We therefore developed CommScores as a comprehensive package for quantifying microbial interaction dimensions within a microbial community, and thereby elucidating the dynamics that govern the given community. CommScores leverages `ModelSEEDpy <https://github.com/ModelSEED/ModelSEEDpy>`_ and `COBRApy <https://github.com/opencobra/cobrapy>`_ packages for metabolic modeling, and the `COBRA-KBase <https://github.com/fliu/cobrakbase>`_ package for acquiring genomic information from KBase. CommScores should accelerate fundamental discoveries in microbial ecology and the rational design of microbial communities for diverse applications in medicine, ecology, and industry.

.. note::

   This project is under active development, and may be subject to losing back-compatibility.

----------------------
Installation
----------------------

CommScores and all of its dependencies should automatically install when it is installed from PyPI::

 pip install commscores

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Andrew Freiburger
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