Metadata-Version: 2.1
Name: commscores
Version: 0.0.7
Summary: A Python package for quantifying microbial interactions
Home-page: https://github.com/freiburgermsu/CommScores
Author: Andrew Freiburger
Author-email: andrewfreiburger@gmail.com
License: MIT 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.
        
Project-URL: Documentation, https://commscores.readthedocs.io/en/latest/
Project-URL: Issues, https://github.com/freiburgermsu/CommScores/issues
Keywords: microbiology,community,scores,interaction,syntrophy,competition
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Natural Language :: English
Description-Content-Type: text/x-rst
License-File: LICENSE

Quantifying microbial interactions within microbial communities
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|PyPI version| |Downloads| |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

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.

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

 pip install commscores


