Metadata-Version: 2.1
Name: micom
Version: 0.20.2
Summary: Microbial community modeling based on cobrapy.
Home-page: https://github.com/micom-dev/micom
Author: Christian Diener
Author-email: mail@cdiener.com
License: Apache License 2.0
Description: .. image:: https://github.com/micom-dev/micom/raw/master/docs/source/_static/micom.png
            :width: 640 px
        
        |actions status| |coverage| |pypi status|
        
        `MICOM` is a Python package for metabolic modeling of microbial
        communities currently developed in the
        `Gibbons Lab <https://gibbons.systemsbiology.org>`_ at the `Institute for Systems
        Biology <https://systemsbiology.org>`_ and the
        `Human Systems Biology Group <https://resendislab.github.io>`_ of
        Prof. Osbaldo Resendis Antonio at the `National Institute of Genomic
        Medicine Mexico <https://inmegen.gob.mx>`_.
        
        `MICOM` allows you to construct a community model from a list on input
        COBRA models and manages exchange fluxes between individuals and individuals
        with the environment. It explicitly accounts for different abundances of
        individuals in the community and can thus incorporate data from 16S rRNA
        sequencing experiments. It allows optimization with a variety of algorithms
        modeling the trade-off between egoistic growth rate maximization and
        cooperative objectives.
        
        Attribution
        -----------
        
        MICOM is published in
        
        ::
        
              MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
              Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio
              mSystems 5:e00606-19
              https://doi.org/10.1128/mSystems.00606-19
        
        Please cite this publication when referencing MICOM. Thanks :smile:
        
        Installation
        ------------
        
        `MICOM` is available on PyPi and can be installed via
        
        .. code:: bash
        
            pip install micom
        
        Getting started
        ---------------
        
        Documentation can be found at https://micom-dev.github.io/micom .
        
        .. |actions status| image:: https://github.com/micom-dev/micom/workflows/Python%20package/badge.svg
           :target: https://github.com/micom-dev/micom/actions
        .. |coverage| image:: https://codecov.io/gh/micom-dev/micom/branch/master/graph/badge.svg
           :target: https://codecov.io/gh/micom-dev/micom
        .. |pypi status| image:: https://img.shields.io/pypi/v/micom.svg
           :target: https://pypi.org/project/micom/
        
Keywords: microbiota modeling metabolism community
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Provides-Extra: dev
Provides-Extra: test
