Metadata-Version: 2.1
Name: micom
Version: 0.33.1
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/main/docs/source/micom.png
            :width: 640 px
        
        |actions status| |coverage| |pypi status| |mastodon|
        
        Welcome
        -------
        
        `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 biomass quantification,
        cytometry, ampliconsequencing, or metagenomic shotgun sequencing.
        
        It identifies a relevant flux space by incorporating an ecological model for the trade-off
        between individual taxa growth and community-wide growth that shows good agreement with
        experimental data.
        
        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
        
        For more info on the installation or setting up the solvers please see the `documentation <https://micom-dev.github.io/micom>`_ .
        
        Getting started
        ---------------
        
        Documentation can be found at https://micom-dev.github.io/micom .
        
        Getting help
        ------------
        
        General questions on usage can be asked in Github Discussions
            https://github.com/micom-dev/micom/discussions
        
        We are also available on the cobrapy Gitter channel
            https://gitter.im/opencobra/cobrapy
        
        Questions specific to the MICOM Qiime2 plugin (q2-micom) can also be asked on the Qiime2 forum
            https://forum.qiime2.org/c/community-plugin-support/
        
        .. |actions status| image:: https://github.com/micom-dev/micom/actions/workflows/pythonpackage.yml/badge.svg
           :target: https://github.com/micom-dev/micom/actions/workflows/pythonpackage.yml
        .. |coverage| image:: https://codecov.io/gh/micom-dev/micom/branch/main/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/
        .. |mastodon| image:: https://img.shields.io/mastodon/follow/109960852316221526?domain=https%3A%2F%2Fmstdn.science&style=social
           :target: https://mstdn.science/@micom
        
        
Keywords: microbiome,microbiota,modeling,metabolism,community,metabolic modeling
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 :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.7
Description-Content-Type: text/x-rst
