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Welcome
-------

`MICOM` is a Python package for metabolic modeling of microbial
communities 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 amplicon
sequencing or metagenomic 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 at https://msystems.asm.org/content/5/1/e00606-19.
Please cite this article when referencing MICOM.

To get an idea which assumptions and strategies MICOM uses we recommend
to start with some background on the :doc:`methods <logic>`. The easiest way to
use MICOM is using the :doc:`workflow API <high_level>`.

Contents
--------

.. toctree::
   :maxdepth: 1

   Strategies used by MICOM <logic>
   Installing MICOM <installing>

   MICOM workflows <high_level>
   Interactions <interactions>
   Visualizations <viz>
   Writing your own workflows <workflows>

   Single Model API <community>
   Growth rates and fluxes <growth_fluxes>
   Growth media <media>
   Knockouts <taxa_knockouts>
   Intervention studies <elasticities>

   Tutorials and Courses <tutorials>
   Release Notes <NEWS>

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/

Indices and tables
------------------

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

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