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micom-dev / micom

Python package to study microbial communities using metabolic modeling.
https://micom-dev.github.io/micom
Apache License 2.0
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biochemistry cobra cobrapy community flux hacktoberfest metabolic-models microbiome microbiota modeling python systems-biology

readme

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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/

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