Micom
Python package to study microbial communities using metabolic modeling.
Install / Use
/learn @micom-dev/MicomREADME
.. image:: https://github.com/micom-dev/micom/raw/main/docs/source/micom.png :width: 640 px
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Welcome
MICOM is a Python package for metabolic modeling of microbial
communities currently developed in the Diener Lab <https://dienerlab.com>_ at the
Medical University of Graz <https://medunigraz.at>. Previous development took place 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, amplicon sequencing, 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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