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Microbial community modeling based on cobrapy.

Project description

https://github.com/micom-dev/micom/raw/master/docs/source/_static/micom.png

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MICOM is a Python package for metabolic modeling of microbial communities currently developed in the Gibbons Lab at the Institute for Systems Biology and the Human Systems Biology Group of Prof. Osbaldo Resendis Antonio at the National Institute of Genomic Medicine Mexico.

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

pip install 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/

Bugs can be reported at https://github.com/micom-dev/micom/issues. If you do so please include the following:

  • version of MICOM that was used
  • solver that was used (CPLEX, Gurobi, OSQP)
  • if possible a small reproducible example

Project details


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