Microbial community modeling based on cobrapy.
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 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.
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:
MICOM is available on PyPi and can be installed via
pip install micom
Documentation can be found at https://micom-dev.github.io/micom .
- General questions on usage can be asked in Github Discussions
- We are also available on the cobrapy Gitter channel
- Questions specific to the MICOM Qiime2 plugin (q2-micom) can also be asked on the Qiime2 forum
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