Microbial community modeling based on cobrapy.
Project description
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 .
Project details
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