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 16S rRNA sequencing experiments. It allows optimization with a variety of algorithms modeling the trade-off between egoistic growth rate maximization and cooperative objectives.
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
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
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