micom 0.6.1

Microbial community modeling based on cobrapy.

Please note that this is still a pre-release and might still lack functionalities. It comes with no guarantees.

micom is a Python package for metabolic modeling of microbial communities developed in 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

If you want to use micom in a scientific publication the attribution clause in the license is covered by citing our relevant publication. However, we are still in the process in pairing micom with validations so that publication still does not exist. If you want to use micom before that article is published please contact us at oresendis (at) inmegen.gob.mx. Thanks :smile:

Installation

micom is available on PyPi and can be installed via

pip install micom

Getting started

Documentation can be found at https://cdiener.github.io/micom .