micom 0.5.0

Microbial community modeling based on cobrapy.

Please note that this is still a pre-release and might still lack functionalities.

micom is a Python package for metabolic modeling of microbial communities.

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.

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 .