Python package to study microbial communities using metabolic modeling.
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
appveyor
docs
micom
tests
.gitattributes
.gitignore
.travis.yml
LICENSE
MANIFEST.in
NEWS.md
README.rst
appveyor.yml
micom.png
setup.cfg
setup.py
versioneer.py

README.rst

https://github.com/cdiener/micom/raw/master/micom.png

travis status appveyor status coverage pypi status

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

Micom is described in a recent preprint that you can cite. If you have any questions contact us at oresendis (at) inmegen.gob.mx. Thanks 😄

Installation

micom is available on PyPi and can be installed via

pip install micom

Getting started

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