Skip to main content

Microbial community modeling based on cobrapy.

Project description

https://github.com/micom-dev/micom/raw/master/docs/source/_static/micom.png

actions status coverage pypi status

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


Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

micom-0.18.1.tar.gz (153.8 kB view hashes)

Uploaded Source

Built Distribution

micom-0.18.1-py2.py3-none-any.whl (171.3 kB view hashes)

Uploaded Python 2 Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page