Quantifying microbial interactions within microbial communities

Microbial communities predicate most biological systems on Earth, yet the interaction dynamics between community members remains opaque. Quantitative metrics offer a means of isolating these complex, multi-dimensional, interactions into single biological dimensions; although, several ostensibly important biological dimensions evade existing metrics and extant metrics have moreover not be consolidated into a single operable package. We therefore developed CommScores as a comprehensive package for quantifying microbial interaction dimensions within a microbial community, and thereby elucidating the dynamics that govern the given community. CommScores leverages ModelSEEDpy and COBRApy packages for metabolic modeling, and the COBRA-KBase package for acquiring genomic information from KBase. CommScores should accelerate fundamental discoveries in microbial ecology and the rational design of microbial communities for diverse applications in medicine, ecology, and industry.

Note

This project is under active development, and may be subject to losing back-compatibility.

Installation

The primary dependency of CommScores is the Freiburgermsu fork of the ModelSEEDpy library, which must be installed via pip in a terminal/command prompt:

pip install git+https://github.com/freiburgermsu/ModelSEEDpy.git

All other dependencies should automatically install when CommScores is installed from PyPI:

pip install commscores