Elhanan Borenstein, Ph.D.

Dept of Genome Sciences
University of Washington

3720 15th Ave NE
Foege Building, S103B
Box 355065
Seattle, WA 98195-5065

Phone: (206) 685-8165
Fax: (206) 685-7301



CoMiDA
CoMiDA is an algorithm for designing simple communities with some predefined metabolic capacities. An implementation of the CoMiDA algorithm is available for download via GitHub.



» CoMiDA>Code (GitHub)
  Download the CoMiDA source code from GitHub repository.

» CoMiDA>ReadMe
  Learn how to obtain, compile, and use CoMiDA in your analysis.



Understanding the CoMiDA algorithm

CoMiDA is a novel algorithm for identifying minimal sets of microbial species that collectively provide the enzymatic capacity required to synthesize a set of desired target product metabolites from a predefined set of available substrates. The CoMiDA algorithm integrates a graph theoretic representation of network flow with the set cover problem in an integer linear programming (ILP) framework to simultaneously identify possible metabolic paths from substrates to products while minimizing the number of species required to catalyze these metabolic reactions.
If you are using CoMiDA please cite the following paper:
Alexander Eng and Elhanan Borenstein, An algorithm for designing minimal microbial communities with desired metabolic capacities. Bioinformatics, 32(13), 2016.