OptCom (2012): A comprehensive modeling framework for the flux balance analysis of microbial communities
Despite the growing availability of this high-throughput data, we still know very little about the metabolic contributions of individual microbial players within an ecological niche and the extent and directionality of metabolic interactions among them. This calls for development of efficient modeling frameworks to elucidate less understood aspects of metabolism in microbial communities.
OptCom, is a comprehensive flux balance analysis framework for microbial communities, which relies on a multi-level optimization description. In contrast to earlier approaches that rely on a single objective function, OptCom’s multi-level/objective structure enables properly assessing trade-offs between individual vs. community level fitness criteria. This modeling framework is general enough to capture any type of interactions (positive, negative or combination of both) for any number of species (or guilds) involved. In addition, OptCom is able to explain in vivo observations in terms of the levels of optimality of growth for each participant of the community.
Zomorrodi, A.R. and C.D. Maranas (2012), "OptCom: A multi-level optimization framework for the metabolic modeling and analysis of microbial communities," PLoS Computational Biology, 8(2):e1002363. PMID: 22319433.
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