A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities.

ABSTRACT: Genome-scale metabolic modeling is a powerful framework for predicting metabolic phenotypes of any organism with an annotated genome. For two decades, this framework has been used for the rational design of microbial cell factories. In the last decade, the range of applications has exploded, and new frontiers have emerged, including the study of the gut microbiome and its health implications and the role of microbial communities in global ecosystems. However, all the critical steps in this framework, from model construction to simulation, require the use of powerful linear optimization solvers, with the choice often relying on commercial solvers for their well-known computational efficiency. In this work, I benchmark a total of six solvers (two commercial and four open source) and measure

SUBMITTER: Machado D 

PROVIDER: S-EPMC10878033 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature