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Open Access Method

FOCAL: an experimental design tool for systematizing metabolic discoveries and model development

Christopher J Tervo and Jennifer L Reed*

Author affiliations

Department of Chemical and Biological Engineering, University of Wisconsin - Madison, WI 53706, USA

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Citation and License

Genome Biology 2012, 13:R116  doi:10.1186/gb-2012-13-12-r116

Published: 13 December 2012

Abstract

Current computational tools can generate and improve genome-scale models based on existing data; however, for many organisms, the data needed to test and refine such models are not available. To facilitate model development, we created the forced coupling algorithm, FOCAL, to identify genetic and environmental conditions such that a reaction becomes essential for an experimentally measurable phenotype. This reaction's conditional essentiality can then be tested experimentally to evaluate whether network connections occur or to create strains with desirable phenotypes. FOCAL allows network connections to be queried, which improves our understanding of metabolism and accuracy of developed models.