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Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic Models

  • Paul A. Jensen
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1716)

Abstract

Genome-scale models have expanded beyond their metabolic origins. Multiple modeling frameworks are required to combine metabolism with enzymatic networks, transcription, translation, and regulation. Mathematical programming offers a powerful set of tools for tackling these “multi-modality” models, although special attention must be paid to the connections between modeling types. This chapter reviews common methods for combining metabolic and discrete logical models into a single mathematical programming framework. Best practices, caveats, and recommendations are presented for the most commonly used software packages. Methods for troubleshooting large sets of logical rules are also discussed.

Key words

Metabolic modeling Flux balance analysis Mixed-integer programming MILP Transcriptional regulation Boolean networks Constraint-based modeling 

Notes

Acknowledgments

The author thanks Caroline Blassick for her assistance with Fig. 1.

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Department of Bioengineering and Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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