Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic Models
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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 wordsMetabolic modeling Flux balance analysis Mixed-integer programming MILP Transcriptional regulation Boolean networks Constraint-based modeling
The author thanks Caroline Blassick for her assistance with Fig. 1.
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