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Curating COBRA Models of Microbial Metabolism

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Microbial Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2349))

Abstract

Constraint-based reconstruction and analysis (COBRA) methods have been used for over 20 years to generate genome-scale models of metabolism in biological systems. The COBRA models have been utilized to gain new insights into the biochemical conversions that occur within organisms and allow their survival and proliferation. Using these models, computational biologists can conduct a variety of different analyses such as examining network structures, predicting metabolic capabilities, resolving unexplained experimental observations, generating and testing new hypotheses, assessing the nutritional requirements of a biosystem and approximating its environmental niche, identifying missing enzymatic functions in the annotated genomes, and engineering desired metabolic capabilities in model organisms. This chapter details the protocol for developing curated system-level COBRA models of metabolism in microbes.

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Acknowledgments

This work was funded in part by the DOE OBER Genomic Science program and LLNL Laboratory Directed Research and Development funding and performed under the auspices of the U.S. Department of Energy at Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

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  1. Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA

    Ali Navid

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  1. Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA

    Ali Navid

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Navid, A. (2022). Curating COBRA Models of Microbial Metabolism. In: Navid, A. (eds) Microbial Systems Biology. Methods in Molecular Biology, vol 2349. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1585-0_14

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  • DOI: https://doi.org/10.1007/978-1-0716-1585-0_14

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