Curating COBRA Models of Microbial Metabolism

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.