Genome-scale reconstruction, modeling, and simulation of E. coli's metabolic network

Since the release of the first genome-scale metabolic reconstruction of the E. coli metabolic network in 2000, there has been a growing number of researchers around the world adapting it for a broad range of studies (Feist 2008). The uses range from practical applications to obtaining basic biological understanding of cellular behavior. This range of uses is further expected to expand as the reconstruction broadens in scope and as new in silico methods are developed, implemented, and put to use. In this chapter, we will describe foundational concepts central to the reconstruction process and model formulation, the history of reconstruction of the E. coli metabolic network, the development of reconstruction technology, genome-scale constraint based modeling with key exemplary case studies of uses of the E. coli metabolic reconstruction, and insights into the future of the field. As such, this chapter should serve as a guide to those interested in either expanding the application of the E. coli reconstruction or adapting established applications to other organisms.