Toward the automated generation of genome-scale metabolic networks in the SEED

Background: Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. Results: We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Matthew DeJongh, Kevin Formsma, Paul Boillot, John Gould, Matthew Rycenga, Aaron A. Best
• Keywords: BMCBI 2007, Current Methods, Genome-scale Metabolic Networks, Reaction Network