OAKLAND, Calif.--Version 4.5 of EcoCyc, a knowledgebase describing the genes and intermediary metabolism of E. coli, is now available on Pangea Systems' web site at http://ecocyc.panbio.com/ecocyc, and for local installation under license from Pangea. Pangea's Peter Karp and Monica Riley of the Marine Biological Laboratory are collaborators on the project.
The knowledgebase is an electronic reference source for biologists who work with E. coli and related microorganisms. Scientists can visualize the layout of genes within a chromosome, in an individual biochemical reaction, or in a complete biochemical pathway, with compound structures displayed. Navigation capabilities allow users to move from displaying an enzyme to displaying a reaction that the enzyme catalyzes, or of the gene that encodes the enzyme. The interface also supports a variety of queries, such as generating a display of the map positions of all genes that code for enzymes within a given biochemical pathway.
As well as serving as a reference, EcoCyc allows complex computations related to metabolism, such as design of novel biochemical pathways for biotechnology, studies of the evolution of metabolic pathways, and simulation of metabolic pathways. EcoCyc is also being used for computer-based education in biochemistry. A US National Institutes of Health Center for Research Resources grant supporting the continued development of EcoCyc was recently renewed.