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SRI, Marine Lab Develop E. Coli Encyclopedia And License It to Pangea


MENLO PARK, Calif.--SRI International here and the Marine Biological Laboratory at Woods Hole, Mass., have announced the development of EcoCyc, a database that offers the most comprehensive collection of information available on the genetic makeup and metabolic pathways of the E. coli bacterium. To compile the database, the laboratory's Monica Riley assembled data from more than 50 scientific journals. Then the information was encoded into an object-oriented database developed by SRI.

EcoCyc has been exclusively licensed to bioinformatics software company Pangea Systems, which will further develop and support the database and other products that derive from it, and offer them to the pharmaceutical industry.

"The EcoCyc database is intended to save scientists time in looking up facts about genes and metabolism and to provide greater accessibility of the E. coli genome," Riley commented, adding that EcoCyc is available over the internet.

To augment the value of EcoCyc, SRI also developed PathoLogic, a proprietary software package that predicts the metabolic pathways of organisms whose genomes have been sequenced, such as H. influenza or H. pylori. PathoLogic uses the EcoCyc database to analyze how the predicted genes of the organisms are organized into pathways, then creates a new database that describes the predicted pathways and enzymes of the organisms.

At the same time, Pangea announced that Peter Karp, an EcoCyc codeveloper with SRI, has joined Pangea as director of pathway research, senior scientist, and a Pangea fellow. A world-renowned bioinformaticist, Karp will specifically focus his contributions to Pangea on the areas of database integration and graphical user interface development, working to expand and improve the company's leading products. At SRI Karp was the senior computer scientist in the company's Artificial Intelligence Center, in charge of research in computer science and bioinformatics. Two of his associates there, Suzanne Paley and Markus Krummenacker, were also involved in the EcoCyc development and have also joined Pangea.

Karp also serves as a consulting assistant professor of medicine in Stanford University's division of medical informatics.

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