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AIC Seminar Series

Pathway/Genome Databases and Software Tools

Peter D KarpAritificial Intelligence Center, SRI International[Home Page]

Date:  2001-10-18 at 16:00

Location:  EJ228  (Directions)

   Abstract

One revolution sweeping molecular biology is the high-throughput generation of massive amounts of experimental data, such as by the human genome project. A second revolution is changing the substrate of biological information from the biological literature to structured knowledge bases. A pathway/genome database (DB) integrates information about the genome, proteins, and biochemical pathways of an organism. For example, the EcoCyc DB describes the full genome and metabolic-pathway complement of E. coli. EcoCyc is the first DB to describe the full biochemical network of an organism, and is used by thousands of scientists for tasks ranging from metabolic engineering of bacteria to analysis of other bacterial genomes. The Pathway Tools software developed in conjunction with EcoCyc includes algorithms for interrogation, visualization, editing, and WWW publishing of pathway/genome DBs. This talk will provide an overview of the past work and future directions for both EcoCyc and the Pathway Tools.

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