Tuesday, July 28, 2009 - 10:30 AM
S66

BioCyc Databases: Symbolic Systems Biology for Metabolic and Regulatory Networks

Peter Karp, Artificial Intelligence Center, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493

BioCyc is a collection of 409 Pathway/Genome Databases for most organisms whose genomes have been completely sequenced. It is a large and comprehensive resource for systems biology research. Pathway/Genome Databases are structured within a rich ontology that describes the genome, the metabolic network, the transport reactions, and the regulatory machinery of an organism.  Most BioCyc databases were created using a computational pipeline whose input is a sequenced genome, and whose output is the inferred metabolic pathways, pathway hole fillers, operons, and transport reactions for the organism.

Symbolic systems biology uses symbolic computation to infer systems  properties of a biochemical network.  Symbolic computation operates on qualitative and topological relationships within a network, as opposed to performing quantitative computations on a network.  An advantage of symbolic computation is that it does not depend on the extensive parameter sets that quantitative methods require.  This talk will review several examples of symbolic systems biology including inference of pathogen drug targets as choke points in a metabolic network; connectivity analysis of metabolic networks; complex queries that integrate regulatory information with metabolic data; and analysis of the complementarity of the transport and metabolic networks of an organism.


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