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Dr. Peter Karp: Databases and Algorithms for Pathway Bioinformatics
December 20th, 2005, 14h 30

CNRS amphitheater

2 Avenue Albert Einstein, 69 Villeurbanne (Lyon)


This talk will provide an overview of the BioCyc collection of 200 Pathway/Genome Databases that is available at URL, and of the Pathway Tools software that underlies BioCyc. The BioCyc collection includes the EcoCyc DB, which describes the full genome and metabolic network of Escherichia coli, and a large portion of its genetic network; the MetaCyc DB, which describes more than 500 metabolic pathways that were experimentally elucidated in more than 300 organisms; and the HumanCyc DB, which describes the metabolic pathway map of humans.

The talk will survey the features of Pathway Tools that facilitate the creation, maintenance, and web publishing of the BioCyc databases. Among the components of Pathway Tools are: a large biological ontology that facilitates the representation of complex biological knowledge with high fidelity; a set of inference modules for inferring new layers of biological information above an annotated genome, including inferring the metabolic pathway map of an organism, predicting which genes fill missing reactions in the predicted pathways, and predicting the operons of the organism; editing tools that allow scientists to interactively refine and curate these databases; and visualization tools that support web publishing, querying, and analyses of these data.

Dr. Peter Karp

Director, Bioinformatics Research Group

Artificial Intelligence Center

SRI International

Menlo Park, CA (USA)

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