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AIC Seminar Series

BioCyc Tools for Visualization of high Throughput Datasets

Peter D KarpArtificial Intelligence Center, SRI International

Date:  Thursday, January 24th 2019 at 4:00pm

Location:  EK255 (SRI E building)  (Directions)

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Please contact braz@ai.sri.com directly for remote viewing.
   Abstract

The BioCyc databases define a large information space of 14,500 sequenced genomes and their associated biochemical pathways and regulatory networks. Each of those databases is a multi-use database that can be queried interactively by users, can be translated to a quantitative metabolic model, and can be queried by other computational tools. In a sense, BioCyc is like an integration of Wikipedia and Google Maps. To speed user navigation through that information space, we have developed a large number of scientific visualization tools, analogous to expanding Google Maps several fold. These visualizations range from compact summaries of relationships among a handful of biological entities to browsers for the complete genome and complete metabolic network of an organism.

   Bio for Peter D Karp

Honors and Awards

Research Interests

Dr. Karp’s research interests include metabolic-pathway bioinformatics, systems biology, and metabolic engineering. He is the bioinformatics architect of the BioCyc collection of Pathway/Genome Databases that includes EcoCyc, HumanCyc, and MetaCyc. He has developed algorithms for prediction of metabolic pathways from sequenced genomes, for visualization of individual pathways and entire metabolic maps, and for generation of metabolic models from pathway databases. He is interested in extending these modeling techniques from individual organisms to communities of interacting microorganisms. His interests also include biological databases and ontologies, and interoperation of bioinformatics databases.

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