Sun awarded two Academic Equipment Grants for two groups supporting the use of open standards and machine augmented data abstraction, the Biopathways Consortium (BPC) and the BioCyc project at SRI International.

The Biopathways Consortium supports the advancement of informatics needs for systems biology through an open, public forum. The BioCyc project is a collection of pathway/genome databases developed using SRI International's Pathway Tools software.

"The rapidly accelerating volume of biological data requires both the use of open standards and machine augmented processing, and we are delighted to support these fine efforts," said Dr. Stefan Unger, business development manager for global education and research, Sun.

Text-mining of scientific articles is a major source of information regarding pathways and biological mechanisms. The Sun servers will be installed at Columbia University and used to run their "Geneways" text-mining algorithm, developed by Andrey Rhzetsky and his group. This facility will enable researchers in the field of automated biological text-mining to offer their tools through the BPC as a public service for the life science community. At the same time, this real-world use and feedback can help to advance similar technologies for large-scale application, possibly including a common public repository for all mined pathways and mechanisms.

The BioCyc Knowledge Library is a collection of pathway/genome databases including the EcoCyc and MetaCyc databases, plus databases from 12 other microorganisms whose genomes have been fully sequenced. Each pathway/genome database describes the genome, proteome and metabolic pathways of a single organism.

The databases in the BioCyc collection resulted from several different collaborations. For example, the Caulobacter crescentus database resulted from a collaboration between SRI International, a nonprofit research institute, and Drs. Harley McAdams and Lucy Shapiro of Stanford University. It is funded by the Department of Energy. MetaCyc is a general database of metabolic pathways that is being developed under a collaboration between SRI and the Department of Plant Biology at the Carnegie Institution of Washington under funding from the National Institute of General Medical Sciences. The database for Agrobacterium tumefaciens resulted from a collaboration between SRI and researchers from the University of Washington, the University of Campinas and DuPont.

"We have named our enhanced Web site 'The BioCyc Knowledge Library' to reflect its important role as a collaborative resource and collection of pathway/genome databases for many different organisms," said Dr. Peter Karp, director of the bioinformatics research group at SRI International and principal investigator for the BioCyc project. "The new dual-processor workstation provided by Sun has increased the performance of the Web site dramatically and makes it possible for us to enable a blast-search capability for each genome in the BioCyc collection."

"The BioCyc projects employ a novel combination of visualization, ontologies and pathway inference methods to ease the production of these very useful databases," Dr. Unger added. "We are very pleased to collaborate with Dr. Karp on this project to help further the life science community's collaborative efforts in systems biology."

http://www.biopathways.org

http://www.biocyc.org [...read more...]

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