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UCSD Launches Cyberinfrastructure

SAN DIEGO -- Scientists and engineers at the University of California, San Diego and the J. Craig Venter Institute (JCVI) have flipped the virtual switch on the first cyberinfrastructure customized to serve the marine microbial metagenomics community. At the heart of the cyberinfrastructure is a new, high-performance computer and storage complex funded by the Gordon and Betty Moore Foundation and located in UC San Diegos Atkinson Hall, headquarters of the California Institute for Telecommunications and Information Technology (Calit2), a partnership of UC San Diego and UC Irvine.

The computer complex enables analysis of a vast array of biocomplexity data housed in the Community Cyberinfrastructure for Advanced Marine Microbial Research and Analysis (CAMERA). It includes environmental metagenomic and genomic sequence data, associated environmental parameters (“metadata”), precomputed search results, and cross-analysis of environmental samples. While end users can manipulate the data over the web or over dedicated optical circuits, CAMERA permits scientists to connect their local laboratory computers directly to the CAMERA database and tools using the National LambdaRail, Internet2’s NewNet, or international optical circuits, resulting in up to a hundred-fold increase in bandwidth over the conventional shared Internet.

CAMERA has been in beta testing since January and today launched the first production version of its database and computational resources. Simultaneously, at a news conference held in Washington D.C., researchers announced the first scientific articles based on sequences and metadata deposited in CAMERA by JCVI’s Global Ocean Sampling (GOS) Expedition. The articles are published in the Oceanic Metagenomics collection in the March 2007 issue of PLoS Biology, including “CAMERA: A Community Resource for Metagenomics,” a four-page introduction to the project by JCVI’s Rekha Seshadri, Saul Kravitz and Marvin Frazier, with Calit2’s Larry Smarr and Paul Gilna [PLoS Biology, March 2007 | Volume 5 | Issue 3 | e75].

“A new cyberinfrastructure architecture is required to support the field of genomics as it transitions to the study of metagenomics,” said CAMERA principal investigator Larry Smarr, a professor of computer science and engineering at UC San Diego and director of Calit2. “The infrastructure will create a virtual domain for global data and knowledge sharing by this emerging research community.”

California Institute for Telecommunications and Information Technology (Calit2)