UCSD Jacobs School of Engineering
University of California San Diego

Studying Genomes of the Sea

The UCSD alumnus who led the first successful effort to decode the human genome now wants to decipher the genetic code of microbial life in the world's oceans. Craig Venter's Sorcerer II Expedition is circumnavigating the globe, gathering undersea microbes and data on their ecosystems. But today's Internet and software tools are not up to the challenge. So Venter turned to a team of UCSD engineers and scientists to build a state-of-the-art computational resource.

“The explosion of data from the collection and sequencing of marine microbes requires a completely novel approach to storing, accessing, mining, analyzing, and drawing conclusions from this rich new wealth of information,” says Venter.

Enter the California Institute for Telecommunications and Information Technology (Calit2). It has pulled together a UCSD-based team to develop and deploy a Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA). With $24.5 million in funding over seven years from the Gordon and Betty Moore Foundation, Calit2 director Larry Smarr will lead a partnership among Venter Institute and UCSD scientists drawn from Calit2, the Center for Earth Observations and Applications at Scripps Institution of Oceanography, San Diego Supercomputer Center, and the university's schools of medicine and pharmaceutical sciences.

The core cyberinfrastructure will provide enhanced connectivity between UCSD and the Rockville, MD-based Venter Institute, using dedicated optical circuits and software developed by the NSF-funded OptIPuter project. Says Smarr, a professor of computer science and engineering in the Jacobs School , “This new infrastructure should result in up to a hundred-fold increase in bandwidth over current standards.”

Scientists will use CAMERA for metagenomics research—analyzing microbial genomic sequence data in the context of other microbial species, as well as in comparison to a variety of other “metadata” such as the chemical and physical conditions under which microbes are sampled. The goal: to help scientists understand how microbes function in their natural ecosystems, enable studies on the effects humans are having on the environment, as well as permit insight into the evolution of life on Earth.

Related Links
News Release: UCSD partners with Venter Institute 1/17/06
Website: OptIPuter Project
Website: Sorcerer II Expedition
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Towards a $1,000 genome sequencing test
Calit2 building opens
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