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UC San Diego partners with Venter Institute to build marine microbial genomics cyberinfrastructure

sident of Venter Institute. "The goal is to create a community resource to house all metagenomic data that will facilitate and advance knowledge of marine microbial ecology, other natural environments, and evolutionary biology."

The CAMERA project builds on pioneering efforts in metagenomics to sequence the genomes of entire microbial communities, often comprising thousands of species. The largest such effort is Venter Institute's Sorcerer II Expedition, for which sequencing is funded by the Moore Foundation. The Expedition is developing the first large-scale genomic survey of microbial life in the world's oceans to produce the largest gene catalogue ever assembled. Sorcerer II is expected to more than double the number of protein sequences currently available in the National Institutes of Health's GenBank. The metagenomics database will include new sequences, genes and gene families, together with their annotations and associated environmental metadata.

The move from traditional organism genome databases to the CAMERA-based environmental metagenomics data storage and computational complex requires development of a more complex cyber-architecture. Using dedicated optical circuits, CAMERA will permit scientists to connect their local laboratory PC clusters directly to the CAMERA database and tools using the National LambdaRail or international optical circuits, resulting in up to a hundred-fold increase in bandwidth over current standards.

The enhanced connectivity is based on a model pioneered by the OptIPuter project and funded by the National Science Foundation. "Linking Venter Institute to Calit2 will be the first persistent application of the OptIPuter high-performance 'collaboratory'," said Calit2 director Larry Smarr, Ph.D., principal investigator on both the OptIPuter and CAMERA projects. "The architecture is quite general and will be quickly adaptable to other areas of data-intensive science." Collaboratories are virtual laborator
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Source:University of California - San Diego


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