First The Body, Now The Oceans - InformationWeek

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First The Body, Now The Oceans

After helping crack the human genome, computer technology, data mining, and optical networking will be put to work to give biologists worldwide a window into ocean life. The Scripps Institution of Oceanography, the J. Craig Venter Institute, and the Calit2 computing facility at the University of California, San Diego, last week launched a joint project to study the DNA of ocean life.

The first phase will involve taking samples of ocean surface water and breaking down the microorganisms found there so their DNA can be extracted and sequenced. "It's a shotgun approach," says project leader Larry Smarr, director of Calit2. "You put the microbes through a blender and sequence the fragments of DNA that are floating around. Then you use a lot of computing power to reconstruct the genomes of this collection of organisms."

The Calit2 facility has been building a new type of 10-Gbps optical network designed to tie supercomputers, terabyte data-storage servers, and wall-sized high-definition displays together. The facility also is linked to the National Lambda Rail optical-computing network and other scientific computing networks.

Biologist J. Craig Venter pioneered the shotgun approach to sequencing the human genome. In Venter's method, sequenced islands of the genome are first created and then fitted together later into the entire sequence.

Most of what's known about microbes has been derived from soil studies, which have led to medical revolutions such as antibiotics. Smarr expects similar discoveries will be made from the project's ocean survey, discovering medically or industrially useful organisms. That should give more people a reason to care about the world's oceans.

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