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Moore Foundation Awards $24.5M to UCSD, Venter

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The emerging field of meta-genomics got a boost from the Gordon and Betty Moore Foundation in January when it awarded $24.5 million to the University of California, San Diego, and the J. Craig Venter Institute to build a publicly available informatics infrastructure to help store, analyze, visualize, and disseminate the massive amounts of data gleaned from environmental sequencing.

The seven-year grant will support a project called the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis — known as CAMERA — which will include hardware, software, and data resources related to marine metagenomics.

The UCSD division of the California Institute for Telecommunications and Information Technology will lead the project, along with the Venter Institute and UCSD’s Center for Earth Observations and Applications at the Scripps Institution of Oceanography. Other partners include UCSD’s San Diego Supercomputer Center, the Scripps Genome Center, and the National Biomedical Computation Resource at UCSD.

The CAMERA project will present challenges in data integration, visualization, and communications infrastructure, says Peter Arzberger, director of the NBCR. Arzberger says that in addition to advancing the understanding of marine ecosystems — the primary goal of the effort — the collaborative aspects of the underlying IT infrastructure will “revolutionize how we work with data.”

The backbone of the system will be the so-called OptIPuter optical network, a project funded by the National Science Foundation that will eventually enable other scientists to plug their compute clusters into the CAMERA infrastructure. NSF kicked off the OptIPuter project in 2002 with a five-year, $13.5 million grant.

OptIPuter is expected to offer a hundred-fold increase over current connectivity standards, meaning that “distance is no longer a bottleneck” for collaborative projects involving large amounts of data, Arzberger says.

On the hardware side, CAMERA will have a dedicated cluster of approximately 1,000 processors and several hundred terabytes of storage, and will also be plugged into the NSF’s TeraGrid distributed computing infrastructure.

— Bernadette Toner

PATENT WATCH

US Patent 6,990,221. Automated DNA array image segmentation and analysis. Inventor: Soheil Shams. Assignee: BioDiscovery. Issued: January 24, 2006.

This patent covers a “segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots,” according to the abstract. The technique utilizes image intensity level information, grid point, and other data to provide analysis.


US Patent 6,988,039. Method for determining sequence alignment significance. Inventor: Aleksandar Poleksic. Assignee: Eidogen. Issued: January 17, 2006.

This invention “relates to methods and systems for quickly determining the statistical significance of a raw alignment score produced by aligning a first sequence to a second sequence,” the abstract says. “The claimed methods and systems determine multiple estimates of the p-value of an alignment score. Each p-value estimate is then compared to a pre-defined threshold p-value” to determine significance.


The Wellcome Trust Sanger Institute announced that the World Trace Archive database of DNA sequences has reached 1 billion entries. The Trace Archive includes all the sequence data produced and published by the world scientific community. The archive is currently 22 terabytes and is doubling every 10 months, according to the institute.

Tripos laid off about half of its Discovery Research employees and closed a temporary laboratory building in Bude, UK, in an attempt to streamline and refine the discovery business and associated cost structure.

Lion Bioscience and the European Molecular Biology Laboratory plan to collaborate on future product developments. EMBL researchers will use the latest version of Lion’s SRS data-integration platform and all its modules, later providing Lion with user feedback on the tool.

Clinical Data and IO Informatics will partner on the final phase of a five-year, $11.7 million Advanced Technology Program grant from the National Institute of Science and Technology. The grant, which started in 2002, is aimed at creating software tools and other technologies that can better support the discovery of novel targets, drugs, and diagnostics using systems biology.

De Novo Pharmaceuticals has entered into a collaboration with Genzyme under which it will use its SkelGen computational drug-design technology to focus on a disease target of interest to Genzyme.

Datapoint
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Number of courses — in molecular biology, computer science, and bioinformatics — students will be required to complete for the new online master’s degree in bioinformatics offered by Johns Hopkins University beginning this spring.
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