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Pittsburgh Supercomputing Center, National Institutes of Health, Science Factory, State University of New York, University of California, Incyte Genomics

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PSC Buys HP Alphas with $1.3M NIH Biomedical Grant

The Pittsburgh Supercomputing Center last week said it received an award of $1.3 million from the National Institutes of Health to provide computational resources for biomedical research.

The award, from NIH’s National Center for Research Resources, will support the acquisition, installation, and operation of a Hewlett-Packard AlphaServer GS1280-based shared-memory computing system built upon HP’s new EV7 Alpha processors.

PSC officials said the new system’s shared-memory architecture, which gives each processor equal access to all of the memory available on the entire system, “will significantly advance a large class of important applications in biomedical research, including protein simulations and genome sequencing.”

Researchers who have already secured cycles on the machine include Eric Lander, Jill Mesirov, and colleagues from the Whitehead Institute; structural biologist Klaus Schulten from the University of Illinois; chemical biologist Michael Klein from the University of Pennsylvania; and neuroscientists Terence Sejnowski and Thomas Bartol of the Salk Institute.

 

Science Factory, IBM Partner for Über-Integration

Science Factory of Cologne, Germany, said last week that it has agreed to integrate its ÜberTool bioinformatics workflow software with IBM’s DiscoveryLink data integration technology.

ÜberTool offers users more than 200 types of bioinformatics analysis methods and also enables access to public and proprietary biological data.

Merging the features of this product with the data federation capabilities of DiscoveryLink “will enable scientists to work with a diverse range of data sources and file types including text, images, numeric files, and relational databases,” according to the Science Factory.

 

UB Bioinformatics Center Gets $7.5 in Congressional Funds

The State University of New York at Buffalo’s bioinformatics center is slated to receive $7.5 million in congressional spending for the current year, the Buffalo News reported on Feb. 14.

The federal funds include $2 million from the defense spending bill, $4.5 million from the veterans/housing appropriation, and $1 million from the labor appropriation.

The appropriations are still far below the $12.3 million the center requested in the spring, but the news is brighter than it appeared in January, when Congress had only approved $2 million [BioInform 01-20-03].

The funding covers the current fiscal year ending Sept. 30.

 

Scientists Map Protein Fold Universe

Researchers from the University of California, Berkeley, and Lawrence Berkeley National Laboratory have created a three-dimensional global map of known protein structures. Armed with empirical data, the DALI (Distance mAtrix ALignment) structural alignment algorithm, and some mathematics, the team led by Berkeley chemist Sung-Hou Kim graphically grouped 498 of the most common SCOP (Structural Classification System of Proteins) domains into four different classes.

“Some have argued that there are really only three classes of protein fold structures but now we can mathematically prove there are four,” said Kim in a statement.

The three-dimensional map, described in last week’s Proceedings of the National Academy of Sciences, shows the distribution in space of the protein folds as represented by points that are spatially separated in proportion to their structural dissimilarities.

The map should prove useful as a “conceptual framework” to organize protein structure and function data in one place, Kim said. “When the structure of a new protein is first solved, we can place it in the appropriate location on the map and immediately know who its neighbors are and its evolutionary history which can help us predict what its function may be.”

Future work for Kim and his colleagues includes access to supercomputer time at Berkeley Lab’s National Energy Research Scientific Computing Center to add the rest of the more than 20,000 known protein structures to their map. They also plan to host a website where researchers can submit new protein structures they have solved.

 

Incyte Buys a Drug Shop

Incyte Genomics said last week that it had completed its acquisition of Maxia Pharmaceuticals, a San Diego-based small-molecule drug discovery and development company.

Maxia will continue to operate in San Diego as a wholly owned subsidiary of Incyte. The company will receive up to $28.3 million in cash and stock and up to $14 million in future clinical performance milestone payments.

Filed under

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