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BIOINFORMATICS BRIEFS: Jan 7, 2002

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HIGH-PERFORMANCE COMPUTING

 

Compaq said it is partnering with the Pittsburgh Supercomputing Center to support CASP5 (Critical Assessment of Techniques for Protein Structure Prediction), scheduled to begin in April.

CASP is held every two years to evaluate computational methodologies for protein structure prediction. Participation in the event has grown from 35 research groups at the first CASP 10 years ago to 158 groups two years ago at CASP4. But according to University of Maryland computational biologist John Moult, president and founder of CASP, “in the past some groups have been at a disadvantage because they lack access to top-flight computational resources.”

In support of Moult’s assertion that “CASP should not be limited by computational capability,” PSC and Compaq will provide computing time on the PSC’s Terascale Computing System, which comprises 3,000 Compaq AlphaServer EV68 processors, and on an additional Compaq 100-processor cluster of AlphaServer systems.

PSC and Compaq will also provide a computational grid environment to offer a common means of access to their computational resources and will provide consulting and engineering support to help participants run their structure-prediction software on the TCS architecture.

In addition, Compaq said it would provide computational and data storage capabilities to collect, assess, and publish the results of CASP5 and will also award small grants for initial development, testing of algorithms, and optimizing on the Compaq AlphaServer system architecture.

Further information on CASP and the application process for computing time is available at http://predictioncenter.llnl.gov.

 

DATA STORAGE

 

Following quickly on the heels of the $200 million in funding it recently received for its planned Center of Excellence in Bioinformatics [BioInform, 12-24-01], the University of Buffalo has been awarded $1 million from the National Science Foundation to support a computational infrastructure to store scientific data.

In addition to the NSF award, approximately $600,000 in matching funds will be contributed to the project by UB and New York State.

“The combination of these two events is a one-two punch in terms of leveraging UB for large-scale center grants from the National Institutes of Health and other federal agencies,” said Jaylan Turkkan, UB vice president for research, in a statement.

Research projects that are named on the grant include protein structure determination, gene expression data analysis, data visualization, and data management.

“The bottom line is if you cannot store the data, you cannot do the research,” said Aidong Zhang, UB associate professor of computer science and engineering and principal investigator on the grant.

By the end of the five-year grant, UB expects to have a total of 20 terabytes of computer storage space.

 

DATABASES

 

SRI International of Menlo Park, Calif., said it has used its Pathway Tools software to analyze the newly sequenced Agrobacterium tumefaciens genome and produce a comprehensive database of its metabolic pathways called AgroCyc.

AgroCyc (available at www.ecocyc.org) will also serve as a collaborative space where other scientists studying A. tumefaciens can share their findings.

SRI researchers worked with researchers from the University of Washington and DuPont on the project and published an article about their findings in the December 14, 2001, issue of Science.

SRI used Pathway Tools to predict A. tumefaciens’ metabolic pathways and analyze the distribution of those pathways across its multiple chromosomes. It identified the metabolic roles of 709 Agrobacterium enzymes in 178 metabolic pathways.

AgroCyc is the twelfth in SRI’s growing collection of pathway/ genome databases. Additional new databases include Pseudomonas aeruginosa and Caulobacter crescentus, the result of a joint effort with Stanford University sponsored by the Department of Energy’s Microbial Cell Project.

 

SOFTWARE

 

In an odd collaboration, Accelrys said it is partnering with General Motors in a three-year DOE-sponsored project to apply its informatics software to identify materials that catalytically reduce NOx pollutants in lean diesel automotive exhaust to harmless nitrogen gas.

The consulting group at Accelrys will customize its software tools for data management and the study of structure/property relationships for use in the project.

Richard Blint, senior staff research scientist at the General Motors Research and Development Center, said, “The range of informatics capabilities gathered within Accelrys satisfies the needs of this discovery program exceptionally well.”

GM announced the automotive catalyst project in October. Other major sub-contractors are Engelhard Corporation, Exxon Mobil Research and Engineering, and Los Alamos National Laboratory. The goal is the development of a new emissions control system that allows compression-ignition, direct-injection diesel engines to achieve future Environmental Protection Agency emissions targets.

But while the project may give us cleaner air, it’s cluttered the informatics lexicon with its newly minted term for the application of informatics tools to materials science — the somewhat clunky “matinformatics.”

 

MERGERS & ACQUISITIONS

 

Exelixis of South San Francisco, Calif., is moving closer to closing its acquisition of Genomica of Boulder, Colo.

The exchange offer for shares of Genomica expired as scheduled on December 28, 2001, and Exelixis said it expects to complete the merger to take place before the end of February.

The final exchange ratio will result in conversion of each share of Genomica common stock into 0.28309 shares of Exelixis common stock.

 

Pharmacopeia’s plan to merge with Eos Biotechnology isn’t proceeding so smoothly, however. The company issued two statments in recent weeks urging its shareholders to ignore the recommendation of a group of stockholders to prevent the merger.

“We are confident that the proposed merger will position both Accelrys and our drug-discovery unit as viable, stand-alone businesses,” Joseph Mollica, Pharmacopeia’s chairman, president and CEO, said in a December 28 letter to company shareholders.

The repeated pleas are in response to a Schedule 13D filed with the SEC on December 19 by OrbiMed, an asset-management firm that owns roughly 10 percent of Pharmacopeia’s common stock, in which it threatened to vote against the deal. OrbiMed said that the proposed acquisition, a $160 million all-stock deal, is “overpriced.”

New York-based OrbiMed, which invests exclusively in the healthcare sector, urged other shareholders to vote against the transaction.

A shareholders’ vote on the merger is set for January 18.

 

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