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Japan’s Yokohama City University Taps Cray To Power Structural Bioinformatics Projects

Cray has added a new bioinformatics customer to its roster, signing on Yokohama City University's Division of Structural Bioinformatics for its new Cray XT4 system.
Two researchers will lead the university in its use of the four-teraflop system, which has 14 terabytes of memory, to study the three-dimensional structures and functions of biomolecules, proteins, and nucleic acids.
Akinori Kidera, a professor in the structural bioinformatics department, said in a statement that the XT4 system “will accelerate analysis of genome function and evolution from protein solid structure information,” and called the acquisition “a key step for the institution and the field of bioinformatics."
Summisho Computer Systems of Japan will install the system later this year.
Representatives from Yokohama City University were unavailable for comment before press time.
Cray's senior vice-president of corporate strategy and business development, Jan Silverman, told BioInform that the XT4’s Intel architecture and ability to run the types of codes the university requires was especially appealing to the university.
Silverman wasn’t intimately involved with the negotiations, but said the agreement should be in the range of $1 million, and that on-site support is always included in such contracts.
The deal is one of several recent bioinformatics agreements for Cray, Silverman said. For example, the Pittsburgh Supercomputer Center is using an ST system to study how bacteria develop resistance to antibodies, and the University of Tennessee and Oak Ridge National Laboratory are using an XT4 Jaguar for protein folding research.
The XT4 has a 3D torus interconnect and can scale to more than 120,000 processor cores for over a petaflop of peak performance. It uses x86 64-bit AMD Opteron processors, employing HyperTransport technology for bandwidth expansion and reduction of latency.

The XT4 system “will accelerate analysis of genome function and evolution from protein solid structure information.”

Cray faces competition from a number of IT vendors in the market for bioinformatics high-performance computing — a sector that IT research firm IDC expects to grow from $5.9 million in 2000 to $2.2 billion in 2010 [BioInform 08-03-07].
Silverman said the company closed the deal with Yokohama after a competitive process. While declining to name names, he said that generally, IBM is a major competitor of Cray's for such business.
As the company rounds out the year, Silverman said, “We are clearly targeting growth for 2008.”
Key drivers for the uptick, he said, will be the Black Widow, Cray XMT system, and Cray XT4 system with quad-core support, which are all targeted for release in the first half of 2008. In addition, “important” upgrades are planned for the Cray XT4 system in the second half of 2008.
He added that the company has signed over $700 million in contracts over the past 18 months across all industries.

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