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GeneProt Employs Compaq Server Farm To Power Large-Scale Proteomics Facility


GeneProt said the large-scale proteomics discovery center it opened last week in Geneva, Switzerland, is supported by the world’s most powerful commercial supercomputer.

“No one in the life sciences has more computing power than GeneProt,” said a company spokesman.

The new center will run 20 hours a day and will use 1,420 Compaq Alpha-based Tru64 Unix computer processors along with Compaq software and StorageWorks systems to capture, store, and analyze the terabytes of data generated by 51 Bruker Daltonics mass spectrometers.

Bioinformatics will be a core component of the proteomics facility, according to Cedric Loiret-Bernal, GeneProt CEO. He said the company’s in-house bioinformatics staff would work with the Swiss Institute of Bioinformatics to develop algorithms to identify and characterize the most promising proteins.

But the compute power provided by the Compaq server farm will give GeneProt the critical ability to work at an industrial scale and with great speed, Loiret-Bernal said.

“Some companies just entering the proteomics industry say they’ll be able to provide candidates for clinical testing within a few years. We believe we will deliver potential therapeutic agents within six months,” said Denis Hochstrasser, co-founder of the company.

Bill Blake, vice president of high performance technical computing at Compaq, said that computational speed “is not just in the instructions per second of a microprocessor; speed is the work done per month.”

Describing the Compaq system as an “industrial tool,” Blake stressed the importance of putting together a system for GeneProt that “would not just be a machine that will run for a few hours in a lab, but something that will continue to churn out useful work on a day-in, day-out basis.”

GeneProt will use the facility to study the development of organisms, maturation of cell types and tissues, and progression of diseases as they vary over time. The company hopes to use the resulting protein profile of healthy and diseased fluids or tissues to speed development of new products by pharmaceutical and biotechnology companies.

The company has no plans to sell its proteomics data. Instead, it intends to identify and produce proteins that can be studied as new drugs, targets for new drugs, and biomarkers for pharmaceutical partners.

Novartis has already recruited GeneProt for a five-year proteomics analysis partnership. In October, the Basel, Swizerland-based pharmaceutical company said it would make a $43 million equity investment in GeneProt, and would pay GeneProt an additional $41 million in fees over the next four years to analyze healthy and diseased human tissues.

In addition, both Bruker Daltonics and Compaq have taken equity investments in GeneProt. Loiret-Bernal said in October that Compaq would invest $10 million in GeneProt in exchange for 2.2 percent of GeneProt’s equity. This investment is managed as part of Compaq’s $100 million Genomics Investment Program unveiled in September.

The amount of Bruker’s investment was not disclosed.

Loiret-Bernal said he expects GeneProt to sign a number of other partnerships with pharmaceutical and technology companies in the future. He noted that these partnerships are a key source of revenue for the company and the core of its business model.

GeneProt is planning to open a second proteomics facility later in the year. The company is currently looking at sites in the Princeton, NJ, area, but said it is also “exploring other options.

Compaq and Bruker Daltonics will supply the technology for the East coast facility, which is expected to be equal in scale to the Geneva center.

— BT

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