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McGill Researchers Prepare to Test Drive Itanium in Proteomics Project

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Robert Kearney, chair of the biomedical engineering department at McGill University, has high hopes for the Itanium processor.

Now he and his research team will be able to see if the technology lives up to their expectations. McGill and 39 other universities have been awarded Hewlett-Packard servers and workstations based on the Itanium as part of HP and Intel’s newly launched Systems Grant program.

The program, a $2.5 million joint effort between Intel and HP, provided HP Workstation i2000 and HP Server rx4610 products to selected universities. Delivery of the systems is expected later this fall.

Robert Fogel of the solutions market development group at Intel told BioInform that the Itanium processor family architecture “is very well suited for the life sciences environment.”

According to Fogel, the Itanium excels in two key aspects of life science computing: memory addressability, which permits large amounts of genomic and proteomics databases to be kept in memory; and floating point performance, which enables computationally intensive applications.

Kearney said his group intends to assess both of these capabilities as part of its work to develop high-throughput proteomics methods for a cell-mapping project.

“One of the things we want to find out is just what are the advantages of using this architecture,” Kearney said. “One of the issues is that as large as the human genome is, the potential number of proteins is even larger, so whatever database size you have for the human genome you’re talking about 10 or 100 times larger for proteins.”

Kearney’s group is seeking to “close the loop” in mass spectrometry analysis in order to attain real-time protein identification. “We’re interested in developing an ability to do the processing of the spectrum in a short enough period of time so you can feed those results back to the mass spectrometer to control what it does as the data comes in,” he said.

This approach could reduce what is currently a 30-45 minute process down to 30 seconds, Kearney said, but it all depends on the processing power of the Itanium.

“Potentially it looks like it will address the issue,” Kearney noted.

The Itanium-based Systems Grant program was developed under the administration of HP University Relations and Intel Academic Relations and the auspices of Intel Research and HP Labs.

— BT

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