Genomics researchers get supercomputing boost

The head of the Ontario Centre for Genomic Computing calls it the most powerful supercomputer in the world dedicated to biological research.

It is the 192-processor SGI Origin 3800 System and on Wednesday Toronto’s Hospital for Sick Children, which houses the OCGC, and the Ontario Research and Development Challenge Fund, which helps support the OCGC, announced the addition of the $25 million Silicon Graphics Inc. supercomputer to the centre.

SGI claims it is the world’s largest publicly-available computational supercomputer. But Dr. Jamie Cuticchia, head of the OCGC, said he believes the 192-processor computer is not only the fastest public system being used for biological study, but is also more powerful than any machine doing such research in the private sphere.

He feels the SGI 3800 supersedes even private cluster systems (groups of PCs working in unison) because the machines composing the latter can not talk to each other or share memory.

“We have 178GB of RAM that can be accessed by one CPU or 192 CPUs,” Cuticchia said of the SGI 3800. “What we have with this upgrade is the fastest supercomputer on the planet dedicated only to biological processes.”

Cuticchia said the system, slated for substantial expansion over the next three years, drastically reduces the time needed to analyze biological information.

“One of the things we’ve done is taken all the short DNA segments (hundreds of thousands of which exist in public databases), and compared them to each other, like pieces in a puzzle,” Cuticchia said. This process, which took three months with the centre’s old system, can be accomplished in a day with the SGI Origin 3800, Cuticchia said.

He added the SGI Origin 3800 allows researchers to begin asking questions about protein to protein interactions and protein folding that are out of reach for scientists without this kind of computing power.

Since it opened a little over a year ago, the OCGC has been a featured part of the Ontario government’s genomics initiative. The Ontario Challenge Fund committed to a $75 million/five-year funding package last April, of which $8 million was earmarked for the OCGC. Government funding accounts for one-third of the centre’s support, with the remainder of financing coming from donations to the hospital and SGI.

Walter Stewart, director of global marketing for SGI’s research and education division, said Mountain View, Calif.-based SGI expects a substantial return from its investment in the OCGC. For example, pharmaceutical companies would purchase SGI solutions in effort to take advantage of advances made at the OCGC.

“We invest in research because we believe that out of that research will come applications that drive demand for SGI solutions,” Stewart said.

SGI investments range from genomics to computer fluid dynamic research, which Stewart said makes SGI a player in the aircraft industry.

SGI has been a partner with the Hospital for Sick Children since 1998, providing technology first to the hospital itself, and more recently, to the OCGC.

“We’ve always been a leader in Ontario, now we’re a leader in the world,” Cuticchia said. “What we’re saying to Ontario researchers is, ‘Now is the time for you to start thinking about large-scale biological research.'”

But it’s not just Ontario researchers who are able to exploit the power of the OCGC to research hot topics like the human genome and human disease genes. Between 300 and 500 scientists access the centre’s computational platform via the Internet. The OCGC serves as an application service provider, with academic researchers in Ontario using the platform free of charge and commercial users and academic researchers outside the process accessing the facilities on a cost-recovery basis.

The OCGC’s system includes applications like EMBOSS, which uses 150 different computer programs to analyze DNA and protein sequences, BLAST, a DNA homology searching program, and HTBLAST, a BLAST program designed to work seamlessly with the new SGI system.

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