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Accelerators Offer Supercomputing for Bioinformatics on a Budget


While Celera, Compaq, and Sandia embark on building a 100 teraflop supercomputer, vendors at the other end of the supercomputing spectrum tout the advantages of hardware accelerators as a cost-effective alternative to pricey compute farms.

“Bioinformatics is a budget-limited process. It’s not a CPU-limited process,” said Jim Lindelien, CEO of TimeLogic. He said that accelerators such as Time-Logic’s DeCypher and Paracel’s newly released GeneMatcher 2 offer far better price/performance ratios than massively parallel general-purpose systems.

Lindelien said that for comparable costs, an accelerator system could yield 30 times more analysis per dollar than an Alpha farm.

Though general-purpose systems offer a level of flexibility not possible with accelerated systems, Lindelien noted that the maintenance and operating expense of massively parallel systems is a “hidden cost” that many buyers do not take into account when shopping around for computing solutions.

In addition, the need for flexibility is waning in many bioinformatics departments, which now run a number of common applications, such as Blast, hidden Markov models, and Smith-Waterman algorithms.
Lindelien said that it still makes sense to use a general-purpose system when optimizing an algorithm that is still in development or if you’re not sure what software will be run on the system. In most cases, however, an accelerator or hybrid system is the best answer, he said.

Paracel’s GeneMatcher 2 configurations start at $150,000 and run as high as $490,000 for systems installed in the United States. TimeLogic’s DeCypher system starts at $100,000 for the equivalent of a 500-CPU system. Lindelien said the system triples in speed for each doubling of price beyond the entry point.

The predecessor to the GeneMatcher 2, Paracel’s GeneMatcher-Plus, is currently installed at 40 pharmaceutical, biotechnology, and academic sites worldwide. Lindelien said that TimeLogic announced a number of new clients, including sales to sites previously using Paracel equipment, during 2000. “We believe DeCypher’s installed base may now be the largest, or soon will be,” he said.

And although Paracel claims the GeneMatcher 2 offers a much better price/performance ratio than DeCypher, Lindelien is not concerned about the competition. “There is plenty of demand for both companies’ products,” he said.

“I think both our DeCypher accelerator and Paracel’s are excellent choices when compared with pure, CPU-only, computing strategies,” Lindelien said. “From both an acquisition and total cost of ownership standpoint, accelerators are now a key component toward maximizing scientific yield at optimal computing cost.”

— BT

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