Paracel is gone, but users who need speed-boosting gear have alternatives.

BY SALVATORE SALAMONE

November 19, 2004 | CRAY, FUJITSU, AND TIMELOGIC are just a few of the hardware companies hoping to fill the void left by the sudden recent demise of Paracel. They all offer products designed to accelerate scientific computations.

In late September, Paracel posted a notice on its Web site stating that it had discontinued all operations with the exception of ongoing support to current contract customers. Paracel would not comment on the business reasons that triggered its demise.

However, the company — which has been a business unit of Applera's Celera Genomics Group since 2000 — was adamant about its commitment to existing customers. "We will maintain staff to provide continual support," a Paracel spokesperson says. "Our primary goal is to [honor] all support contracts through the length of those contracts."

The shutdown came as a surprise. After all, in late June, Paracel announced that the Nestlé Research Center in Switzerland, the University of Würzburg in Germany, and the Institute of Molecular Pathology in Austria had all selected Paracel's GeneMatcher2 system to support their computational biology work. The GeneMatcher2 is a massively parallel supercomputer based on application-specific integrated circuits (ASICs) and designed to run sequence similarity search algorithms such as GeneWise, Hidden Markov Models, and Smith-Waterman. (See "Smokin' Supercomputing," Feb. 2004 Bio·IT World, page 26.)

One Paracel customer, who wished to remain anonymous, said he was sad to see the company go, but will investigate alternatives. "We use a combination of Linux clusters and the Paracel systems. When the service contracts run out, we will rethink our approach. It may be that the incremental improvements in cluster nodes between now and then will raise the clusters' performance to a level where they are comparable to Paracel's performance. We will also look at some of the other hardware accelerator alternatives on the market."


Increasing Options for Acceleration 
Paracel wasn't the only game in town when it came to hardware accelerators to improve the performance of life science software. For instance, TimeLogic offers DeCypher, which uses field-programmable gate array (FPGA) technology to speed the performance of bioinformatics applications. The two companies often would compete head-to-head. For instance, a recent paper in Nucleic Acids Research (Gordon, P.M.K., 32 (17); 2004) compared the use of hardware accelerators from Paracel and TimeLogic to run an oligonucleotides design program called Osprey.

In early October, Cray entered the market when it announced general availability of its Cray XD1 Supercomputer, the fruition of Cray's acquisition of OctigaBay. The OctigaBay system, and thus the Cray XD1, is a tightly integrated Linux computer that uses the Opteron processor and FPGA technology (see "Hanging Tight," Nov. 2003 Bio·IT World, page 70). It is well suited for search and sort algorithms.

"The Cray XD1 is not merely an Opteron and Linux parallel system," says Rich Partridge, enterprise systems analyst at the research and consulting firm D.H. Brown Associates. "This is a true supercomputer with balanced performance that commodity designed [systems] just cannot achieve."

The Cray XD1 joins a market that includes Star Bridge Systems' Hypercomputers, which also use FPGAs to improve the performance of applications.

And there are more options to come. Fujitsu is planning to soon release a 192-processor version of its BioServer, a high-speed informatics machine based on the company's commodity FR-V processors (low-cost chips that are typically used in consumer goods such as printers and digital cameras). One version will be a pre-configured appliance for drug discovery research — essentially a hardware accelerator for life science applications.

Fujitsu plans to develop a way for the BioServer to accelerate CAChe and BioMedCAChe software. The company says it will release the new BioServer in Japan later this year, and in the United States in 2005.






ILLUSTRATION BY ART VALERO