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Active Motif s TimeLogic to Expand DeCypher Market With Upcoming CodeQuest Workstation

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Active Motif's TimeLogic biocomputing business is preparing to launch a new product this September that will place its familiar DeCypher accelerator technology in a not-so-familiar environment — a desktop workstation.

TimeLogic, known for its enterprise-scale FPGA-based Decypher bioinformatics accelerator, is "diverging" its product line with the new tool, Chris Hoover, TimeLogic marketing manager at Active Motif, told BioInform last week. The upcoming product, called CodeQuest, has been developed for Active Motif's core market of bench biologists, rather than TimeLogic's historic user base of bioinformaticists running high-throughput analysis pipelines.

Hoover said the growing product line signals the successful integration of the TimeLogic business into Active Motif, following its acquisition by the reagent provider in late 2003 [BioInform 09-01-03].

"A lot of this has to do with the conclusion of the acquisition," he said. "We've been working closely on products that appeal to the Active Motif customer base." CodeQuest represents the first of these "bridge products," Hoover said, adding that the strategy "will evolve rapidly to include many wetlab-focused computing applications."


"While many new genome projects are being funded, we're seeing more people just using bioinformatics as standard tools in their research, and it hasn't gotten that much easier for them to do that. People still have to build large clusters."

In addition, Hoover said, demand for high-powered but easy-to-use bioinformatics tools is growing within the broader biology community. "While many new genome projects are being funded, we're seeing more people just using bioinformatics as standard tools in their research, and it hasn't gotten that much easier for them to do that. People still have to build large clusters."

Chris Wasden, marketing director at Active Motif, added, "Our belief is pretty much that the core customer of Active Motif — who isn't necessarily a bioinformaticist — would really love the information that bioinformatics can provide if only he or she could figure out how to do it."

Hoover did not disclose pricing information for CodeQuest, but said that it will be priced "in the range of a typical lab appliance."

CodeQuest includes a DeCypher accelerator card in a dual-CPU workstation — a choice of HP's xw8200 or xw9300. It comes with around 50 sequence-analysis packages, including several of TimeLogic's accelerated bioinformatics applications, such as DeCypherBlast, DeCypher HMM, DeCypherSW, and GeneDetective.

In addition, CodeQuest has its own drag-and-drop pipelining interface, called PipeWorks, which is expected to appeal to biologists because "you don't need complex scripting to build genome annotation pipelines," Hoover said. Users can use PipeWorks to build analytical workflows using tools within CodeQuest as well as their own applications.

Active Motif also announced a collaboration last week with Spain's BioAlma to co-develop a text-mining module for CodeQuest based on the company's AlmaKnowledgeServer literature-extraction technology. This module is expected to be available some time after the release of CodeQuest in the fall.

Hoover said that the text-mining capabilities will enable CodeQuest users to view the results of their bioinformatics analysis within a broader biological context. "We expect that by coupling literature mining with genome analysis, researchers will produce higher quality annotations," he said.

The text-mining tool may also help set the system apart in a growing field of preconfigured bioinformatics boxes targeted at smaller labs. IT vendors like Sun, Apple, and IBM are marketing mini-clusters bundled with bioinformatics software that can fit under a lab bench, while Orion Multisystems has released several versions of its hybrid "cluster workstation" pre-loaded with the BioTeam's iNquiry bioinformatics suite [BioInform 09-06-04].

More recently, at the Bio-IT World conference in May, new smaller-scale bundled software/hardware products were on display from cluster provider Microway and Unleashed Informatics [BioInform 05-23-05].

None of these systems includes text-mining capability, however, and none offers the performance gains of the DeCypher FPGA card, according to Hoover. "If you really are planning to do some serious throughput, I don't think you'll be able to approach the performance we get," he said.

But it's still unclear what kind of adoption rate any of these vendors are seeing for their preconfigured bioinformatics systems among end-user biologists.

Hoover admitted that TimeLogic's own customer base for DeCypher has remained "in the realm of the high-throughput people, and those people are generally not in the lab at all." The company has yet to see what kind of demand it will see in the market for CodeQuest.

In the meantime, TimeLogic is also embarking on a campaign that's more in line with its traditional customer base by targeting former customers of Paracel, its primary competitor in the bioinformatics accelerator market, which shut its doors last October [BioInform 10-04-04].

Paracel, a subsidiary of Celera, has maintained a small staff to support its existing contracts, but that support will run out this September — presenting an opportunity for TimeLogic to step in.

Hoover estimated that there are around 100 facilities with Paracel GeneMatcher or BlastMachine systems that could migrate to TimeLogic's platform. "A DeCypher system that fits in 4U of rack space makes a space-efficient replacement, and is much less expensive to purchase and operate than a cluster of equivalent performance," he said.

Hoover said that the company has already converted at least one former Paracel customer to its system — the Nijmegen Center for Molecular and Biomolecular Informatics in the Netherlands — and is in talks with several others, but he acknowledged that the expiration of Paracel's support contract has left many of the company's former customers undecided as to whether to stick with an unsupported system, switch to DeCypher, or opt for a cluster or other hardware platform.

Although "many of the sites are just beginning to explore options for replacing their Paracel gear," said Hoover, TimeLogic is confident that it will be able to switch over at least a few of them.

"The absence of support and software updates will become a liability for these groups since their critical pipelines depend upon uninterrupted processing," he said.

— Bernadette Toner ([email protected])

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