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Accelerator Sector Shift: TimeLogic Sold, Paracel Peddles Linux Clusters


Like much of the bioinformatics sector, companies selling accelerated hardware solutions to the life science research community are evolving to address a broader customer base. Last week, TimeLogic was acquired by reagent provider Active Motif in a move to “connect wet lab biology with computational biology methods,” according to a company statement. Meanwhile, TimeLogic’s primary competitor, Paracel, took a step away from its core bioinformatics customer base with a new initiative to sell low-cost turnkey Linux clusters for general-purpose computing applications.

The moves follow closely behind Compugen’s announcement in July that it plans to sell its Bioccelerator product line to Biocceleration Ltd., a startup headed by Compugen founder Simchon Faigler.

The sector’s recent realignment doesn’t appear to stem from a lack of business. Paracel just installed a 28,800-CPU GeneMatcher2 system at the University of Calgary’s Faculty of Medicine, while TimeLogic recently announced deals with Myriad Proteomics, the Virginia Bioinformatics Institute, and the Japan Patent Office. But according to Chris Wasden, marketing manager at Active Motif, accelerator firms like TimeLogic could fare even better by getting the message to the right person at prospective client firms: “One of the things we thought [TimeLogic was] missing with their sales strategies is that they were going more after the IT person rather than the biologist … We think that when you’re dealing with the person at the bench who needs to use the hardware and software as opposed to the one who’s going to maintain it, you’re going to do a much better job of selling it to them.”

Chris Hoover, marketing manager at TimeLogic, agreed with Wasden’s assessment. “We grew up as an engineering-focused company, and computational biology is making inroads,” he said. “More people are getting used to these ideas and biologists are realizing the power of these big tools … so we think there’s going to be more and more overlap moving forward.”

The sentiment reflects the strategy Paracel embarked upon in May, when it relaunched with a revamped product line and a vow to focus more on end-users than systems administrators [BioInform 05-19-03]. Paracel’s latest product launch, its Cyclone Linux cluster, is a push in the opposite direction, extending its customer base — and competitor list — into the general-purpose computing realm.

Acceleration, Acquisition, Accessibility

As part of its relaunch in May, Paracel split its ASIC-based GeneMatcher accelerated hardware line into three separate models, each optimized to run different algorithms and priced between $69,000 and $99,000. TimeLogic is planning to follow a similar path following its acquisition by Active Motif. Within a month, Hoover said, TimeLogic will offer three separate versions of its FPGA-based DeCypher accelerated hardware product: one for Blast searches, one for Smith-Waterman alignments, and one for hidden Markov model analysis.

Pricing for the modules starts at $36,000, Hoover said — “considerably less” than the previous DeCypher product. “That will make it a little bit more accessible to people,” he said. “It will make it easier for departmental budgets. Sometimes there is an interest in one key area, and that’s the computational bottleneck, but our price point before made it a little bit hard for people to get into the system.”

TimeLogic will operate as a subsidiary of Active Motif and will retain the “TimeLogic” and “DeCypher” trademarks. Around six employees — mostly in sales, marketing, and manufacturing — will be relocated from TimeLogic’s current Crystal Bay, Nev., offices to Active Motif’s Carlsbad, Calif., headquarters. The move to Carlsbad — about 20 minutes north of San Diego — should be an instant benefit, according to Hoover. “It was hard to reach people in Crystal Bay,” he admitted.

The remainder of the company’s employees will continue to work from home, as they did under the “fairly virtual” working conditions at Time Logic, Hoover said. No other personnel changes are planned, he added.

“Customers of TimeLogic probably won’t even notice the change,” said Wadsen.

Dedicated Fan of Dedicated Computing

Paracel, meanwhile, is hoping to expand its reach into the general-purpose Beowulf market by packaging the Linux cluster backend it developed for its BlastMachine product — sans Blast — as a turnkey stack that starts at $13,500 for an 8-CPU system.

The company’s latest customer win, however, proves that Paracel doesn’t intend to veer too far away from its core customer base of compute-hungry bioinformaticists. Christoph Sensen, director of the Sun Center of Excellence for Visual Genomics at the University of Calgary’s Faculty of Medicine, said that he’s sworn off using clusters for database searches and other bioinformatics tasks in favor of dedicated hardware like GeneMatcher.

The 28,800-CPU system Paracel recently installed in his lab — an upgrade of a smaller GeneMatcher system installed three years ago — is able to process six genomes a day on the MAGPIE automated genome annotation system, Sensen said. Annotation data generated with the system for about 90 genomes will be available by the end of September via a browser called Bluejay at, he said.

Sensen is also providing access to the Calgary GeneMatcher system via the web at

Citing the high maintenance costs of Linux clusters, the large amount of space they take up, and the higher likelihood of “some student playing Doom” on a Beowulf system, Sensen opined that “the time of the cluster is nearing it’s end” for bioinformatics. Calling for a larger repertoire of accelerated algorithms for bioinformatics tasks such as protein folding and phylogenetic tree construction, Sensen said, “my prediction is that in the future we’ll have these dedicated devices doing their work, and then a main brain in the middle that farms out jobs … All the main brain does is integrate results with results from other systems. With that, you can get a fairly small server room with fairly low-maintenance systems that out-performs any cluster that you can think of — even the ASCI White at Los Alamos.”

— BT


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