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Eyeing End-Users, TimeLogic Adds New Gene Modeling Software to Modular DeCypher Line

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TimeLogic has taken another step in an effort to steer its FPGA-based DeCypher platform toward end-user bioinformatics tasks with the launch of a new software module for gene modeling.

The software, called GeneDetective, includes proprietary algorithms for aligning EST/cDNA or protein sequences to genomic regions, and identifying alternative splice forms for gene modeling. It is the fourth software package in the DeCypher line, which TimeLogic began offering in a modular format late last year.

DeCypher used to come preconfigured with a comprehensive bioinformatics software suite, but the company split those capabilities into three configurations in order to lower the price of the product: DeCypherBlast, DeCypherSW (with the Smith-Waterman algorithm), and DeCypherHMM (with hidden Markov modeling analysis).

GeneDetective rounds out the product offering and also gives the company some ammunition against Paracel, a competitor in the accelerated bioinformatics marketplace, which sells the GeneWise gene modeling algorithm as part of its GeneMatcher2 system.

Christopher Hoover, marketing manager for TimeLogic, said that GeneDetective “matched or exceeded” Genewise on a test set of independently validated genes.

Hoover did not disclose pricing information for GeneDetective, but said the software is priced lower than other commercial gene modeling algorithms. The company said previously that its DeCypher software/hardware modules start at $36,000 [BioInform 09-01-03]. GeneDetective is available as a software addition to an existing DeCypher system, or as a standalone system.

Hoover said that TimeLogic is seeing “strong growth from academic groups involved in large annotation projects,” and cited the University of Oklahoma Genome Center, the Duke Center for Human Genetics, the Salk Institute, and the University of Illinois, Urbana-Champaign among recent customer wins.

The new modular format of the DeCypher system appeals to academic customers, he said, because of its lower price as well as its flexibility. This combination, he said, “lets academic groups address their immediate computing bottlenecks with a dedicated resource, yet allows them to “extend their systems capabilities and performance over time” as their needs evolve.

Other New Additions

TimeLogic has also upgraded the DeCypher Engine FPGA card that it sells with the system. DeCypher Engine G4 offers a performance improvement of 83 percent over previous versions, Hoover said, and customers can swap their old cards for new ones and get “double the performance for often one-tenth the cost” of other systems, he said.

In addition, Hoover said that the latest version of DeCypher, version 7.5, includes a new web interface that enables users to build “personal” databases, of up to 200 megabytes, through their browser. The new release can also be integrated with company intranets, he said, so that search results from DeCypher can link to proprietary databases. The release also includes a simplified command line interface to enable “power users” to access the access the system from Windows, Linux, Solaris, or Mac OS X.

“We’re trying to focus on ease-of-use issues,” both for end-user biologists and for bioinformaticists, Hoover said. “It’s clear from publication trends that more comprehensive, high-quality bioinformatics is being done in research labs.

“Bioinformatics is migrating into the larger community as a research tool and is being embraced by wetlab scientists,” he added.

For companies like TimeLogic, the challenge is successfully marketing a tool originally designed for hardcore bioinformatics to that broader end-user community.

The wetlab market is potentially much larger than the company’s core bioinformatics user base, but TimeLogic faces stiff competition from bigger names — like IBM, Sun, Apple, and others — who are also targeting that community with pre-configured bioinformatics hardware/software systems.

The added competition “is validating our market, especially for smaller research groups, where researchers require a powerful and easy-to-implement solution for their BLAST-based sequence annotation and HMM-PFAM based protein function analysis,” Hoover said.

In addition, he said, TimeLogic’s new parent company, Active Motif, has increased TimeLogic’s sales capabilities. “Using their distribution channels brings us improved exposure in Europe,” he explained.

Hoover added that Active Motif’s cell biology product focus brings with it “a strong connection with research scientists” — which is a foot in the door of the end-user community that TimeLogic is trying to reach.

— BT

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