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Champions computing TimeLogic

March 7, 2002

TimeLogic Corp.
Jim Lindelien

Fascination with Science; Nose for Opportunity

What is the history of your organization’s involvement in life sciences?
Lindelien: I was motivated by a personal fascination with the science and an entrepreneurial nose that smelled an opportunity. In 1989, TimeLogic, a computer-engineering firm I founded in 1981, became involved with the development of hardware-accelerated genetic database search and analysis systems. I became aware of the great potential of bioinformatics, both as an exceptional growth market and for its potential research benefits, during a weekend visit with a friend working as a post-doc at Caltech. That’s where the prototype of the fluorescent DNA sequencer was developed. Although I did not fully appreciate all the molecular biology behind the workings of this device, I could understand that it was a high-performance “DNA to ASCII converter.”

What is your vision for the development of the life sciences market?
Lindelien: Working as a computer hardware and software engineer in the film and television industry, I was familiar with digital-signal-processing hardware, and I saw that it could be applied to genomics. Buried in the raw DNA sequence text stream of A, C, G, and T’s were instructions for building a molecular-scale self-replicating computing and information-processing machine—that’s what life is. But the DNA genome of each species is a cryptogram written in the strangely foreign hand of deep time and evolutionary change. You can’t just call IEEE and order the standards document describing how this information is encoded. Working on that puzzle struck me as a fascinating endeavor to undertake.

What organizational assets have you developed to serve this community?
Lindelien: We formed a team of key designers and scientific advisors who are able to apply the relatively new field of so-called “reconfigurable computing” (where the chips and computing topology of the processor arrays can be synthesized on-the-fly to suit each job) to the algorithms most important to bioinformatics. This combination of talents in two arcane fields—one science, one technology—forms our unfair advantage and barrier to entry to our market. Reconfigurable computing is like having “soft hardware,” or hardware that changes to suit the needs of the algorithm, rather than compiling a high-level C description of the algorithm into the fixed instruction set of a CPU. Our reconfigurable computer for bioinformatics, called DeCypher, uses this FPGA-chip-based form of computing to beat Moore’s Law and its constraint on CPU-based computing costs and speeds.

What products and services does your company provide to the life sciences market?
Lindelien: Our DeCypher biocomputing accelerators are designed to yield 100- to 1,000-fold raw speed gain per server, at 10- to 100-fold better price-performance ratio versus CPU-only execution. They do so for those bioinformatics algorithms that for a majority of the marketplace represent the worst IT computing loads on the most rapidly growing genetic databases. The raw speed gain per server means that each 3.5-inch rack mount DeCypher-accelerated Dell, Sun, or Compaq server replaces several racks of CPU-only servers with the RAM and disk system costs, while delivering the same throughput and with savings in all the other areas I mentioned.

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