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CLC Bio Partners with SciEngines to Offer FPGA-Accelerated Bioinformatics

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CLC Bio said this week that it is partnering with high-performance computing firm SciEngine to integrate its server and desktop-based sequence analysis software tools with SciEngines' field programmable gate array-based platform.

Initially, SciEngines' Rivyera system will offer implementations of Blastn, Blastp, and the Smith-Waterman algorithm, with other algorithms added later, CLC Bio said.

The platform can offer up to 128 FPGAs per machine and scales to 1,792 FPGAs per rack. It also offers up to 320 gigabytes of distributed random access memory and up to 128 GB of shared memory with over 100 GB/s total bandwidth.

Preliminary Blastp runs to align 920,000 amino acids from the black cottonwood tree, Populus trichocarpa, to a database demonstrated a 188-fold increase in speed using a Rivyera S3-5000 computer with 64 FPGA chips when compared to a Xeon E5520 core, Jost Bissel, SciEngines' chief software architect, said in a statement.

He also said that the company has seen a similar speedup "in early benchmark tests of Blastn," adding that "we expect both Blast implementations to be accelerated even further before the final release."

Last year, CLC Bio's competitor, Auckland, NZ-based Biomatters said it was partnering with ActiveMotif's TimeLogic to allow users of its Geneious Server software to run bioinformatics jobs on Time Logic's accelerated DeCypher system, a field programmable gate array-based technology (BI 1/14/2011).

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