[Bioclusters] Use of FPGA based BLAST accelerators?

James Cuff bioclusters@bioinformatics.org
Thu, 12 Dec 2002 08:19:19 +0000 (GMT)

On Wed, 11 Dec 2002, Amar Shan wrote:

> Does anyone on the list have any experience with using some of the
> commercially available FPGA accelerators for Bioinformatics applications
> (e.g. from Timelogic)?

I run one of each here, a DeCypher and a Paracel system.  Integrating
them seamlessly with the farm is the tricky part.  The Pfam group here
manage to use the DeCypher with fair amount of success.  We are still
working on the Paracel system, as it it more tricky to pipeline, as we
have one of the older machines.  Paracel now sell a product that includes
20odd Intel CPUs in conjunction with an accelerator.

I don't think this is too bad an idea at all if it comes out cost
neutral...  Depends on how much genewise/hmm's you plan to run.  The
accelerators really win in this segment.


Dr. James Cuff
Group Leader - Informatics Systems Group
Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
Tel: +44 (0) 1223-494880  Fax: +44 (0) 1223-494919