Pico announces bioinformatics results on FPGA cluster

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Pico Computing announced performance results for its FPGA-accelerated computing platform on a dot plot algorithm

Pico Computing…announced that it has achieved greater than 5000X acceleration of a bioinformatics sequence analysis and dot plot algorithm using a cluster of 112 commodity FPGA devices. The FPGA computing platform consumes less than 300 Watts of power and fits into a standard 4U server case.

A dot plot provides a way to understand the relationship between two DNA sequences; Greg Edvenson, a Senior Software Engineer at Pico Computing, developed on a single local FPGA before running on a larger system

Edvenson used a single FPGA device during initial algorithm development. The FPGA was encapsulated in a Pico Computing E-17 card attached directly to a laptop computer via an ExpressCard interface. After the algorithm was tested and working as a single hardware process, Edvenson then scaled up and replicated the algorithm for deployment on the FPGA cluster. C-to-FPGA tools provided by Impulse Accelerated Technologies were used during the development of the algorithms, reducing the need to write low-level HDL code.

There isn’t a customer involved here — the development and demonstration is all in-house. Still, it’s a interesting data point for the technology. More information about the demonstration in the press release [PDF].