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Clusters and Coordinates

Oct. 10, 2007 | “We generate a lot of data,” says Steve Lombardi, rather stating the obvious. “We do near real-time image processing. We take an image of an XY coordinate, we do that 45,000 times, switch the cells, do the other, then switch again.

“We’re reading these images through time and connecting the dots. In real time, we’re taking the entire data set and compressing it into XY space where we only have the signal. That’s a pretty heavy computational process, but it keeps up with the instrument.

At the end of the run, you don’t have to process the data and wait — you can start the next run while you’re porting the data off to the informatics.

“It’s a tower, with graphic processing chips used in the gaming industry, incredibly inexpensive and phenomenally compute intensive. We can do it for a relatively reasonable amount of money, but it’s a significant part of the cost of the box.”

In reference to the bioinformatics alignment engine Lombardi said, “We’ll source this — an informatics tower that at today’s costs is $150,000.  It’s a 10-multiprocessor Linux Cluster Blade that has field programmable gate arrays that can take 30 billion bases and align them to a reference sequence in less than 24 hours.”

Lombardi and Kristen Stoops, the company’s head of bioinformatics business development, are evaluating potential informatics collaborators. “We’re going open source with the image processing software and the informatics...  Then we’ll be working with partners to figure out who are the best partners to source this. The Broad Institute isn’t going to buy this, but the academic health centers will.”  --K.D.

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