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Solving DNA puzzles is overwhelming computer systems, researchers warn
Date:7/15/2013

netic jigsaw pieces, and a computer is needed to assemble the picture. Therein lies the problem, Schatz and Langmead say: Improvements in computer programs have not kept pace with the enhancements and widespread use of the sequencers that are cranking out huge amounts of data. The result is, the puzzle cannot be pieced together in a timely manner.

"It's a problem that threatens to hold back this revolutionary technology," the authors say in their article. "Computing, not sequencing, is now the slower and more costly aspect of genomics research."

The authors then detail possible computing solutions that could help erase this digital bottleneck. In his own research at Johns Hopkins, co-author Langmead is working on some of these remedies.

"The battle is really taking place on two fronts," he said. "We need algorithms that are more clever at solving these data issues, and we need to harness more computing power."

An algorithm is a recipe or a series of steps -- such as searching through data or doing math calculations -- that a computer must complete to accomplish a task.

"With cleverer algorithms," Langmead said, "you can do more steps with a fixed amount of computing power and time -- and get more work done."

The Johns Hopkins researcher has also had extensive experience in the second digital battle zone: assembling more computing power. This can be accomplished by putting multiple computers to work on assembling the DNA jigsaw puzzle. The linked machines can be at a single location or at multiple sites connected over the Internet through cloud computing. For the latter option, Langmead said, scientists may be able to do their work more quickly by tapping into the huge computing centers run by companies such as Amazon and "renting" time on these systems.

Langmead said he and Schatz wrote the IEEE Spectrum article to call attention to a significant computing problem and to jumpstart efforts to address i
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Contact: Phil Sneiderman
prs@jhu.edu
443-287-9960
Johns Hopkins University
Source:Eurekalert

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