Solving DNA puzzles is overwhelming computer systems, researchers warn

Jul 15, 2013

(Phys.org) —Imagine millions of jigsaw puzzle pieces scattered across a football field, with too few people and too little time available to assemble the picture.

Scientists in the new but fast-growing field of computational genomics are facing a similar dilemma. In recent decades, these researchers have begun to assemble the chemical blueprints of the DNA found in humans, animals, plants and microbes, unlocking a door that will likely lead to better healthcare and greatly expanded life-. But a major obstacle now threatens the speedy movement of DNA's secrets into research labs, two scholars in the field are warning.

This logjam has occurred, the researchers say, because the flood of unassembled is being produced much faster than current computers can turn it into useful information. That's the premise of a new article, co-written by a Johns Hopkins bioinformatics expert and published in the July 2013 issue of IEEE Spectrum. The piece, titled "DNA and the Data Deluge," was co-authored by Michael C. Schatz, an assistant professor of quantitative biology at Cold Spring Harbor Laboratory, in New York state; and Ben Langmead, an assistant professor of computer science in Johns Hopkins' Whiting School of Engineering.

In their article, the authors trace the rapidly increasing speed and declining cost of machines called DNA sequencers, which chop extremely long strands of biochemical components into more manageable small segments. But, the authors point out, these sequencers do not yield important biological information that researchers "can read like a book."

Instead, the article says, the sequencing machines "generate something like an enormous stack of shredded newspapers, without any organization of the fragments. The stack is far too large to deal with manually, so the problem of sifting through all the fragments is delegated to computer programs."

In other words, the sequencers produce the genetic 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 it. The magazine describes itself as the flagship publication of the IEEE, the world's largest professional technology association.

"We hope the people who read our article can contribute to some solutions and make the work of genomic scientist much easier," he said.

Explore further: Designing exascale computers

More information: spectrum.ieee.org/biomedical/d… /the-dna-data-deluge

Related Stories

Cloud computing method greatly increases gene analysis

Sep 08, 2010

Researchers at the Johns Hopkins Bloomberg School of Public Health have developed new software that greatly improves the speed at which scientists can analyze RNA sequencing data. RNA sequencing is used to compare differences ...

'Condor' brings genome assembly down to Earth

Jul 20, 2010

(PhysOrg.com) -- Borrowing computing power from idle sources will help geneticists sidestep the multimillion-dollar cost of reconstituting the flood of data produced by next-generation genome-sequencing machines.

Cornell jigsaw solver uses shape-blind algorithm

Jun 17, 2012

(Phys.org) -- A Cornell scientist has come up with an algorithm that can sift through 10,000 pieces of a jigsaw in 24 hours to complete the puzzle. Andrew Gallagher at Cornell University in Ithaca, New York, ...

A genomic CluE for cloud computing

Apr 23, 2009

DNA sequencing is the next frontier in biological research. As new sequencing technology becomes more efficient and affordable, it is increasingly available to small laboratories. Thus, sequencing data is being generated ...

Recommended for you

Designing exascale computers

13 hours ago

"Imagine a heart surgeon operating to repair a blocked coronary artery. Someday soon, the surgeon might run a detailed computer simulation of blood flowing through the patient's arteries, showing how millions ...

User comments : 1

Adjust slider to filter visible comments by rank

Display comments: newest first

Lischyn
1 / 5 (2) Jul 15, 2013
I hope they are getting rid of the bloated operating systems i.e. windows, mac, etc. and writing an operating system from scratch specifically to deal with DNA.