Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Solving DNA Puzzles is Overwhelming Computer Systems, Researchers Warn

16.07.2013
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-science knowledge. 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 a flood of unassembled genetic data 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, [they] 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 these 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 in order 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 the approach known as 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.

The article can be viewed online at:
http://spectrum.ieee.org/biomedical/devices/the-dna-data-deluge
Related links:
Ben Langmead’s website: http://www.cs.jhu.edu/~langmea/
Department of Computer Science: http://www.cs.jhu.edu/
Whiting School of Engineering: http://engineering.jhu.edu
Johns Hopkins University news releases can be found on the World Wide Web at http://www.jhu.edu/news_info/news/ Information on automatic E-mail delivery of science and medical news releases is available at the same address.
July 12, 2013 Tags: bioinformatics, computational genomics, computer science, DNA sequencers, human genome

Posted in Engineering, Medicine and Nursing, Technology

Office of Communications
Johns Hopkins University
901 South Bond Street, Suite 540
Baltimore, Maryland 21231
Phone: 443-287-9960 | Fax: 443-287-9920

Phil Sneiderman | EurekAlert!
Further information:
http://www.jhu.edu

More articles from Life Sciences:

nachricht Multi-institutional collaboration uncovers how molecular machines assemble
02.12.2016 | Salk Institute

nachricht Fertilized egg cells trigger and monitor loss of sperm’s epigenetic memory
02.12.2016 | IMBA - Institut für Molekulare Biotechnologie der Österreichischen Akademie der Wissenschaften GmbH

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

Im Focus: Molecules change shape when wet

Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water

In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...

Im Focus: Fraunhofer ISE Develops Highly Compact, High Frequency DC/DC Converter for Aviation

The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.

Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

UTSA study describes new minimally invasive device to treat cancer and other illnesses

02.12.2016 | Medical Engineering

Plasma-zapping process could yield trans fat-free soybean oil product

02.12.2016 | Agricultural and Forestry Science

What do Netflix, Google and planetary systems have in common?

02.12.2016 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>