Featured Research

from universities, journals, and other organizations

Researchers developing 'BIGDATA' toolbox to help genome researchers

Date:
October 3, 2012
Source:
Iowa State University
Summary:
The latest DNA sequencing technology is burying researchers in trillions of bytes of data. Researchers are now developing high performance computing tools that will help researchers analyze all that data.

Today's life scientists are producing genomes galore. But there's a problem: The latest DNA sequencing instruments are burying researchers in trillions of bytes of data and overwhelming existing tools in biological computing. It doesn't help that there's a variety of sequencing instruments feeding a diverse set of applications.

Iowa State University's Srinivas Aluru is leading a research team that's developing a set of solutions using high performance computing. The researchers want to develop core techniques, parallel algorithms and software libraries to help researchers adapt parallel computing techniques to high-throughput DNA sequencing, the next generation of sequencing technologies.

Those technologies are now ubiquitous, "enabling single investigators with limited budgets to carry out what could only be accomplished by an international network of major sequencing centers just a decade ago," said Aluru, the Ross Martin Mehl and Marylyne Munas Mehl Professor of Computer Engineering at Iowa State.

"Seven years ago we were able to sequence DNA one fragment at a time," he said. "Now researchers can read up to 6 billion DNA sequences in one experiment.

"How do we address these big data issues?"

A three-year, $2 million grant from the BIGDATA program of the National Science Foundation and the National Institutes of Health will support the search for a solution by Aluru and researchers from Iowa State, Stanford University, Virginia Tech and the University of Michigan. In addition to Aluru, the project's leaders at Iowa State are Patrick Schnable, Iowa State's Baker Professor of Agronomy and director of the centers for Plant Genomics and Carbon Capturing Crops, and Jaroslaw Zola, a former research assistant professor in electrical and computer engineering who recently moved to Rutgers University.

The majority of the grant -- $1.3 million -- will support research at Iowa State. And Aluru is quick to say that none of the grant will support hardware development.

Researchers will start by identifying a large set of building blocks frequently used in genomic studies. They'll develop the parallel algorithms and high performance implementations needed to do the necessary data analysis. And they'll wrap all of those technologies in software libraries researchers can access for help. On top of all that, they'll design a domain specific language that automatically generates computing codes for researchers.

Aluru said that should be much more effective than asking high performance computing specialists to develop parallel approaches to each and every application.

"The goal is to empower the broader community to benefit from clever parallel algorithms, highly tuned implementations and specialized high performance computing hardware, without requiring expertise in any of these," says a summary of the research project.

Aluru said the resulting software libraries will be fully open-sourced. Researchers will be free to use the libraries while developing, editing and modifying them as needed.

"We're hoping this approach can be the most cost-effective and fastest way to gain adoption in the research community," Aluru said. "We want to get everybody up to speed using high performance computing."


Story Source:

The above story is based on materials provided by Iowa State University. Note: Materials may be edited for content and length.


Cite This Page:

Iowa State University. "Researchers developing 'BIGDATA' toolbox to help genome researchers." ScienceDaily. ScienceDaily, 3 October 2012. <www.sciencedaily.com/releases/2012/10/121003141058.htm>.
Iowa State University. (2012, October 3). Researchers developing 'BIGDATA' toolbox to help genome researchers. ScienceDaily. Retrieved September 17, 2014 from www.sciencedaily.com/releases/2012/10/121003141058.htm
Iowa State University. "Researchers developing 'BIGDATA' toolbox to help genome researchers." ScienceDaily. www.sciencedaily.com/releases/2012/10/121003141058.htm (accessed September 17, 2014).

Share This



More Computers & Math News

Wednesday, September 17, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

FBI Finishes $1 Billion Facial Recognition System

FBI Finishes $1 Billion Facial Recognition System

Newsy (Sep. 15, 2014) The FBI announced it plans to make its Next Generation Identification System available to law enforcement, but some privacy advocates are worried. Video provided by Newsy
Powered by NewsLook.com
A+ for Apple iPhone Pre-Sales

A+ for Apple iPhone Pre-Sales

Reuters - Business Video Online (Sep. 15, 2014) Apple says it received a record 4 million first-day pre-orders for its new iPhone 6 and iPhone 6 Plus, pushing delivery dates into October. Bobbi Rebell reports. Video provided by Reuters
Powered by NewsLook.com
Microsoft to Buy 'Minecraft' Maker for $2.5B

Microsoft to Buy 'Minecraft' Maker for $2.5B

AP (Sep. 15, 2014) Microsoft will acquire the maker of the long-running hit game Minecraft for $2.5 billion as the company continues to invest in its Xbox gaming platform and looks to grab attention on mobile phones. (Sept. 15) Video provided by AP
Powered by NewsLook.com
Manufacturer Prints 3-D Car In Record Time

Manufacturer Prints 3-D Car In Record Time

Newsy (Sep. 15, 2014) Automobile manufacturer Local Motors created a drivable electric car using a 3-D printer. Printing the body only took 44 hours. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

    Environment News

      Technology News



      Save/Print:
      Share:

      Free Subscriptions


      Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

      Get Social & Mobile


      Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

      Have Feedback?


      Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
      Mobile: iPhone Android Web
      Follow: Facebook Twitter Google+
      Subscribe: RSS Feeds Email Newsletters
      Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins