Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Iowa State Researchers Developing ‘BIGDATA’ Toolbox to Help Genome Researchers

05.10.2012
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.”

Srinivas Aluru, Electrical and Computer Engineering,
515-294-3539, aluru@iastate.edu
Mike Krapfl, News Service, 515-294-4917, mkrapfl@iastate.edu

Mike Krapfl | Newswise Science News
Further information:
http://www.iastate.edu

More articles from Information Technology:

nachricht Cutting edge research for the industries of tomorrow – DFKI and NICT expand cooperation
21.03.2017 | Deutsches Forschungszentrum für Künstliche Intelligenz GmbH, DFKI

nachricht Molecular motor-powered biocomputers
20.03.2017 | Technische Universität Dresden

All articles from Information Technology >>>

The most recent press releases about innovation >>>

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

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Argon is not the 'dope' for metallic hydrogen

24.03.2017 | Materials Sciences

Astronomers find unexpected, dust-obscured star formation in distant galaxy

24.03.2017 | Physics and Astronomy

Gravitational wave kicks monster black hole out of galactic core

24.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>