Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

The Internet Was Delivered to the Masses; Parallel Computing Is Not Far Behind

22.08.2014

During the past few years, Virginia Tech’s Wu Feng has built upon a National Science Foundation (NSF) / Microsoft grant from the “Computing in the Cloud” program, and synergistically complemented it with subsequent collaborative grants, including a $6 million award from the Air Force on “big computing” for mini-drones and a $1 million award from NSF and the National Institutes of Health on “big data” for the life sciences.

As he wove together the “parallel computing” aspects from each grant, he was able to tell a much larger, more interconnected story –– one of delivering parallel computing to the masses. In doing so, he has worked to apply this democratization of parallel computing to an area of emerging importance -- the promise of personalized medicine.


Virginia Tech

Virginia Tech College of Engineering Professor Wu Feng has garnered support from NSF, Microsoft, the Air Force, and NIH among others, putting together a way to deliver parallel computing to the masses, much like the Internet's worldwide accessibility.

Microsoft took particular notice of Feng’s leadership in this cutting-edge research and succinctly worked the supercomputing expert’s collaborative ideas into one of its global advertising campaigns, describing Virginia Tech scientists and engineers as “leaders in harnessing supercomputer powers to deliver lifesaving treatments.”

This full-page ad ran this summer in the Washington Post, New York Times, USA Today, Wall Street Journal, Bloomberg Businessweek, United Hemispheres, The Economist, Forbes, Fortune, TIME, Popular Mechanics, and Golf Digest, as well as a host of other venues in Philadelphia, Washington, D.C., and Baltimore.

... more about:
»BIGDATA »NGS »Technology »cybersecurity »resources

“Delivering personalized medicine to the masses is just one of the grand challenge problems facing society,” said Feng, the Elizabeth and James E. Turner Fellow in Virginia Tech’s Department of Computer Science http://www.cs.vt.edu/  .

“To accelerate the discovery to such grand challenge problems requires more than the traditional pillars of scientific inquiry, namely theory and experimentation. It requires computing. Computing has become our ‘third pillar’ of scientific inquiry, complementing theory and experimentation. This third pillar can empower researchers to tackle problems previously viewed as infeasible.”

So, if computing faster and more efficiently holds the promise of accelerating discovery and innovation, why can’t we simply build faster and faster computers to tackle these grand challenge problems?

“In short, with the rise of ‘big data’, data is being generated faster than our ability to compute on it,” said Feng. “For instance, next-generation sequencers (NGS) double the amount of data generated every eight to nine months while our computational capability doubles only every 24 months, relative to Moore’s Law. Clearly, tripling our institutional computational resources every eight months is not a sustainable solution… and clearly not a fiscally responsible one either. This is where parallel computing in the cloud comes in.”

As noted by the National Institute of Standards and Technology, cloud computing is “a model for enabling convenient, on-demand network access to a shared pool of configurable computing resources (e.g., networks, servers, storage, applications, and services) that can be rapidly provisioned and released with minimal management effort or service provider interaction.”

“The implicit takeaway here is that the configurable computing resources are hosted and maintained by cloud providers such as Microsoft rather than the institution requiring the computing resources. So, rather than having an institution set-up, maintain, and support an information technology infrastructure that is seldom utilized anywhere near its capacity… and having to triple these resources every eight to nine months to keep up with the data deluge of next-generation sequencing, cloud computing is a viable and more cost effective avenue for accessing necessary computational resources on the fly and then releasing them when not needed,” Feng said.

Whether for traditional high-performance computing or cloud computing, Feng is seeking to transform the way that parallel computing systems and environments are designed and the way that people interact with them.

“My analogy would be the Internet, and how it has transformed the way people interact with information,” Feng added. “We need to make a similar transition with parallel computing, whether with the cloud or with traditional high-performance computing such as supercomputers.”

The groundwork for Feng’s big data research in a “cloud” began in the mid-2000s with a multi-institutional effort to identify missing gene annotations in genomes. This effort combined supercomputers from six U.S. institutions into an ad-hoc cloud and generated 0.5 petabytes of data that could only be stored in Tokyo, Japan.

By combining software Feng developed called mpiBLAST with his ad-hoc ‘big data’ framework called ParaMEDIC: Parallel Metadata Environment for Distributed I/O and Computing, he and his colleagues successfully addressed an important problem in genomics via supercomputing. They were able to reduce the time it took to identify and store missing gene annotations remotely in Japan from more than three years down to two weeks by simply changing the software infrastructure via parallel computing in their ad-hoc cloud.

This work is now being formalized and extended as part of an NSF/Microsoft Computing in the Cloud grant that seeks to commoditize biocomputing in the cloud.

The advent of NGS, on the heels of the above “missing genes” work, created a larger “big data” problem that resulted in an interdisciplinary grant from NVIDIA Foundation to Compute the Cure (for cancer) and the creation of the Open Genomics Engine, which was presented in a talk at the 2012 Graphic Processing Units (GPU) Technology Conference. Other related “big data” biocomputing tools that Feng and his group have created include Burrows-Wheeler Aligner (BWA)-Multicore, SeqInCloud, cuBLASTP, and GPU-RMAP. In turn, this research provided the basis for the recent $1 million NSF-NIH BIGDATA grant on parallel computing for next-generation sequencing in the life sciences.
.
The research from the above grants have provided the impetus for a new center at Virginia Tech -- Synergistic Environments for Experimental Computing (SEEC) -- co-funded by Virginia Tech’s Institute for Critical Technology and Applied Science http://www.ictas.vt.edu/ (ICTAS), the Office of Information Technology, and the Department of Computer Science. This center seeks to democratize parallel computing by synergistically co-designing algorithms, software, and hardware to accelerate discovery and innovation. As the founder and director of SEEC, Feng is concentrating on five areas for synergistic computing: cyber-physical systems where computing and physical systems intersect; health and life sciences, including the medical sciences; business and financial analytics; cybersecurity; and scientific simulation.

The members of the center represent some 20 different disciplines in seven different colleges and three institutes at Virginia Tech.

Feng, who also holds courtesy appointments in electrical and computer engineering http://www.ece.vt.edu/ and in health sciences http://www.fhs.vt.edu/ , has garnered more than $32 million in research funding during his career. Among his achievements, he founded the Supercomputing in Small Spaces http://sss.cs.vt.edu/ project in 2001 that created Green Destiny, a 240-node supercomputer, an energy efficient machine that would fit inside a closet.

These achievements led to the founding of the Green500, a project that identifies the greenest supercomputers in the world, and more recently, HokieSpeed, a computing resource for science and engineering that debuted as the greenest commodity supercomputer in the U.S. in 2011.

HPCwire named him twice to its Top People to Watch List in 2004 and in 2011.

Contact Information

Lynn Nystrom
Director of News
tansy@vt.edu
Phone: 540-231-4371

Lynn Nystrom | newswise

Further reports about: BIGDATA NGS Technology cybersecurity resources

More articles from Information Technology:

nachricht NASA CubeSat to test miniaturized weather satellite technology
10.11.2017 | NASA/Goddard Space Flight Center

nachricht New approach uses light instead of robots to assemble electronic components
08.11.2017 | The Optical Society

All articles from Information Technology >>>

The most recent press releases about innovation >>>

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

Im Focus: A “cosmic snake” reveals the structure of remote galaxies

The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.

Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...

Im Focus: Visual intelligence is not the same as IQ

Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.

That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...

Im Focus: Novel Nano-CT device creates high-resolution 3D-X-rays of tiny velvet worm legs

Computer Tomography (CT) is a standard procedure in hospitals, but so far, the technology has not been suitable for imaging extremely small objects. In PNAS, a team from the Technical University of Munich (TUM) describes a Nano-CT device that creates three-dimensional x-ray images at resolutions up to 100 nanometers. The first test application: Together with colleagues from the University of Kassel and Helmholtz-Zentrum Geesthacht the researchers analyzed the locomotory system of a velvet worm.

During a CT analysis, the object under investigation is x-rayed and a detector measures the respective amount of radiation absorbed from various angles....

Im Focus: Researchers Develop Data Bus for Quantum Computer

The quantum world is fragile; error correction codes are needed to protect the information stored in a quantum object from the deteriorating effects of noise. Quantum physicists in Innsbruck have developed a protocol to pass quantum information between differently encoded building blocks of a future quantum computer, such as processors and memories. Scientists may use this protocol in the future to build a data bus for quantum computers. The researchers have published their work in the journal Nature Communications.

Future quantum computers will be able to solve problems where conventional computers fail today. We are still far away from any large-scale implementation,...

Im Focus: Wrinkles give heat a jolt in pillared graphene

Rice University researchers test 3-D carbon nanostructures' thermal transport abilities

Pillared graphene would transfer heat better if the theoretical material had a few asymmetric junctions that caused wrinkles, according to Rice University...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Ecology Across Borders: International conference brings together 1,500 ecologists

15.11.2017 | Event News

Road into laboratory: Users discuss biaxial fatigue-testing for car and truck wheel

15.11.2017 | Event News

#Berlin5GWeek: The right network for Industry 4.0

30.10.2017 | Event News

 
Latest News

NASA detects solar flare pulses at Sun and Earth

17.11.2017 | Physics and Astronomy

NIST scientists discover how to switch liver cancer cell growth from 2-D to 3-D structures

17.11.2017 | Health and Medicine

The importance of biodiversity in forests could increase due to climate change

17.11.2017 | Studies and Analyses

VideoLinks
B2B-VideoLinks
More VideoLinks >>>