Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Scientists use world's fastest supercomputer to create the largest HIV evolutionary tree

29.10.2009
Mapping Darwinian evolutionary relationships results in an HIV family tree that may lead researchers to new vaccine focus areas

Supporting Los Alamos National Laboratory's role in the international Center for HIV/AIDS Vaccine Immunology (CHAVI) consortium, researchers are using the Roadrunner supercomputer to analyze vast quantities of genetic sequences from HIV infected people in the hope of zeroing in on possible vaccine target areas.

Physicist Tanmoy Bhattacharya and HIV researcher Bette Korber have used samples taken by CHAVI across the globe – from both chronic and acute HIV patients – and created an evolutionary genetic family tree, known as a phylogenetic tree, to look for similarities in the acute versus chronic sequences that may identify areas where vaccines would be most effective.

In this study the evolutionary history of more than 10,000 sequences from more than 400 HIV-infected individuals was compared.

The idea, according to Korber, is to identify common features of the transmitted virus, and attempt to create a vaccine that enables recognition the original transmitted virus before the body's immune response causes the virus to react and mutate.

"DNA Sequencing technology, however, is currently being revolutionized, and we are at the cusp of being able to obtain more than 100,000 viral sequences from a single person," said Korber. "For this new kind data to be useful, computational advances will have to keep pace with the experimental, and the current study begins to move us into this new era."

"The petascale supercomputer gives us the capacity to look for similarities across whole populations of acute patients," said Bhattacharya. "At this scale we can begin to figure out the relationships between chronic and acute infections using statistics to determine the interconnecting branches – and it is these interconnections where a specially-designed vaccine might be most effective.

The goal of CHAVI, established by the National Institute of Allergy and Infectious diseases, is to solve major problems in HIV vaccine development and design.

About Roadrunner, the world's fastest supercomputer, first to break the petaflop barrier

On Memorial Day, May 26, 2008, the "Roadrunner" supercomputer exceeded a sustained speed of 1 petaflop/s, or 1 million billion calculations per second. "Petaflop/s" is computer jargon—peta signifying the number 1 followed by 15 zeros (sometimes called a quadrillion) and flop/s meaning "floating point operation per second." Shortly after that it was named the world's fastest supercomputer by the TOP500 organization at the June 2008 International Supercomputing Conference in Dresden Germany.

The Roadrunner supercomputer, developed by IBM in partnership with the Laboratory and the National Nuclear Security Administration, will be used to perform advanced physics and predictive simulations in a classified mode to assure the safety, security, and reliability of the U.S. nuclear deterrent. The system will be used by scientists at the NNSA's Los Alamos, Sandia, and Lawrence Livermore national laboratories.

The secret to its record-breaking performance is a unique hybrid design. Each compute node in this cluster consists of two AMD Opteron™ dual-core processors plus four PowerXCell 8i™ processors used as computational accelerators. The accelerators used in Roadrunner are a special IBM-developed variant of the Cell processor used in the Sony PlayStation 3®. The node-attached Cell accelerators are what make Roadrunner different than typical clusters.

Roadrunner is still currently the world's fastest with a speed of 1.105 petaflop/s per second, according to the TOP500 announcement at the November 2008 Supercomputing Conference in Austin Texas, and it again retained the #1 position at the June ISC09 conference.

About Los Alamos National Laboratory (www.lanl.gov)

Los Alamos National Laboratory, a multidisciplinary research institution engaged in strategic science on behalf of national security, is operated by Los Alamos National Security, LLC, a team composed of Bechtel National, the University of California, The Babcock & Wilcox Company, and the Washington Division of URS for the Department of Energy's National Nuclear Security Administration.

Los Alamos enhances national security by ensuring the safety and reliability of the U.S. nuclear stockpile, developing technologies to reduce threats from weapons of mass destruction, and solving problems related to energy, environment, infrastructure, health, and global security concerns.

Kevin Roark | EurekAlert!
Further information:
http://www.lanl.gov

More articles from Information Technology:

nachricht Smarter robot vacuum cleaners for automated office cleaning
15.08.2017 | Fraunhofer-Institut für Arbeitswirtschaft und Organisation IAO

nachricht Researchers 3-D print first truly microfluidic 'lab on a chipl devices
15.08.2017 | Brigham Young University

All articles from Information Technology >>>

The most recent press releases about innovation >>>

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

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

Gold shines through properties of nano biosensors

17.08.2017 | Physics and Astronomy

Greenland ice flow likely to speed up: New data assert glaciers move over sediment, which gets more slippery as it gets wetter

17.08.2017 | Earth Sciences

Mars 2020 mission to use smart methods to seek signs of past life

17.08.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>