Tech Shout

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For centuries, HIV has been the center of attention for medical experts around the world. With advancing technology we seem to be getting slowly yet steadily close to possible treatments for the dreaded disease. It has now come to light that scientists have used the world’s fastest supercomputer namely the Roadrunner to bring to existence what is claimed to be the largest HIV evolutionary tree. This has been done by researchers supporting Los Alamos National Laboratory’s role in the international Center for HIV/AIDS Vaccine Immunology (CHAVI) consortium.

Researchers may probably get closer to novel vaccine focus areas by mapping Darwinian evolutionary relationships which results in an HIV family tree. Using the Roadrunner supercomputer, researchers were able to analyze vast quantities of genetic sequences from HIV infected people. This they hoped would allow them to zero in on possible vaccine target areas.

Thanks to the supercomputer physicist Tanmoy Bhattacharya and HIV researcher Bette Korber were able to develop an evolutionary genetic family tree, known as a phylogenetic tree. This was done using samples taken by CHAVI across the globe from both chronic and acute HIV patients. Possibly identifying areas where vaccines would be most effective, with this tree, experts could look for similarities in the acute versus chronic sequences.

The evolutionary history of more than 10,000 sequences from over 400 HIV-infected individuals was compared in this study. Korber revealed that the idea was to identify common features of the transmitted virus that would aid them in their attempt to create a vaccine that would enable recognition of 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,” explains 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,” mentioned 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.

Developed by IBM in partnership with the Laboratory and the National Nuclear Security Administration, the Roadrunner supercomputer will finds its place in advanced physics and predictive simulations functions in a classified mode. Courtesy its robust performance, it assures the safety, security, and reliability of the U.S. nuclear deterrent. According to the TOP500 announcement at the November 2008 Supercomputing Conference in Austin Texas, the supercomputer is currently the worlds fastest with a speed of 1.105petaflop/s per second. It is believed to have again retained the leading position at the June ISC09 conference.

A distinct hybrid design is claimed to be the secret to the computer’s record-breaking performance. Two AMD Opteron dual-core processors plus four PowerXCell 8i processors used as computational accelerators are contained in each compute node in this cluster. Unique IBM-developed variant of the Cell processor used in the Sony PS3 are the accelerators used in the computer.

The CHAVI, established by the National Institute of Allergy and Infectious diseases aims at solving major problems in HIV vaccine development and design. With help from innovative devices like the Roadrunner, we seem to be efficiently getting a step closer.