Now, 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 Roadrunner supercomputer, developed by IBM in partnership with the Laboratory and the National Nuclear Security Administration, is a 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.
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.
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