Tackling Ebola With GPUs

A team of researchers from University of Illinois at Urbana-Champaign and Stanford University are using the Blue Waters supercomputer at the National Center for Supercomputing Applications (NCSA) to predict what antibody would most likely pair best with a protein that coats a virus. The work focuses on two strains of the Ebola virus, and multiple possible mutants of both strains.

Using CUDA and the 4,228 NVIDIA Tesla accelerators in the supercomputer, the researchers simulated the evolution of the Ebola virus and the most likely mutations of antibody that would combat that evolution. In nature, this is a trial and error process that results in many members of a population dying as it evolves to become resistant.

Team researcher and senior research scientist at the NCSA Eric Jakobsson hopes they may be able to “shortcut” that process and team up with the biotechnology industry to design synthetic antibodies that can be produced on a massive scale.

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Blue Waters is one of the most powerful supercomputers in the world and uses hundreds of thousands of computational cores to achieve peak performance of more than 13 quadrillion calculations per second.

Ebola isn’t the only virus the team is concerned about – tackling influenza is next in line.

“People are moving all around the world, people are carrying viruses with them. It’s really in the interests of the developed world to really attack viral infections all over the world, because we are not going to be isolated,” Jakobsson says. “We can’t effectively quarantine ourselves. So from self-interest, and also because it’s the right thing to do, we should gear up to attack the problem of viral infections around the world.”

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