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September 30, 2013

Biomedicine Soars on HPC’s Wings

Tiffany Trader

Computing and simulation methods have had a transformative effect on science and research. From computational biology to the recently coined petascale humanities, the computer sciences are pervasive throughout the academic and research landscape. And as the computer resources become both more powerful and easier to use, this transformative potential is even greater. The biomedical research sector is perhaps particularly illustrative of this on-going paradigm shift.

At a recent conference, prominent experts in biomedicine from government, academia and industry gathered to discuss HPC’s role in transforming bioscience. The event, titled “Current Challenges in Computing 2013: Biomedical Research,” or CCubed, was held earlier this month in Napa thanks to support from Lawrence Livermore National Laboratory and funding from IBM.

The attendees identified two key points:

+ The latest generation of high performance computers has the potential to transform the biomedical field in ways unthinkable just a few years ago.

+ There are further opportunities for accelerating the development of biomedical tools using petaflop class supercomputers.

“Computing is at a tipping point where it can play a much larger role in biomedical research,” said Fred Streitz, director of LLNL’s Institute for Scientific Computing Research and the High Performance Computing Innovation Center. “This is because of the level of computing power we’re now reaching and the fact that the biomedical community is becoming aware of HPC potential.”

Streitz added that “the promise of computing in the biology space was overhyped 10 years ago.” According to him the claims were on-target, but a decade too early. The best systems of the time were outmatched in terms of scale and sophistication. In the last ten years, however, both biology and computing have improved sufficiently to tackle these complex modeling challenges.

The current generation of leadership-class machines has crossed over into new territory by being able to model entire systems and not just parts of a system. For example, scientists can now model organs, like the human heart, beating in almost real-time. “The field is starting to realize they can use computing as a tool in a way they were not able to five years ago,” observed Streitz.

The inflection point does not only apply to computing; the event also emphasized the co-occurring need for data-based insight. The big data aspect of bioscience is the purview of bioinformatics. The two sides – HPC and big data – will inform and shape each other.

As Anna Barker, director, Transformative Healthcare Knowledge Networks, said: “Events like CCubed help advance biomedical research by bringing together eclectic thinkers who offer fresh perspective on how we can begin to manage and analyze this data, and how we can turn it into real knowledge.”

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