Slideshow: Berkeley wields big data to beat cancer

BERKELEY, Calif. – Researchers showed progress accelerating the search for gene-based cures for cancer and expanding the field of computer theory at an annual event sponsored by the University of California at Berkeley. They also discussed work on next-generation processor architectures and an effort to speed the development of an Internet of Things.

Computer scientist David A. Patterson called for a million genome warehouse to advance work on a cure for cancer. Today separate repositories hold less than 10,000 pieces of genetic information, many of them only partial representations of genes.

"There’s a chance for computer science to help build fast and accurate genetic pipelines and accelerate the move to personalized therapies--I want this in time to help me and my family," he said, noting researchers today often delete genetic data after completing experiments.

Patterson helped develop a tool called SNAP that provides significantly faster and more accurate genetic analysis that tools typically used by cancer researchers today (see below). Benchmarking tools are still needed to improve what are still highly subjective methods used in the field, he said.


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Separately, the university will spend $60 million over ten years on a new institute aimed to stake out new frontiers in computer science. "We want to develop a new theory of computing that extends far beyond its current reach and encompasses problems in other fields," said Richard Karp who will direct the effort.

"Many phenomena can be viewed as computational," he said. "If you look at how a living cell operates we can think of it as information processing; an economy is an information processing activity," he added.

The institute will host a symposium in late May in one of its first efforts to gather experts from a broad range of fields to study the possibilities.