Georgia Tech announced today that the NSF, using money from the American Recovery and Reinvestment Act of 2009, has funded a four year, $1M effort to develop new petascale tools for genomic sequencing
Even on today’s fastest parallel computers, it could take centuries to analyze genome rearrangements for large, complex organisms. That is why the research team — which also includes Jijun Tang, an associate professor in the Department of Computer Science and Engineering at the University of South Carolina; and Stephen Schaeffer, an associate professor of biology at Penn State — is focusing on future generations of petascale machines, which will be able to process more than a thousand trillion, or 10^15, calculations per second. Today, most personal computers can only process a few hundred thousand calculations per second.
The researchers plan to develop new algorithms in an open-source software framework that will utilize the capabilities of parallel, petascale computing platforms to infer ancestral rearrangement events. The starting point for developing these new algorithms will be GRAPPA, an open-source code co-developed by Bader and initially released in 2000 that reconstructed the evolutionary relatedness among species.