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IMPACT October 2012

O C T O B E R 2 0 1 2

"What's New in XSEDE" is a monthly e-newsletter providing information on scientific discoveries made possible by the Extreme Science and Engineering Discovery Environment, as well as the people, places, and programs involved. XSEDE is a five-year high-performance computing project supported by the National Science Foundation.

John Towns of XSEDE named to Compute Canada board of directors

John Towns, project director for XSEDE, joins leaders in industry, academia, and computational research as a newly elected member of the board of directors for Compute Canada. This inaugural board is a part of a new governance model the group launched in October to develop and support the shared use of advanced computing to enable research and innovation in Canada. The board's first meeting is scheduled for Nov. 19, 2012.

A tree depicting evolutionary relationships among frogs used in the study. Each branching point represents a speciation event from a common ancestor, and the timing of speciation is indicated on the scale bar. (Dates from Bossyut F and Roelants K, 2009, in Timetree of Life, eds Hedges SB, Kumar S, Oxford University Press, New York, pp 357-364.)

Growing the frog family tree through supercomputing

With the help of a new method of target enrichment for genome analysis, researchers are using the Ranger supercomputer at the Texas Advanced Computing Center (TACC) to help determine relationships among frog species and speed up the process of comparing species. David Hillis at The University of Texas at Austin developed the method with the help of Shannon Hedtke, David Cannatella, and Matt Morgan. When applying the new method to 16 frog species, representing 265 million years of evolutionary divergence, Ranger helped generate a new phylogenetic family tree for the frogs faster and more economically than ever before. The project shows the potential of target enrichment to accurately identify appropriate regions of genomic analysis and to overcome much of the data overload that currently inhibits the field.

Bridging models and research communities

ECSS couples climate, hydro models on Kraken

Climate change affects watersheds, and changes in watersheds affect climate change.

To examine the impact of hydological and climate changes, Cecilia DeLuca, a computational scientist at the National and Oceanic Atmospheric Administration, turned to XSEDE-allocated resources and assistance. XSEDE's Extended Collaborative Support Service (ECSS) and the National Institute for Computational Sciences (NICS) provided DeLuca and members of her research team with access to the resources and user support to help overcome obstacles. Led by DeLuca and Richard Rood of the University of Michigan, the team is using the Kraken supercomputer at NICS to bring together two separate data sets and simulations and gain valuable scientific feedback.

Pie chart showing approximate percentage of trades canceled within seconds or nanoseconds. See caption for details.

Fleeting Orders
On August 30, 2011, about 3 million orders were submitted to the NASDAQ exchange to trade the stock SPDR S&P 500 Trust (ticker symbol SPY). This image shows that 18.3 percent of the orders were cancelled within one millisecond, and 42.5 percent of orders had a lifespan of less than 50 milliseconds, less time than it takes to transfer a signal between New York and California. More than 40 percent of orders, in other words, disappeared before a trader in California could react.

Catching up with Wall Street

Strange things have been happening on Wall Street as the high-frequency trading (HFT) race escalates. To examine the impact of trading done by supercomputers, it takes a supercomputer, so Mao Ye, assistant professor of finance at the University of Illinois at Urbana-Champaign, and colleagues Chen Yao, also of Illinois, and Maureen O'Hara of Cornell used XSEDE resources and assistance to analyze the impact of HFT on the stock market.

Their study recently generated media attention and aroused policy debate. In November, the Financial Industry Regulatory Authority (FINRA), plans to vote on Ye's proposal to eliminate odd-lot trades, and the U.S. Senate is discussing another Ye proposal that would put a speed limit on HFT.

Scientists use TACC's Ranger supercomputer to analyze unusual genomes in garden-variety geraniums just like the blooms shown here.

Scholars test garden-variety mutants

Robert Jansen, professor of biology at The University of Texas at Austin, is applying next-generation sequencing methods to better understand why geraniums have evolved differently and faster than other plants. Speculation is that there is a direct connection between the high rate of change and the genes involved in DNA repair and recombination.

Jansen and his research team currently are gathering sequence data and assembling and analyzing it with the assistance of the Ranger supercomputer at the Texas Advanced Computing Center (TACC). Ranger speeds up sequence analyses by breaking down the process into small chunks and distributing them to thousands of computer processors. Ranger also served as a testbed for method development, allowing the researchers to compare multiple experimental approaches to find the best one. The examination of the genetic makeup of this unusual plant could lead to future agricultural breakthroughs.

XSEDE headed to Salt Lake City for SC12

XSEDE is well represented at SC12, this year's Supercomputing Conference in Salt Lake City, coming up in mid-November. Participation includes everything from XSEDE speakers and presenters in the technical program to XSEDE events to an XSEDE booth on the main aisle of the exhibit floor. If you are attending, visit Booth 2031 to learn more about XSEDE and talk with staff, and don't forget to also visit the XSEDE partners.

See XSEDE speakers, presenters, events and partner booth locations at SC12

XSEDE in a nutshell

Following are events, deadlines and opportunities related to XSEDE.

XSEDE issues Call For Participation in annual conference, XSEDE13, July 22-25 in San Diego