[hpc-announce] What's New in XSEDE

Thu Sep 27 11:21:56 CDT 2012

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[XSEDE, Extreme Science and Engineering Discovery Environment]<https://xsede.org/>

What's New in XSEDE

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S E P T E M B E R   2 0 1 2

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"What's New in XSEDE" (previously "News from 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.

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[An atomic model of the tobacco mosaic virus (PDBID: 2OM3) visualized at several scales from a full length rod-like virus (top, tens of millions of atoms) to the atomic level details (bottom).]
An atomic model of the tobacco mosaic virus (PDBID: 2OM3) visualized at several scales from a full length rod-like virus (top, tens of millions of atoms) to the atomic level details (bottom).

Molecular matchmaking for drug discovery

In a world of potential compounds, how does a scientist find the one drug molecule that might match and bind to a disease molecule? Researchers at The University of Texas at Austin are working on faster ways for a supercomputer to find matching molecules using nanoscale images of the molecules. According to J. Tinsley Oden, director of the university's Institute for Computational Engineering and Sciences (ICES), the research has the potential to transform the way the drug discovery process works.

To solve these problems, Chandrajit Bajaj, computer science professor at The University of Texas at Austin, uses XSEDE-allocated resources Ranger and Lonestar, TACC's high-performance computing systems, and Longhorn, TACC's remote visualization system.

Read more about molecular matchmaking with XSEDE-allocated resources at TACC [arrow to link] <http://www.tacc.utexas.edu/news/feature-stories/2012/molecular-matchmaking>

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Four institutions awarded planning grant for Science Gateways Institute

The San Diego Supercomputer Center (SDSC) at the University of California, San Diego is the lead institution on a National Science Foundation (NSF) planning grant for a Science Gateways Institute. Through a one-year, $500,000 conceptualization award, the team has been asked to develop a strategic plan as part of the NSF's Software Institutes program. The Science Gateways Institute would connect often diverse resources in a scalable way that saves researchers and institutions both time and money by providing access to many of the tools used in cutting-edge research – telescopes, seismic shake tables, supercomputers, sky surveys, undersea sensors, and more. Other XSEDE partner institutions included in this grant are Indiana University, Purdue University and the Texas Advanced Computing Center (TACC) at The University of Texas at Austin.

Read more about the NSF planning grant for a Science Gateways Institute [arrow to link] <https://www.xsede.org/gateway-institute-planning-grant>

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Enhancing life sciences' use of PSC's Blacklight

Genomics has shifted into data-intensive overdrive. While it's an unprecedented blessing for the life sciences, it's also an unprecedented challenge for data processing and analysis.Pittsburgh Supercomputing Center (PSC) scientist and XSEDE consultant Phil Blood says that many large genomics assemblies simply couldn't be done without large shared memory, and with two partitions of 16 terabytes of shared memory, PSC's Blacklight is the largest shared-memory system in the world. To enhance PSC's Blacklight genomics capabilities, XSEDE's Extended Collaborative Support Services (ECSS) has made nearly all genomics software tools available for easy use — saving much time for researchers. This genomics work includes tracing the genetic underpinnings of mammalian social behavior and identifying enzymes that can degrade non-food plants, such as switchgrass and wheat straw, for more efficient production of biofuel.

Read more about genomics' use of PSC's Blacklight [arrow to link] <http://www.psc.edu/science/2012/assembly/>

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[Phylogeny of the 16S rRNA sequences used in this study. Gray branches correspond to the bacterial sequences recovered from the monogamous P. californicus, while the black branches related to the promiscuous P. maniculatus.]
Phylogeny of the 16S rRNA sequences used in this study. Gray branches correspond to the bacterial sequences recovered from the monogamous P. californicus, while the black branches relate to the promiscuous P. maniculatus.

Monogamy and the immune system

Researchers at the University of California, Berkeley recently conducted one of the first studies to use next-generation gene sequencing and high-performance computers to assess the influence of behavior on genes in a non-model species. As a National Science Foundation (NSF) graduate research fellow at Berkeley, Matthew MacManes learned that researchers could access NSF supercomputers through XSEDE. The alignment and analysis that MacManes accomplished on Ranger at the Texas Advanced Computing Center in a few weeks would have taken years with his local resources.

The California mouse (Peromyscus californicus) is characterized by a lifetime of monogamy; the deer mouse (Peromyscus maniculatus) is sexually promiscuous. MacManes and members of the research group discovered that the lifestyles of the two mice had a direct impact on the bacterial communities; furthermore, these differences correlate with enhanced diversifying selection on genes related to immunity against bacterial diseases. The results show that differences in social behavior can lead to changes in the selection pressures and gene-level evolutionary changes in a species and match findings in humans and other species with differential mating habits.

Read more about MacManes' research at TACC [arrow to link] <http://www.tacc.utexas.edu/news/feature-stories/2012/monogamy-and-the-immune-system>

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XSEDE names first cohort of Campus Champions Fellows

XSEDE recently selected the first four Campus Champions Fellows, pairing each Champion with a member of XSEDE's Extended Collaborative Support Services (ECSS) staff to work on science and engineering projects for about one year. Campus Champions are volunteers at their respective campuses who advise researchers on the use of high-end computing resources. The fellows program helps Champions increase their expertise while working in partnership with ECSS staff.

The four fellows selected to participate in the first round are:

  *   Dirk Colbry, a research specialist at the Institute for Cyber-Enabled Research at Michigan State University;
  *   Nasseer Idrisi, an assistant professor at the University of the Virgin Islands' Center for Marine and Environmental Studies;
  *   Liwen Shih, professor and computer engineering chair at the University of Houston-Clear Lake;
  *   Jack Smith, a research staff member with Marshall University and cyberinfrastructure coordinator at the West Virginia Higher Education Policy Commission.

Read more about the Campus Champions Fellows [arrow to link] <https://www.xsede.org/ccfellows-july2012>

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[Fluorish representing nutshell.]XSEDE in a nutshell

Following are events, deadlines and opportunities related to XSEDE.

  *   Agenda now online for the October 8 XSEDE workshop during iEEE conference in Chicago [arrow to link] <http://www.psc.edu/index.php/escience-2012-workshop>
  *   XSEDE celebrates Petascale Day at the National Center for Supercomputing Applications -- Check out all the events scheduled for October 15 (10/15, otherwise known as "ten to the fifteenth power") [arrow to link] <http://petascale.ncsa.illinois.edu/events.html>
  *   Visit XSEDE in Booth 2031 at SC12 in Salt Lake City, November 12-15 [arrow to link] <http://sc12.supercomputing.org/>

[National Science Foundation.]
XSEDE is supported by the National Science Foundation.

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