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Placing Landmarks on the Genome

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Placing Landmarks on the Genome What is XSEDE? The Extreme ScienceXSEDE and Engineering Discovery The five-year, $121 million project is supported by XSEDE is led by the University of Illinois’s National Environment (XSEDE) is the most advanced, powerful, the National Science Foundation. It replaces and Center for Supercomputing Applications. and robust collection of integrated digital resources expands on the National Science Foundation TeraGrid The partnership includes: and services in the world. It is a single virtual system project. More than 10,000 scientists used the TeraGrid • Carnegie Mellon University/Pittsburgh that scientists can use to interactively share to complete thousands of research projects, at no Supercomputing Center - University of Pittsburgh computing resources, data, and expertise. cost to the scientists. XSEDE continues that same • Center for Advanced Computing - Cornell University sort of work—with an expanded scope, generating • Indiana University • Jülich Supercomputing Centre more knowledge, and improving our world in an even • National Center for Atmospheric Research broader range of fields. • Ohio Supercomputer Center - The Ohio State University • Purdue University • Rice University • Shodor Education Foundation • Southeastern Universities Research Association • University of California Berkeley • San Diego Supercomputer Center - University of California San Diego • University of Chicago • National Center for Supercomputing Applications - University of Illinois at Urbana-Champaign • National Institute for Computational Sciences - University of Tennessee Knoxville/Oak Ridge National Laboratory • Texas Advanced Computing Center - The University of Texas at Austin • University of Virginia xsede.org Dawn of the XSEDE Era 2 No Charge Double Helix 20 Researchers derive the first accurate 3D John Towns, leader of the National Science structure of a synthetic double-helical Foundation’s new Extreme Science and molecule that holds promise for applications Engineering Discovery Environment, talks in biomedicine and nanotechnology about the vision for XSEDE and how it will build on the TeraGrid. A Recipe for Science Success 22 Collaboration between Open Science Grid and TeraGrid aims to give Science highlights researchers the right tools For the Birds 6 Table of Supercomputers and citizen scientists Education, Outreach, and Contents converge to pinpoint avian populations Training highlights Malaria Mystery Solved 8 Building Skills that Count 26 On the cover: Humans likely source of malarial infections XSEDE The Advanced Visualization A sampling of the education and outreach in great apes, not the other way around as Laboratory at the National programs offered by TeraGrid partners Center for Supercomputing previously thought Applications generated this Champions Help 28 visualization of supernova Ice, Ice, Baby 10 data from Volker Bromm at University of Washington researchers Campuses Connect The University of Texas at Austin. explore mysterious Antarctic sea ice Swarthmore exemplifies how dedicated The image represents an initial champions broaden TeraGrid/XSEDE reach data study, and the collaboration eventually yielded a final Improving Nature’s Top Recyclers 12 rendered scene for the feature The National Renewable Energy Laboratory Compelling, Ferocious Beauty 30 film ‘The Tree of Life.’ uses TeraGrid supercomputers to explore Cosmic simulations and visualization skill Courtesy of the Advanced new enzymes for renewable fuels contribute to acclaimed feature film Visualization Laboratory at ‘The Tree of Life’ the National Center for Supercomputing Applications Placing Landmarks on the 14 Taking Training on the Road 32 Genome Map Collaboration with Southeastern Researchers show for the first time that Universities Research Association differences in DNA between individuals provides visualization workshops can affect the binding of transcription factors to minority-serving institutions Turbulent Times 16 Being ‘Smart’ at Home 34 TeraGrid aids scientists in developing TeraGrid storage and visualization novel technique to reduce jet noise resources aid ‘smart grid’ research Cold Dark Matter Lives 18 An international team led by University of Washington astrophysicists appears to have solved the problem of dwarf galaxies XSEDE TERAGRID Dawn of the XSEDE era John Towns, leader of the National Science Foundation’s new Extreme Science and Engineering Discovery Environment, talks about the vision for XSEDE and how it will build on the TeraGrid. 02 03 John Towns XSEDE Project Director Research no longer typically happens in the context of a single XSEDE will also leverage GlobusOnline services to easily move investigator on a single campus. Instead, today’s investigators data from campus servers, laptops, and desktops, allowing are collaborating across institutional and geographic bound- high-performance data movement to and from XSEDE Dawn of the XSEDE era aries. To be successful, researchers need access to dispersed resources. resources, including instruments, data stores, and high-perfor- mance computers and, critically, to the tools and services that Of course, along with new services and tools, we also want to enable coordinated use and sharing of those resources. continue providing the strong support that people relied on throughout the TeraGrid’s decade of operation; we want to The intent with XSEDE is to create the integrated environment make the transition from TeraGrid to XSEDE as non-disruptive in which all of these resources and services are available. We as possible. Ralph Roskies and Nancy Wilkins-Diehr jointly lead aim to establish a cyberinfrastructure ecosystem that allows us XSEDE’s Extended Collaborative Support Services (ECSS), to interoperate with other resources, with other infrastructure which encompasses Advanced Support for Research Teams providers, and in which researchers and educators can be much (a continuation of TeraGrid’s Advanced Support for TeraGrid more productive and can begin to develop new capabilities. Applications), Advanced Support of Community Capabilities, and Advanced Support for Training, Education and Outreach. For example, we will lower the entry barrier for institutions and collaborations to connect to XSEDEnet by using National XSEDE ECSS will also include support for Novel and Innovative LambdaRail’s (NLR) FrameNet services. In Year 1, XSEDEnet will Projects, an effort led by Sergiu Sanielevici at PSC. This effort provide dedicated 10 Gbps connectivity to the core XD will extend support to domain areas that have not typically Service Providers (Indiana, NCSA, NICS, NCAR, PSC, Purdue, tapped into high-performance computing, such as economics SDSC and TACC); then in Year 2 XSEDE will add a service to and computational linguistics, and to under-represented enable collaborators to create on-demand high-performance communities and institutions. networks between XSEDE service providers and many other potential sites around the country. As XSEDE gets under way, what I find most exciting is the potential to include a lot more disciplinary areas and a lot more researchers who might not have had easy access to the resources in the past. New disciplines, new users, and being able to increase productivity in order to enable new science and engineering—that’s what makes the XSEDE project really exciting. XSEDE TERAGRID Science highlights 04 05 SCIENCE HIGHLIGHTS Discussion of cyberinfrastructure projects such as TeraGrid and XSEDE often focuses on flops and bytes and data transfer rates, on hardware and software, on code and computers. But what these projects are really about is gaining new knowledge. Over the past decade, thousands of researchers used the resources, tools, and support provided by TeraGrid to better Science highlights understand climate change, the flow of blood in our bodies, and the evolution of the universe. Thousands more investigators will use XSEDE to tackle these and many other challenges. The following pages offer just a small sampling of the research enabled by TeraGrid over the past year, and a hint of what may be to come with XSEDE. XSEDE TERAGRID For the Birds Supercomputers and citizen scientists converge to pinpoint avian populations Sometimes everything just comes together, creating a sum much greater than its parts. Such is the case with eBird, a bird-monitoring project by the Cornell Laboratory of Ornithology that is using a unique National Science Foundation (NSF) collaboration to revolutionize bird conservation and numerous areas of environmental science. “Three distinct entities came together to make this possible: citizen scientists, a unique statistical algorithm, and the existence of large-scale (high-performance computing) facilities,” says John Cobb, a principal investigator for TeraGrid at Oak Ridge National Laboratory (ORNL) in Tennessee. Birds are often the first to suffer when damage hits an ecosystem. For that reason they are a widely acknowledged environmental indicator. Thanks to the NSF’s Office of Cyberinfrastructure DataONE and TeraGrid initiatives, along with support from the Leon Levy Foundation, eBird was able to show, for the first time, how bird populations move week-by-week across Indigo Bunting (Passerina cyanea) distribution for June 28, 2008. America and identify the environmental conditions The map shows the predicted occurrence corrected for variation associated with these population movements. in detectability associated with search effort. This estimate was derived from a model using data from eBird and data describing the local environment.
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