News from the San Diego Supercomputer Center
October 2006
Friends and Colleagues,
This month, SDSC staff have been making the final preparations for Supercomputing 2006, which will be held in Tampa, Florida Sunday, November 12 through Friday, November 17. SDSC will host a booth (number 1915 on the Conference Exhibit Floor) with the theme "SDSC: Data to Discovery," highlighting SDSC's many activities in data-oriented high performance computing and Cyberinfrastructure. Come visit the booth for in-depth Discovery Sessions on timely topics in science and technology, as well as the much-requested return of the SDSC Booth Coffee Cart (would you like foam on that latte?)
SDSC Discovery Sessions (all held at the SDSC booth) will include:- From Data to Discovery (Tues., 10:30am-12:00pm)
- Everything you wanted to Know About Observing Systems (Tues., 2:00-3:00pm)
- Getting to Know the TeraGrid (Tues., 3:30-4:30pm)
- Petascale Science -- Scaling to 10,000+ Processors (Wed., 10:30-11:30am)
- Virtual Grid Application Development Software or VGrADS (Wed., 1:00-2:00pm)
- The Cyberinfrastructure Partnership (Wed., 2:30-3:30pm)
SDSC staff will also be active in the Technical Program. On Sunday, SDSC?s Ilkay Altintas will participate in a tutorial on "Introduction to Scientific Workflow Management and the Kepler System," and Jeff Sale will present an education tutorial on "Discover Data." The Poster Session on Tuesday will include a poster by SDSC computational scientist Ross Walker on "High Resolution, High Throughput Protein Structure Prediction Using IBM Blue Gene Supercomputers: Predicting CASP Targets in Record Time" with Srivatsan Raman and David Baker. Also on Tuesday, SDSC Director Fran Berman will co-lead a BOF session on "The Pathway to Petascale Science"" with Thom Dunning of NCSA and John Boisseau of TACC, and Nancy Wilkins-Diehr will chair a BOF on "Science Gateway, Portal and Other Community Interfaces to High End Resources."" On Wednesday, SDSC's Phil Andrews will participate in a panel on "Data Intensive Computing."
On the final day of the Conference, SDSC Director Fran Berman will lead a Panel on "100 Years of Digital Data"" (Friday morning from 10:30am-12:00pm). Distinguished members of the Panel include Tony Hey from MicroSoft, Chris Greer from NSF's Office of Cyberinfrastructure, Robert Chadduck from the National Archives and Records Administration, and William LeFurgy from the Library of Congress, who will offer their views on the challenges and opportunities involved in preserving today's increasing deluge of digital data. View a complete agenda of SDSC SC06 activities online.
We hope to see you at SC06 in Tampa and wish Nuggets readers a great month.
| More than Google – Sharper Views of Earth’s Surface for Geoscientists | |
 |  Geoscientists require higher resolution and more integrated information about the Earth’s topography than most of us who enjoy using Google Earth. SDSC staff in the NSF GEON project have collaborated with Arizona State University (ASU) researchers led by Professor Ramón Arrowsmith to democratize access to high resolution topography for geoscience research. As part of the GEON collaboration, the ASU and SDSC teams have developed a workflow (GEON LIDAR Workflow – GDW) that has integrated four Light Detection And Ranging (LiDAR) datasets to date, making these massive collections of high quality topographic data easily available to geoscientists for the first time. This Cyberinfrastructure lets geoscientists study the processes that shape the Earth’s surface in far greater detail than previously possible. The most recent data in the collection is the Southern San Andreas Laser Scan (or B4 Project - OSU/USGS/NCALM/NSF) with some 35 billion points. Users can interact with the system through the GEON portal. For more information see the article LiDAR Data Processing and the Active Tectonics Research Group at ASU. |
| Cyberinfrastructure for the Molecular Sciences – SDSC Releases GEMSTONE Version 1.0 | |
 | Researchers in the molecular sciences study some of the most challenging problems in science, such as protein-ligand interactions, which are important in rational drug design and understanding complex mechanisms in enzymes. To assist scientists with sophisticated hybrid techniques that combine the accuracy of ab initio quantum mechanical methods with the numerical scalability of classical methods, SDSC and its collaborators have developed GEMSTONE -- Grid Enabled Molecular Science Through Online Networked Environments. GEMSTONE is a full end-to-end Web services architecture for grid computing, including services for data management, remote job creation, and access to computation. Users access GEMSTONE grid services through a rich GUI-based front-end, integrated with the local desktop environment. The project is being developed with support from the NSF National Middleware Initiative, and collaborators span SDSC, the National Biomedical Computation Resource (NBCR) at UCSD, the University of Zurich, the University of Texas, El Paso, and UCSD's Center for Theoretical Biological Physics. For more information see the Release of Gemstone story on the Web and for downloads, screenshots, and tutorials see the GEMSTONE site. |
| The Science of Learning – New UCSD Center Partners with SDSC | |
 | Understanding how we learn is a key challenge for science and society. UCSD’s new NSF-funded Temporal Dynamics of Learning Center will focus on time-related factors, such as the pace at which new ideas are presented, that underlie effective learning and memory. This knowledge can lead to improved teaching techniques. The Center is led by UCSD Computer Science professor Gary Cottrell and colleagues at Vanderbilt University, Rutgers University, and other institutions. SDSC will contribute data sharing Cyberinfrastructure and expertise to the new Center, through a partnership between SDSC’s Reagan Moore and Professor Mark Appelbaum of UCSD’s Psychology department. The Learning Center’s Data Sharing Facility will enable the researchers to do large-scale data mining critical to understanding the wealth of data from projects, many of which will involve human subjects. The facility is also expected to serve as a data-sharing model for other interdisciplinary communities. For more information see Science of Learning Center comes to UC San Diego. |
| Natural History Magazine Features SDSC's TeacherTECH Website | |
 | SDSC?s TeacherTECH website was recognized in the Highlights column of this month's October Natural History. The TeacherTECH program brings together K-12 teachers and SDSC staff for science and technology education and training. The program provides on-site training at SDSC, a wealth of online materials, and follow-up groups for teachers to help them increase the science and technology expertise at their institutions. The October Natural History focused on earthquakes, directing readers to SDSC's TeacherTECH educational website for resources such as animations of a "virtual" 7.7 earthquake on the southern San Andreas Fault. The animation was created from a large-scale simulation of seismic activity conducted by Southern California Earthquake Center (SCEC) on SDSC's DataStar high performance computer. TeacherTECH was described as a remarkable resource for understanding earthquakes and other computational science topics. Visit the TeacherTECH website for more information. |
| A Historical Record of “Redlining” | |
 | “Redlining” is the practice of discriminating in housing or insurance, and is illegal when done on the basis of race. Of great historical significance, valuable documents on redlining of neighborhoods in the 1930s and 1940s in eight California cities will now be available online in a new project. The documents include neighborhood maps, interviews, financial and banking documents, and detailed city surveys. SDSC’s Richard Marciano, the University of California Humanities Research Institute’s (UCHRI) Director and UCI Professor David Theo Goldberg, and their collaborators were recently awarded an Institute of Museum and Library Services (IMLS) National Leadership Grant to support a “Testbed for the Redlining Archives of California’s Exclusionary Spaces (T-RACES)”. The project will develop and deploy data Cyberinfrastructure to bring the historical documents online. In addition to the immediate benefits of making this important historical information widely available to scholars, community groups, students, and the general public, this innovative project will serve as an important model of Cyberinfrastructure use. It is expected to encourage wider adoption of these powerful technologies in the humanities community. For more about the T-RACES project visit the UCHRI website and SDSC’s Sustainable Archives and Library Technologies lab. |
