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News About the NPACI and SDSC Community

SDSC Receives Six ITR Awards

SDSC has been awarded six highly competitive National Science Foundation Information Technology Research (ITR) awards. SDSC researchers will participate in projects ranging from earthquake modeling and prediction to building the National Virtual Observatory and integrating wireless real-time oceanographic and environmental data. Researchers from SDSC’s Data and Knowledge Systems program (DAKS) are participating in all six of the awards.

“It’s a real sign of the recognized quality of SDSC’s work that so many of the projects we’re participating in were funded,” said Fran Berman, SDSC and NPACI director. “Through this NSF program, SDSC researchers will make major contributions to both basic research and practical solutions to advance science and engineering in the new century.”

Although the average ITR award rate is only 15 percent, six out of eight proposals in which SDSC participated were awarded. ITR projects focus on fundamental research in information technology and its innovative uses in science and engineering.

ITR projects in which SDSC researchers are participating include:

• The Southern California Earthquake Center’s “SCEC Community Modeling Environment: An Information Infrastructure for System-Level Earthquake Research.” This is a $10 million, five-year project with collaborators in many institutions.

• Exploring the Environment in Time: Wireless Networks and Real-Time Management. This three-year, $3.2 million project will use sensor arrays to monitor such interrelated environmental factors as weather, fire hazard, water availability and quality, snow pack in the Sierras, wildlife distribution and movement, and seismic hazards in southern California.

• SIO Explorer: Bridging the Gap between Libraries and Data Archives. In this three-year award, UCSD researchers at the Institute for Geophysics and Planetary Physics, SIO, and SDSC will build on recent developments in database and digital library technology to create a model that can rescue irreplaceable scientific archives while they are still accessible, place them under cost-effective modern database control, and make them available to a wide set of users.

• Enabling Creation and Use of GeoGrids for Next-Generation Geospatial Information. In this three-year, $1.5 million project, researchers at the University of Maine, SDSC, and Iowa State University will develop concepts, algorithms, and system architectures to enable users on a geographical or spatial grid to query, analyze, and contribute to quality-aware geospatial information that can encompass multiple variables.

• The International Virtual Data Grid Laboratory (iVDGL). This five-year, $13.6 million project will be carried out by a consortium of 15 universities and four national laboratories. In partnership with the European Union, Japan, Australia, and, later, other nations and international groups, the iVDGL will provide a large-scale computational resource for scientific experiments in academic fields such as physics, astronomy, biology, and engineering. (v 5.21)

Computational Chemist Kim Baldridge Elected Fellow of AAAS

Computational chemist Kim K. Baldridge, SDSC associate director for Integrative Biology and adjunct professor of chemistry at UCSD, has been elected a fellow with the American Association for the Advancement of Science (AAAS). She was being honored “for the development of important tools in quantum chemistry and the insightful application of these tools in chemistry and biochemistry.” Baldridge will be recognized at the annual meeting of AAAS in Boston on February 16, 2002.

Baldridge, also a fellow of the American Physical Society, received the Agnes Faye Morgan Research Award in 2000 from Iota Sigma Pi, the national honor society for women in chemistry.

Baldridge’s research uses computationally derived chemical and physical properties in conjunction with laboratory experiments to enhance the understanding of technologically important chemical structures and reaction processes. (v 5.21)

SDSC Focusing on Five Strategic Areas

Under the leadership of Director Fran Berman, SDSC has refined the focus of its activities to five strategic program areas: Integrative Biosciences, Data and Knowledge Systems, Grid and Cluster Computing, High-End Computing, and Computational Sciences.

“SDSC is uniquely positioned to conduct research and development at a scale and with a level of synergy that cannot be achieved within traditional academic departments,” said Berman. “Through these program areas, SDSC will pursue large, integrated projects of national importance with the potential for significant impact.”

In a process in which the entire staff of SDSC contributed, the strategic areas were selected to focus on the center’s strengths and to increase the impact of its technical accomplishments. “The key metric of SDSC’s success is the impact of its research results, technology, and infrastructure,” Berman said. “Deep impact is achieved when our projects directly promote scientific breakthroughs. Broad impact is achieved when large communities of users adopt our technologies. And future impact is achieved when our activities provide a window to science for new audiences, such as students, potential user communities, and the general public.” (v 5.20)

Grid Teams Joining in $12 Million Project

Research centers from across the nation will collaborate on a $12 million project to develop middleware, software that allows scientists to share applications, scientific instruments and data, and collaborate with colleagues across the Internet.

The NSF Middleware Initiative (NMI) will create and deploy advanced network services that will make it easier for researchers to access a wide range of resources available through high-performance networks. For example, they will be able to share scientific tools, such as telescopes or modeling software, access supercomputing systems and databases, and run simulations in real-time with colleagues across the country and around the world.

Two groups will receive the awards. The Grids Research Integration Deployment and Support (GRIDS) Center, including Information Sciences Institute, Chicago, NCSA, SDSC, and the University of Wisconsin. A team formed by Internet2 includes EDUCAUSE and the Southeastern Universities Research Association.

“We believe that middleware and a comprehensive middleware infrastructure will be the key to creating a network infrastructure that can be used by the worldwide research community to share ideas, conduct research, and make new discoveries,” said Carl Kesselman, co-leader of NPACI’s Metasystems (Grid Computing) thrust area. “There is a world of resources and information out there, and we intend to bring it to members of the scientific community in a seamless manner, so that they can focus specifically on their research.” (v 5.20)

SDSC Researcher Wins Molecular Docking Grant

Researchers investigating molecular docking recently won a three-year, $1 million grant from the U.S. Department of Energy to model how proteins interact. The researchers, led by Julie Mitchell, assistant research scientist at SDSC, are developing ways to improve computational models that describe the structure of biomolecules.

“Our goal in this project is to model protein interactions in a way that accurately approximates the biology while remaining computationally efficient,” said Mitchell. Her work has focused on ways of making parallel code used for molecular docking run more efficiently utilizing resources such as the IBM Blue Horizon at SDSC.

Mitchell has been collaborating with Lynn Ten Eyck at SDSC, Victoria Roberts at The Scripps Research Institute, and Michael Holst, J. Ben Rosen, and J. Andrew McCammon at UCSD. (v 5.20)

SDSC Collaborating on Project to Study Endangered Primates

SDSC will participate in a five-year, $3.8 million NSF-supported collaboration to establish an Integrated Primate Biomaterials and Information Resource to preserve biomaterials such as blood from primate species. Other partners in the consortium include the Zoological Society of San Diego’s Center for Research in Endangered Species (CRES), the International Species Inventory System (ISIS), the Coriell Institute for Medical Research, and Princeton University.

The resource will provide primate biomaterials such as DNA samples and cell lines for research. This program will probe questions that range from wild primate distribution and conservation to human and primate origins and human behavior and cognition.

“As wild primate populations are endangered worldwide, it is important for future research studies to preserve primate biomaterials together with pedigree and other information,” said David Stockwell, an environmental informatics research scientist at SDSC. “The leadership of SDSC in applying advanced information technologies to biomaterials from zoos and field collections will make a significant contribution to this important new resource, complementing the work we have done with biodiversity informatics in the museum community.”

The ability of scientists to conduct advanced research to conserve endangered species and to learn more about human genetics requires open access to high-quality, well-documented biological samples. However, until now such access has been sporadic and the quality control of information and samples highly variable. This new resource will make an important contribution to overcoming these obstacles. (v 5.19)

Cray/Tera MTA Retired at SDSC

On September 14, the Cray/Tera MTA at SDSC was retired. The 3-year-old multithreaded computer was developed and manufactured by Tera Computer of Seattle, WA, during the 1990s. Cray Inc., formed from the March 2000 merger of Tera Computer Company and Cray Research, had provided maintenance of the MTA.

The MTA at SDSC was the largest and only one outside of Seattle. It was installed in stages, beginning with one processor in December 1997 and growing to eight processors in May 1999. A further upgrade to 16 processors was planned, but difficulties in manufacturing its GaAs chips prevented that implementation.(v 5.19)