News Archive

San Diego Supercomputer Center to Play Major Role in Six NSF Information Technology Research Awards

Building the Information Technology Framework for the Geosciences, Environmental Sciences, Optically Networked Grids, and Theoretical Biological Physics

Published 09/25/2002

San Diego, September 25, 2002 - From helping build the crucial information technology underpinnings for a leading-edge geosciences network to a science environment for ecological knowledge, an optically networked grid, and a center for theoretical biological physics, the San Diego Supercomputer Center (SDSC) at the University of California, San Diego (UCSD) will play a key role in enabling future scientific advances through four large Information Technology Research (ITR) initiatives announced today by the National Science Foundation (NSF). These awards are designed to support "visionary work" that could lead to major advances in information technology (IT) and its applications. Four of the projects involve large $5 million-plus ITR awards, among only seven highly competitive such awards made. SDSC is also participating in two medium-sized ITR awards.

"Tomorrow's scientific breakthroughs depend critically on the advances we make in today's information infrastructure," said Fran Berman, director of SDSC and the National Partnership for Advanced Computational Infrastructure (NPACI). "Each of these ITR projects will leverage SDSC and NPACI experience and technologies to lay the groundwork for new discoveries in the Earth sciences, biology, and other disciplines. Such new science requires collaborative research to bring together new tools, new ideas, and powerful IT infrastructure."

All together, UCSD has principal investigators (PIs) or co-PIs on seven ITR projects that were awarded approximately $40 million over five years. Of this amount, UCSD research teams will receive more than $21 million (80% for four large ITR projects, defined by NSF as $5 million or more), with the balance going to partner institutions collaborating on the projects.

SDSC is the lead institution in the Geosciences Network (GEON), an $11.25 million award, and is participating as data component lead in the $12.25 million Science Environment for Ecological Knowledge (SEEK) program, led by the University of New Mexico. SDSC is also participating in the $13.5 million OptIPuter research project led by the California Institute for Telecommunications and Information Technologies, Cal-(IT)2, and in UCSD's Center for Theoretical Biological Physics, a $10.5-million program. Half of the funding for the Center for Theoretical Biological Physics is under the NSF Physics Frontier Centers program. These four projects are five year large awards under the NSF ITR program. The two medium-sized ITR awards that SDSC is part of are the $2.9 million Monitoring Civil Infrastructure effort and the $3 million Network Framework project.

Geosciences Network

The GEOsciences Network (GEON) project is a collaboration between IT and Geoscience researchers with the goal of creating a modern information technology framework for the earth sciences. IT research is coordinated by Chaitan Baru of SDSC, and colleagues Bertram Ludäscher, Phil Papadopoulos, and Mike Bailey, as well as scientists from Pennsylvania State University and San Diego State University. Geoscience research coordinated by A. Krishna Sinha of Virginia Tech includes 10 additional universities (Arizona State University, Bryn Mawr College, Cornell University, Rice University, University of Arizona, University of Idaho, University of Missouri, University of Texas, El Paso, University of Utah, and UNAVCO). The Digital Library for Earth Sciences Education (DLESE) will lead the GEON education and outreach program.

A major partner in GEON is the U.S. Geological Survey (USGS), which will collaborate in building broader access through GEON to selected USGS national scale geological databases. "GEON will seamlessly integrate USGS data with those of the broader geoscience community," said Charles G. Groat, USGS Director. "And this will significantly speed the pace of geological research."

Many key questions in earth systems science can only be answered through the discovery of relationships between disciplines. Questions GEON can help answer include understanding the processes that control the growth of continents, and investigating the interaction between tectonics, regional climate, and the evolution and distribution of organisms.

"Many interdisciplinary questions posed within GEON by the earth science team will require a research partnership between geoscientists and information technologists," said Chaitan Baru, co-director of SDSC's Data and Knowledge Systems program. "Our goal is to develop geoinformatics cyberinfrastructure that will provide interlinked information systems to enable the geosciences community at large to share not only data and information but also tools and programs that will let them collaborate more effectively than ever before." GEON cyberinfrastructure will be critical for integrating and interpreting data collected by projects such as the NSF EarthScope initiative.

The IT part of the project encompasses the three core components of a national information infrastructure - grid computing, data management, and visualization. The earth science research will emphasize the development of information and concept integration procedures, as well as research that bridges traditional subdisciplines. "Because of this balanced design, the GEON cyberinfrastructure will serve not only the geosciences community, but will be a valuable technology model for many other communities as well," said Baru. For more information on GEON, go to (or

Science Environment for Ecological Knowledge

The SEEK project involves a multidisciplinary team of ecologists, computer scientists, and technologists from the Partnership for Biodiversity Informatics (PBI), a consortium consisting of the University of New Mexico (UNM); SDSC; the National Center for Ecological Analysis and Synthesis (NCEAS) at the University of California Santa Barbara (UCSB); and the University of Kansas (KU); and as well as partner institutions Arizona State University, University of North Carolina, University of Vermont, and Napier University in Scotland.

SEEK will provide ecologists and other researchers access to a large-scale network of information resources and computational services. The project will provide fundamental improvements in how researchers can gain global access to data and information, rapidly locate and use distributed computational services, and exercise powerful new methods for capturing, reproducing, and extending the analysis process itself.

"These capabilities will help researchers address global research, management, and policy issues in environmental biology," said William Michener of the NSF Long-Term Ecological Research (LTER) Network Office at UNM, which leads this collaborative proposal. "Increasingly, these issues require efficient, automated access to diverse and widespread data."

SEEK will be built as a layered system, with EcoGrid as the foundation layer for seamless data sharing, querying, and computation. EcoGrid will be based on the SDSC Storage Resource Broker (SRB), leveraging and extending this proven system for data sharing and interoperation.

The other two core components of SEEK IT research are the Analysis and Modeling System, led by NCEAS, and the SDSC-led Semantic Mediation System for mapping descriptions of analytical pipelines and workflows to distributed query plans in the EcoGrid. "Analyzing and compiling such semantically enriched workflow descriptions into executable 'EcoGrid plans' is a formidable IT research challenge," said Bertram Ludäscher, SEEK principal investigator at SDSC and director of the DAKS Knowledge-based Information Systems lab. "It will take collaboration among ecologists, ecoinformatics technologists, and researchers in UCSD's Computer Science and Engineering Department to accomplish this," said Ludäscher. The SEEK researchers will also collaborate with the GEON team, which faces some similar IT challenges. (For more on SEEK, go to


Led by Larry Smarr, director of Cal-(IT)2, the OptIPuter project will explore next-generation distributed cyber "infostructure" to support scientific research and collaboration. Initial application efforts will be in biomedical imaging and geoscience research, including environmental, seismic, and remote sensing.

UCSD and the University of Illinois at Chicago will lead the research team, in partnership with Northwestern University, San Diego State University, the University of Southern California, and the University of California, Irvine [a partner of UCSD in Cal-(IT)2]. SDSC will provide grid and cluster computing expertise, as well as facilities and services, including access to the NSF-funded TeraGrid. Co-principal investigators on the project are UCSD's Mark Ellisman and SDSC's Philip Papadopoulos.

The OptIPuter research will be carried out in close conjunction with two data-intensive e-science efforts already underway, the NSF-funded EarthScope, and the Biomedical Informatics Research Network funded by the National Institutes of Health. They will provide applications to test the OptIPuter design. "Because of our emphasis on geosciences applications, we also plan to work in close collaboration with the GEON project," said principal investigator Larry Smarr, who is also a professor of Computer Science and Engineering in UCSD's Jacobs School of Engineering. (For more information go to

Center for Theoretical Biological Physics

Scientists at UCSD and SDSC are creating a new NSF-funded Center for Theoretical Biological Physics to be the world's leading center in the emerging field of theoretical biological physics. Co-directed by Jose N. Onuchic and Herbert Levine, professors of physics at UCSD, and managed by the university's Division of Physical Sciences, the new center will advance research and educate scientists in a discipline that uses the theoretical tools of physics to understand the fundamental principles governing complex biological systems. This interdisciplinary approach - a joint effort by physicists, chemists, mathematicians and biologists at UCSD and scientists at neighboring institutions in La Jolla - will provide biologists with a better understanding of the underlying mechanisms governing complex biological systems, such as networks of neurons or biochemical pathways in the assembly of proteins, while allowing physicists to develop new principles and models based on complex biological phenomena. "SDSC will participate in this groundbreaking program in three ways," said SDSC co-principal investigator Kim Baldridge. "We will contribute molecular-level quantum chemistry algorithmic integration, knowledge and support efforts in hardware infrastructure, and education and outreach."

The program will focus on four central research thrusts: biopolymer structure and function; gene regulation and function; the non-equilibrium physics of cellular and developmental systems; and computational networks in neurobiology. The close collaboration between physicists and life scientists is expected to challenge and enrich both disciplines as they confront increasingly complex systems, speeding the pace of research physics as well as rapid, targeted discoveries in biology that will yield powerful benefits in medicine and beyond.

Network Framework

SDSC's Amarnath Gupta and professor Fan Chung Graham, who has joint appointments in CSE and Mathematics, are co-PIs on a medium-sized ITR project to develop a framework to analyze, model, and design robust, complex networks based on biological and computational principles. The Keck Graduate Institute of Applied Life Sciences is the lead institution on the project. SDSC researchers will construct a graph-structured data model to encode the behavior of the genes in a "gene regulatory network." The researchers will try to learn from and model the example of such networks in which, although the various genes have specific functions, when one gene is removed the system can often compensate without drastic impact.

Monitoring Civil Infrastructure

SDSC's Tony Fountain is part of an interdisciplinary effort led by structural engineer Ahmed Elgamel of UCSD's Jacobs School to create an integrated framework for real-time health monitoring of highway bridges and other civil infrastructure, to detect both sudden and gradually accumulating damage. A flexible and scalable software architecture to which Fountain will contribute data mining capabilities and SDSC's Amarnath Gupta will contribute advanced query processing will integrate real-time data from thousands of sensors as well as heterogeneous inputs from database and archiving systems, computer vision, data analysis and interpretation, numerical simulation of complex structural systems, visualization, probabilistic risk analysis, and rational decision-making procedures. The framework will speed the discovery of new knowledge related to infrastructure health, which will provide significant economic benefits to society.

About SDSC

The San Diego Supercomputer Center (SDSC) is an organized research unit of UCSD and the leading-edge site of the National Partnership for Advanced Computational Infrastructure (NPACI). SDSC's mission is to develop and use technology to advance science, and SDSC provides leadership both nationally and internationally in computing, data management, biosciences, and other areas. As a national laboratory for computational science and engineering, SDSC is funded by the National Science Foundation through NPACI and other federal agencies, the State and University of California, and private organizations. For more information, see or contact David L. Hart, SDSC Communications, 858-534-8314,

Media Contacts: Dave Hart (858) 534-8314
Geosciences Network (GEON): Paul Tooby (858) 822-3654
Science Environment for Ecological Knowledge (SEEK):
Frank Martinez (505) 277-1811
Paul Tooby (858) 822-3654
OptIPuter: Doug Ramsey (858) 822-5825
Center for Theoretical Biological Physics:
Kim McDonald (858) 534-7572

Related Links

For more details on institutions involved, visit the following websites:

Geosciences Network (GEON)

GEON (or

San Diego Supercomputer Center (SDSC)

University of California, San Diego (UCSD)

Arizona State University

Bryn Mawr College

Cornell University

Penn State Univ

Rice University

San Diego State University


University of Arizona,

University of Idaho

University of Missouri

University of Texas, El Paso

University of Utah

Virginia Polytechnic Institute and State University

California Institute for Telecommunications and Information Technology

Science Environment for Ecological Knowledge (SEEK)

Science Environment for Ecological Knowledge (SEEK)

NSF Long-Term Ecological Research (LTER) Network Office

University of New Mexico

San Diego Supercomputer Center (SDSC)

National Center for Environmental Analysis and Synthesis (NCEAS)

University of Kansas Natural History Museum and Biodiversity Research Center


California Institute for Telecommunications and Information Technology

San Diego Supercomputer Center (SDSC)

University of California, San Diego (UCSD)

University of Illinois at Chicago (UIC)

Northwestern University (NU)

San Diego State University (SDSU)

Information Sciences Institute

University of California-Irvine