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Tree of Life and Virtual Grid Development among Four ITR Awards to SDSC

NSF Middleware Projects Receive $9 Million

NSF Awards $1.2 Million to Extend PRAGMA Program
Teachers Bring Technology They Developed at SDSC to Their Classrooms
Texas Installs Lonestar Cluster
SDSC Education Department Efforts Recognized in SIGKids Awards

September 17, 2003

SDSC Press Release


San Diego Supercomputer Center to Play a Key Role in NSF Information Technology Research Awards


Media contact:
Greg Lund
(858) 534-8314

Projects range from a "Tree of Life" for all of Earth's known flora and fauna to "virtual" Grid development

The San Diego Supercomputer Center at the University of California, San Diego (SDSC) will participate in several National Science Foundation (NSF) Information Technology Research (ITR) awards. ITR projects focus on fundamental research in information technology (IT) and innovative uses of IT in science and engineering.

Announced today, of the two large ITRs, one, funded at $11.6 million, will create a "Tree of Life" that will allow researchers to explore the evolutionary relationships between all species of living organisms. The second, Virtual Grid Application Development Software (VGrADS), funded at $8.25 million, aims to simplify and accelerate the development of Grid applications and services, making the Grid more accessible to users.

The first award to develop the "Tree of Life" will support an alliance of 13 institutions coordinated by  Bernard Moret, Professor of Computer Science at University of New Mexico. SDSC's Director, Francine Berman, and SDSC's Director of Integrative Biosciences, Philip Bourne, will serve as co-PIs, and Program Coordinator Mark Miller will act as SDSC point of contact.  The project is an alliance of 13 institutions to develop the "Tree of Life."

"We are very excited about this opportunity," said Berman. "The Tree of Life team is a stellar group and the project uses data technologies to provide a foundation for new advances in the biosciences.  The Tree of Life will provide an important building block for Cyberinfrastructure and complements the wide spectrum of technology-enabled bioscience activities at SDSC."

The "Tree of Life" effort includes developing computational tools to explore the evolutionary relationships between all species of living organisms.  Researchers will be able to use comparisons of DNA sequences to predict the relationships of existing plants and animals to their common ancestors. The result will be a map, long sought-after by biologists, that describes which species have close common ancestors and which have more distant relations. SDSC resources, including its new DataStar machine and the TeraGrid will be applied to the project.

Berman will also participate in a $8.25 million ITR award for VGrADS, a project led by Ken Kennedy, the Ann and John Doerr Professor in Computational Engineering at Rice University. Berman, Henri Casanova, director of SDSC and UCSD's Grid Research and Applications Laboratory, and SDSC strategic advisor Andrew Chien, the Science Applications International Corporation Chaired Professor at UCSD, will collaborate with researchers at seven other institutions to extend previous work in the Grid Application Development Software (GrADS) Project. VGrADS will simplify and accelerate the development of Grid applications and services, while making the Grid accessible to a larger community of users and developers. Ultimately, VGrADS will assist researchers in areas such as bioinformatics, weather prediction, and bioimaging; and act as a model for other scientific communities interested in using the Grid.

"It takes a degree in computer science to understand today's parallel computers and several more years of training to write code to use them efficiently," said Kennedy, who is the director of HiPerSoft, Rice's Center for High Performance Software Research. "VGrADS hopes to change that with tools that bring the power of Grid computing within reach of the average scientist."

Director of the Knowledge-Based Information Systems Lab at SDSC, Bertram Ludäscher, and Director of Data Grid Technologies Lab at SDSC Arcot Rajasekar, will serve as co-PIs on a $2.3 million medium ITR for Real-Time Data Aware System for Earth, Oceanographic, and Environmental Applications. Working with PI John Orcutt of Scripps Institution of Oceanography and other collaborators, this project will focus on dynamically adapting downstream processing and modeling as sensors are added to or removed from a real-time data network. The research will include work on methods to detect automatically the occurrence of interesting phenomena in real-time data streams and to trigger responses such as data analysis, modeling computations or turning on or off parts of the sensor network. The project will also investigate how to extend data Grid ideas to include real-time data streams and permit feedback between observations and the operation of the observing network.

Ludäscher will also participate as a co-PI on a small ITR for $375,000 to investigate new approaches for querying data streams in XML form, covering the spectrum from formal foundations all the way to systems. The expected outcome of the project will be a qualitatively new architecture, technology and query processor for XML data streams, with impact on a wide range of applications. The methods will be tested on seismic data provided by the UCSD-based ROADNet project and is expected to have a broad impact on voluminous XML data streams.

About SDSC

The San Diego Supercomputer Center (SDSC) is leading the way in developing a national Cyberinfrastructure that will provide the technological foundation for the next generation of science and engineering advances. 

Founded in 1985, SDSC is an organized research unit of the University of California, San Diego. With a staff of more than 400 scientists, software developers and support personnel, SDSC is an international leader in data management, biosciences, geosciences, Grid computing and visualization.

Primarily funded by the National Science Foundation (NSF), SDSC is the leading-edge site for The National Partnership for Advanced Computational Infrastructure (NPACI), a 41-institution partnership to create computational environments for tomorrow’s scientific discovery.  For more information, visit