Press Archive

Undergraduates Get Experience in World of Research at SDSC

Published 07/11/1996

For more information, contact:
Ann Redelfs, SDSC
619-534-5032/5113 (fax)

San Diego, CA -- To get a feel for the world of research, a group of undergraduates are spending this summer exploring problems in chemistry, molecular biology, and computer science, as participants in the 1996 Research Experiences for Undergraduates (REU) program sponsored by the National Science Foundation at the San Diego Supercomputer Center (SDSC).

For 10 weeks from June to August, the REU participants are given an intensive exposure to computational science and the process of conducting research. Students work on projects in their fields of interest, supervised by an SDSC staff member and either a faculty member at his or her home institution or a faculty member at University of California, San Diego (UCSD).

"The objective is to give each student a taste of research in computational science, albeit within a condensed time frame," said Bob Leary, SDSC computational scientist who coordinates the program with Mike Bailey, SDSC senior staff scientist. "Rather than being taken on as cheap programming labor, REU students perform all the essential aspects of the research themselves."

The program also includes workshops on high performance computing and special lectures on such topics as parallel computing, graphics and scientific visualization, and numerical analysis.

This year's REU participants, all between their junior and senior undergraduate years, have selected topics within their supervisor's existing or planned research project, while others have an interest in a certain area and are using the REU program to take the first steps in their own research.

Matt Lundy from UCSD is creating, with Phil Bourne, SDSC computational biologist, a prototype of a global registry of data on protein kinases. Protein kinases are an important class of enzymes that regulate cellular processes, but no single online resource has compiled all of the available data in one place where the data could be compared.

"Basically I will create a Web page, or a group of Web pages, with links to the various databases for each protein kinase," Lundy said. "I also hope to prototype a mechanism for database administrators to submit new data. The administrators of some online resources have already agreed to participate in the registry idea." Such an electronic resource for existing data would allow researchers to accelerate the pace of further protein kinase research.

Susan Kanda from UCLA is working with SDSC computational biologist Michael Gribskov on a structural walk-through of a protein kinase that plays an important role in the regulation of the cellular life cycle. The structure of this kinase, cyclin-dependent kinase 2 (cdk2), is critical to its function. A single mutation can cause the kinase to malfunction and disrupt the cell cycle, a disruption often seen in tumor cells.

Sarah Wustner from UCSD is exploring the suitability of Java, the new programming language on the Web, for more complex applications. Working with Scott Baden, UCSD associate professor of computer science, Wustner will be creating an image processor in Java. "I want to create a program that is not just a toy," Wustner said. "I will try to make a functional, useful image processor, geared toward use in schools."

The other REU participants, all from UCSD, and their projects are Randall Harris, who is working with Leary on the global optimization problem of finding the lowest energy states of atomic clusters; Lawrence Li, who with Andrew McCammon, UCSD professor of chemistry and biochemistry, is looking at the structure of organic molecules using simulated annealing; Neil Spring, who is working with UCSD's Rich Wolski and SDSC's Reagan Moore to incorporate the Mentat and Legion software into the AppLeS project; and Michelle Strout, who with Jeanne Ferrante, UCSD professor of computer science, is generating code for the hierarchical tiling of parallel programs.

All REU students are given access to appropriate computer resources at SDSC and receive a $4,000 stipend. Students are expected to work full-time on their research during the program, and are required to attend regular seminars and present a poster paper at a concluding meeting, which is open to the public. The program is open to U.S. citizens or permanent residents enrolled full-time in an undergraduate program at a U.S. college or university. For more information on the program, visit the REU Web page on SDSC's Web server (

SDSC, a national laboratory for computational science and engineering, is sponsored by NSF, other federal agencies, the State and University of California, and private organizations; is affiliated with the University of California, San Diego; and is administered by General Atomics. For more information, see or contact Ann Redelfs, SDSC,, 619-534-5032.