News About the NPACI and SDSC Community

TeacherTECH a Summer Hit at SDSC

The participants in TeacherTECH, a training sequence for middle school science teachers held in July at SDSC, learned about everything from Web page design and scientific visualization to computational science and Internet resources. Teachers spoke highly of those classes and others devoted to such topics as robotics, rocketry, and the design of scientific games.

"It was one of the best training sessions I’ve ever attended," said Michael Senise, who teaches science, English, and serves as faculty advisor for the Science Olympiad at Standley Middle School in San Diego. "It differed from other such courses, especially in the complete engagement and enthusiasm of the staff. Everyone who taught or helped us in the computer laboratories was awesome."

There was even a field trip to Legoland in Carlsbad, where teachers learned about the theme park’s robotics kits. They discovered how robotics and other Legoland resources could be incorporated into a technology curriculum. Several sessions focused on the use of Envision, Explore, Engage, the multimedia science resource constructed at SDSC by senior staff chemist Rozeanne Steckler and her colleagues.

Steckler organized TeacherTECH. SDSC staff who served as teachers for the program included Michael Bailey, director of the Center for Visualization Prototypes, and Jason Wiskerchen, Anne Bowen, Apryl Bailey, and Zack Schumann from Steckler’s science education group. Three guest teachers–Cynthia Lanius from Rice University, Susan Boone of the Houston Independent School District, and Nancy Stubbs of the Sweetwater Union School District in San Diego County–discussed ways to diversify the demographics of students in math and science classes.

"I learned a great deal about ways to involve the young women in my classes in scientific activity," said Senise. "It means choosing projects of more general interest and assigning project work groups in such a way that the more voluble kids–often boys at this age–don’t overwhelm the rest."

Miriam Nason, a teacher at O’Farrell Middle School in San Diego, said the increasingly high-tech world makes it imperative that teachers learn effective ways to encourage every student to learn about science and technology in the classroom.

"I’m certain that these dedicated teachers, who have already been making an impact on science education in San Diego, received support from us and each other," said Steckler. "We loved working with them, and we admire them for their dedication and insight." (v5.16)

SDSC Collaborating with DOE to Manage Deluge of Scientific Data

In recognition of the increasing importance of huge data sets in research, SDSC, a leader in data-intensive computing, will collaborate in a three-year, $12 million Department of Energy (DOE) data project.

SDSC will collaborate in the DOE’s Scientific Data Management Center, which is part of the DOE’s Integrated Software Infrastructure Centers component of the Scientific Discovery through Advanced Computing (SciDAC) program. As part of the effort, Argonne, Lawrence Berkeley, Lawrence Livermore, and Oak Ridge National Laboratories are working with Georgia Institute of Technology, North Carolina State University, and Northwestern University. The scientific application areas that will initially be supported by the Scientific Data Management Center include scientific disciplines with large data sets, such as climate modeling, astrophysics, genomics, and high-energy and nuclear physics.

"The goal of this new center is to provide additional tools to scientists that will allow them to concentrate on their research by minimizing the effort they have to spend managing very large data sets," said Reagan Moore, leader of SDSC’s Data-Intensive Computing Environments (DICE) group.

Under the direction of DICE researchers and co-PIs Bertram Ludäescher and Amarnath Gupta, researchers involved in the project will address the problems of access to distributed, heterogeneous data, storage and retrieval of very large data sets, optimization of access to distributed data, and data mining and discovery of access patterns. The researchers want to develop scalable, intuitive systems for moving, storing, analyzing, querying, manipulating, and visualizing petabytes of scientific data. (v5.16)

SDSC’s Mike Vildibill Appointed to CENIC Board

The Corporation for Education Network Initiatives in California (CENIC), a not-for-profit consortium founded by California’s higher education community, has appointed Mike Vildibill to its board of directors. Vildibill is deputy director for computational infrastructure at SDSC.

CENIC’s board members are selected to represent its charter institutions–the California Institute of Technology, California State University, Stanford University, the University of California, and the University of Southern California. The board also includes representatives of other education and research organizations.

John Bruno, vice provost for Information and Educational Technology at UC Davis, and Larry Smarr, director of the California Institute for Telecommunications and Information Technology, also were named to the CENIC board.

"Our new board members bring a wealth of skills and expertise to help shape a set of bold, new initiatives to sustain California’s legacy as the center of the digital universe," said CENIC chair John Silvester. (v5.15)

UCSD Biologists: Human Genetic Diseases Have Counterparts in Fly

Biologists at UCSD have identified genes in the common fruit fly, Drosophila melanogaster, that appear to be counterparts of genes responsible for more than 700 different diseases in humans. The results published in the June issue of Genome Research provide geneticists with a tool to identify human counterparts of fruit fly genes that may play roles in human diseases. The results also revealed biochemical mechanisms involved in the diseases, a step toward developing effective treatments.

The study began two years ago when the co-authors, Lawrence T. Reiter, a postdoctoral researcher at UCSD, and Ethan Bier, a UCSD biology professor who runs a Drosophila-genetics laboratory, began collaborating. They wanted to compare genes in fruit flies to possible counterparts in the human genome. Michael Gribskov, a computational biologist at SDSC, helped them create a database of human and fly genes and human genetic diseases. They call the database Homophila (http://homophila.sdsc.edu/).

"Scientists have known that humans share many genes with fruit flies," said Bier, who headed the research. "The surprise was the depth of these similarities. Basically, every category of human genetic disease is well represented with a counterpart in the fly."

The team screened the genes involved in 929 human genetic diseases against the genes in the complete Drosophila genome. They identified 548 fruit-fly genes that are strikingly similar to genes involved in 714 human genetic disorders.

Based on these results, Lorraine Potocki, a clinical geneticist at Baylor College of Medicine, categorized the human genetic disorders that might be studied in Drosophila. These diseases fell into essentially every major category, including neurological, immunological, cardiovascular, auditory, visual, developmental, and metabolic, as well as many forms of cancer.

In addition, Reiter and Bier found that more than 200 fruit fly genes are so similar to their human counterparts that they likely carry out equivalent biochemical functions. "Most people don’t think of studying blindness, hearing or cancer in Drosophila," said Reiter. "But human genetics has hit a wall with regards to function. And the fly turns out to be an ideal model for analyzing genes and placing them in the context of known genetic pathways." (v5.13)

SDSC and UCSD Partner with Mondeca in Topic Map Research

T opic Maps are powerful navigational tools to organize, retrieve, and access information. Mondeca, a French developer of advanced XML Topic Map technology, and SDSC have entered a partnership to explore innovative applications of the increasingly important research tool.

Under the agreement, Mondeca will provide its advanced Topic Map software, which includes a suite of components and an SDK platform. SDSC’s Data-Intensive Computing Environments (DICE) group will use the software to develop prototypes and evaluate XML Topic Map standards. The research is aimed at creating an independent "knowledge layer" above the information resources.

"We’re looking forward to this partnership with SDSC," said Mondeca CEO Jean Delahousse. "This is our first collaboration with a research group in the United States. We expect this partnership to be very helpful in making Topic Map technology a practical reality for a broad range of scientific, cultural, and enterprise applications."

Part of the research will focus on the Regional Workbench (RWB), a project involving DICE researchers and Keith Pezzoli, a professor in UCSD’s Urban Studies and Planning Program. The RWB is a Web-based network of researchers and community groups planning for sustainable development in a region that includes San Diego, CA, and Tijuana, Mexico. Research-ers will use Topic Maps to create an integrated view of land use in the area. (v5.13)

NPACI’s NetSolve Grid Project Releases New Software

T he NetSolve project, which is being developed at the University of Tennessee’s Innovative Computing Laboratory to enable users to solve complex scientific problems using grid technology, has released a new version of its software. The system allows users to access hardware and software resources distributed across a network in a computational grid. NetSolve searches for computational resources on the grid, chooses the best one available, and using retry for fault-tolerance solves a problem, and returns the answer to the user.

A load-balancing policy is used by the NetSolve system to ensure good performance by enabling the system to efficiently use computational resources available.

NetSolve 1.4 integrates the Internet Backplane Protocol middleware to optimize data movement, enables the Network Weather Service, uses Kerberos for security, and has several other features. The software provides computational resources via its many client application-programming interfaces. Client programs implemented in C, Fortran, Matlab, and Mathematica can access the NetSolve system and its services from libraries such as LAPACK, ScaLAPACK, PETSc, Aztec, SuperLU, and others. All components have been tested on a number of Unix operating systems. (v5.18)