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
"It was one of
the best training sessions Ive 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 parks 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.
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 Stecklers science education group. Three
guest teachersCynthia Lanius from Rice University, Susan
Boone of the Houston Independent School District, and Nancy Stubbs
of the Sweetwater Union School District in San Diego Countydiscussed
ways to diversify the demographics of students in math and science
"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 kidsoften boys at this
agedont overwhelm the rest."
Miriam Nason, a teacher
at OFarrell 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.
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."
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 DOEs Scientific Data Management Center, which is
part of the DOEs 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
"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 SDSCs 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)
Mike Vildibill Appointed to CENIC Board
The Corporation for
Education Network Initiatives in California (CENIC), a not-for-profit
consortium founded by Californias higher education community,
has appointed Mike Vildibill to its board of directors. Vildibill
is deputy director for computational infrastructure at SDSC.
members are selected to represent its charter institutionsthe
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 Californias legacy
as the center of the digital universe," said CENIC chair
John Silvester. (v5.15)
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
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/).
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
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 dont 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."
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. SDSCs 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.
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
Part of the research
will focus on the Regional Workbench (RWB), a project involving
DICE researchers and Keith Pezzoli, a professor in UCSDs
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)
NetSolve Grid Project Releases New Software
T he NetSolve project,
which is being developed at the University of Tennessees
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