Skip to content

NEWS | Contents | Next


Subscribe to Online or ENVISION| Front Cover

RCSB Rolls out Phase II PDB Query Interface, Announces Accelerated Transition Schedule

The RCSB rolled out the Phase II search interface for the Protein Data Bank (PDB) May 15. Called SearchFields, the interface provides customizable forms for creating more complex queries.

The Phase II query also allows users to determine the status of an entry. Even though structures are generally processed within two weeks of receipt, it remains important to find structures that are on hold and determine when they will be available.

The RCSB also announced it will assume full responsibility for the PDB on July 1, 1999--a full three months ahead of schedule. This progress is possible because all aspects of the project involving the RCSB have proceeded smoothly and because of the cooperation of the Brookhaven National Laboratory (BNL) staff.

The RCSB PDB is supported by the NSF, the Department of Energy, and two units of the National Institutes of Health: The National Institute of General Medical Sciences and the National Library of Medicine. The RCSB is a consortium of Rutgers University, SDSC, and the National Institute of Standards and Technology. (v3.7, v3.11)

SDSC Accomplishments Highlighted at Annual NAVO PET Review

To an attentive and impressed audience at the Naval Oceanographic Office (NAVO) annual review April 13-14, SDSC staff presented the accomplishments of the past year from eight Programming Environments and Training (PET) program projects ranging across user collaborations, tool development, and systems improvement.

SDSC's work on the PET project was conducted by members of the Scientific Computing, Advanced Systems, and Science Visualization groups. The PET program is part of the Department of Defense's High-Performance Modernization Program, which established four major shared-resource centers, including one at the NAVO office at the Stennis Space Center in Mississippi.

"The SDSC presentation went very well," said Walter Shackelford, chief technologist for the NAVO PET program. "I received a number of compliments from people at HPCMO and the other sites regarding the SDSC project. Many were not aware of the scope of the effort and were very impressed with the leveraging from the NPACI partnership." (v3.9)

Trans-Pacific Microscopy Enabled by International Advanced Networks

Scientists in Osaka, Japan, and La Jolla, California, used international research networks April 28–29 to couple the world's largest and most powerful transmission electron microscope, at Japan's Research Center for Ultra High Voltage Electron Microscopy (UHVEM), to a remote computer pavilion at the National Center for Microscopy and Imaging Research (NCMIR) at UC San Diego. The research marks a milestone in international scientific collaboration.

"We were very happy that the connections went so smoothly," said UHVEM Director Hirotaro Mori, professor of materials science at Osaka University. "The ability to use this powerful facility from a distance of 10,000 kilometers increases its utility for all the sciences that can share it."

Scientists from the Osaka materials research group visiting the NCMIR lab in California were also able to view samples and control the microscope remotely during the two-day test. NCMIR is an important resource of the NPACI Neuroscience thrust area. (v3.10)

Web Cache Bake-off Results Released at Fourth International Web Caching Workshop at UCSD

Results of the first Web Cache "Bake-off"
were released at the Fourth International Web Caching Workshop at UCSD on April 2. The competition was organized by the National Laboratory for Applied Network Research (NLANR), an independent research and support organization for high-performance networking funded by the NSF. SDSC is one of several sites at which NLANR researchers are based.

Six major Web cache vendors--IBM, InfoLibria, Network Appliance, Novell (in an OEM agreement with Dell), the University of Wisconsin, and NLANR itself--participated in the competition, which was open to any company or organization with a Web cache product. Several other vendors, while initially interested, declined to participate in a head-to-head comparison. (v3.8)

NPACI and SDSC Host Workshops on the Future of High-Performance Networking

In March, NPACI and SDSC hosted two workshops to examine the state of high-performance networks and prospects for their future in research and education.

On March 1–2, the Computing Research Association (CRA) sponsored a workshop of 32 individuals from the computing research community called "Future Scenarios--NSF Networking Research and Associated Infrastructure Support." Mary Jane Irwin of Pennsylvania State University and Sid Karin of SDSC were co-chairs.

Karin and Larry Smarr, director of NCSA and the Alliance, chaired the second workshop "Future Scenarios: NSF Networking Research and Associated Infrastructure Support for PACI" March 4–5.

Participants urged NSF to assume the leadership role defined for it in the President's Information Technology Advisory Committee (PITAC), taking steps to stimulate new programs that target the needs of the various communities dependent on networking infrastructure. (v3.7)

NPACI Hosts IBM SP Development and Optimization Meeting at SDSC

Nearly 100 attendees met for three days to discuss developing and optimizing applications for the newest generation of IBM RS/6000 SP systems at a workshop sponsored by NPACI and IBM's Advanced Computing Technology Center (ACTC) and hosted by SDSC March 17-19.

ACTC staff presented talks on porting to the SP, optimizing for processor and parallel communication, and using performance and monitoring tools. Users from Lawrence Livermore National Laboratory, Pacific Northwest National Laboratory, and other sites discussed their issues and experiences.

NPACI is installing a teraflops IBM SP at SDSC later this year. The workshop was designed to help users of SP systems benefit from ACTC expertise and the experience with current large SP systems. (v3.7)

Science Enrichment Students Celebrate Science at SDSC

SDSC's Science Enrichment Program held a "Celebration of Science," May 13, at SDSC for students to show off their projects in bridge-building, electronics, solar power, and robotics.

Led by SDSC scientists Rozeanne Steckler and Mike Bailey, the program provides equipment, curriculum development, and support to middle-school teachers who run after-school science enrichment programs in San Diego County. The participating schools are Keiller, Memorial, Montgomery, Mountain Empire, Taft, and Wilson.

Steckler and Bailey also won the Educator Pinnacle award for leading the development of women in science and math at the first UCSD CONNECT Athena Awards April 20. The Athena Awards recognize executives, companies, and educators who foster professional change and help women attain senior management positions. (v3.11)

NPACI, SDSC Internet2 Demonstrations Enliven Networking Conferences

At the Internet2 Spring Members Meeting
in Washington, D.C., UCAID sponsored demonstrations, including three by NPACI and SDSC, at the Highway 1 Technology Center April 27–29. The demos were also open to attendees of two other conferences, the Coalition for Networked Information Task Force Members Meeting and EDUCAUSE Net '99.

The Mediation of Information using XML project of the SDSC Data-Intensive Computing group and the Database Lab of the UC San Diego Computer Science and Engineering Department showed tools and techniques for XML-based data mediation.

Greg Johnson of SDSC's Interaction Technologies group demonstrated volume-rendering of a large 3-D data set in "MPIRE: Distributed Computing to View the National Library of Medicine's 'Visible Human'."

From SDSC, David Moore of the Cooperative Association for Internet Data Analysis (CAIDA) presented the Otter, Skitter, and Coral network measurement and visualization tools. Internet2 deployment will benefit greatly from such tools. (v3.11)

NLANR Packets Makes Web Debut

The premiere issue of NLANR Packets, a quarterly Web publication of the National Laboratory for Applied Network Research (NLANR), hit the Web on April 20, 1999. The newsletter is intended to serve scientists and engineers at NSF High Performance Connections sites and in the general high-performance networking community. (v3.9)

SDSC TeleManufacturing Facility Acquires Z402 Fabrication Machine

The SDSC TeleManufacturing Facility (TMF) has acquired a Z Corporation Model Z402 fabrication machine, which constructs solid objects by bonding layers of fine powder together. The Z402 complements the TMF's existing Helisys 1015 laminated-object manufacturing device.

The Z402 is used by industry to build models and castings of prototype parts. Michael Bailey, leader of the SDSC TMF project, has pioneered the use of rapid prototyping machines for scientific purposes. (v3.8)

NPACI Director Joins Advisory Board of IBM Deep Computing Institute

NPACI Director Sid Karin is among the members of the advisory board helping to guide the $29 million Deep Computing Institute announced by IBM May 24, 1999. Led by William Pullyblank, director of Mathematical Sciences at IBM Research, the institute will join experts in academia and industry to address some of the world's most challenging problems.

One of the first actions of the institute was the open-source release of IBM Visualization Data Explorer. NPACI is supporting the open-source project, OpenDX, by hosting a Web site from which downloads will be made. Developers can now collaborate with IBM to improve the software. (v3.11)

Top| Contents | Next