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RCSB Opens Protein Data Bank Web Site, Assumes Responsibility for Distributing New Entries

The Research Collaboratory for Structural Bioinformatics (RCSB) opened its new Protein Data Bank (PDB) Web site and ftp archive and assumed primary responsibility for distributing new entries to the PDB on February 3, 1999. Following the first five successful updates, the PDB now contains 9,419 coordinate entries for proteins, nucleic acids, and carbohydrates.

During its first two weeks of operation in February, the RCSB PDB Web site ( recorded an average of 3,682 hits per day. The ftp site (, containing the structural data, transmitted an average of 5,040 files per day.

A highlight of the new site is a search engine developed at SDSC, SearchLite, that represents the first phase in the development of new tools for querying the data bank. Another key service is a validation server ( developed at Rutgers. This server may be used to detect possible errors in atomic models before final submission. (v3.5)

Nature Features Paper on CAIDA and Internet Tomography

The Web Matters section of the January 7, 1999, issue of Nature featured a paper by CAIDA staff K.C. Claffy, Tracie Monk, and Daniel McRobb on "Internet Tomography." It gives an interesting overview of some of CAIDA's activities and of some of the issues involved in keeping track of the Internet.

To gain insights into Internet traffic and workloads, the Cooperative Association for Internet Data Analysis (CAIDA) is developing and deploying tools to collect, analyze and visualize data on connectivity and performance across a large proportion of the Internet. These tools and analyses will provide windows on the infrastructure for network operators, designers and researchers, using a process analogous to medical CAT scans. The CAIDA researchers regard what they're doing as a form of computerized tomography -- but the body that they are analyzing is the vast structure of the Net.

"Web Matters" is an occasional section presenting short essays exploring the use of the Web as a medium for scientific communication. (v3.2)

NPACI and SDSC to Present Demos at Internet2 Member Meeting in April

Four SDSC and NPACI projects have been selected to demonstrate the potential and reality of an advanced Internet at the April 27-29, 1999, Internet2 member meeting in Washington, D.C.

From SDSC, David Moore of the Cooperative Association for Internet Data Analysis (CAIDA) will demonstrate several network measurement and visualization tools. Greg Johnson and Jon Genetti of SDSC's Interaction Technologies group will show how MPIRE allows interactive viewing of the National Library of Medicine's "Visible Human."

Members of SDSC's Data-Intensive Computing group and UCSD's Computer Science and Engineering Department will demonstrate technology for modeling and querying mediated Web sites using XML-based technologies. And researchers from NPACI partner UCLA will show the Virtual World Server project, part of NPACI's Interaction Environments and Data-Intensive Computing thrust areas. (v3.5)

NPACI Welcomes New Partners in Molecular Science, Neuroscience, Earth Systems Science, and EOT-PACI

The NPACI partnership roster has grown by five sites, extending NPACI's activities in Molecular Science; Neuroscience; Earth Systems Science; Programming Tools and Environments; and Education, Outreach, and Training. In addition, two associate partner sites joined the ranks of NPACI's development and education partners.

The new sites are Johns Hopkins University, MIT, the University of Chicago, and the University of Minnesota. Montana State University and UC Irvine have become development and education partners after being associate partners last year.

Johns Hopkins: Michael Miller directs the Center for Imaging Science and participates in a Neuroscience thrust area project on refining and linking brain data.

MIT: Carl Wunsch, director the Program in Atmospheres, Oceans, and Climate and faculty member of the Center for Global Change Science, has joined the Earth Systems Science thrust area, leading a project on ocean circulation and climate.

University of Chicago: Ridgway Scott, a faculty member in the Computer Science Department, is leading a project on Pfortran and PC Compilers in the Programming Tools and Environments thrust area and a Molecular Science project on Enhanced Imaging of Biological Structures.

University of Minnesota: Paul Woodward, as director of the Laboratory for Computational Science and Engineering, is leading an Education, Outreach, and Training project through the Secondary Education in Computational Science (SpECS) program.

Montana State University: Gwen Jacobs and John Miller of the Center for Computational Biology have become development and education partners for their work on Neuroscience thrust area projects on federating brain data and refining and linking brain data.

UC Irvine: Donald Dabdub, of the Atmospheric Sciences and Engineering program, is leading an Earth Systems Science project on Atmospheric Chemistry. (v3.3)

NPACI External Visiting Committee Holds First Meeting

During the 1999 All-hands Meeting, NPACI's External Visiting Committee (EVC) convened its first meeting to provide external assessment of NPACI activities, progress, and plans.

The EVC members are:

  • Ann Hayes, EVC Chair, Los Alamos National Laboratory
  • William Carlson, IDA Center for Computing Sciences
  • Dona Crawford, Sandia National Laboratories
  • Jill Dahlburg, Naval Research Laboratory
  • John Ingram (Retired), Schlumberger Limited
  • Mary Jane Irwin, Department of Computer Science and Engineering, Pennsylvania State University
  • David Kingsbury, Chiron Corporation
  • Michael Klein, University of Pennsylvania
  • Carl Kukkonen, ViaSpace Technologies
  • William Lester, UC Berkeley and Chemical Sciences Division, LBNL
  • Juan Meza, Sandia National Laboratories
  • Lori Perine (observer), White House Office of Science and Technology Policy
  • William Press, LANL
  • Stephen Wolff, Cisco Systems, Inc.

The EVC will prepare a written report of its findings for NPACI's Institutional Oversight Board and the National Science Foundation. The report represents feedback to NPACI's leadership to help NPACI achieve the goals of the NSF and the partnership. (v3.4)

University of Michigan Upgrades IBM SP System Available to NPACI Users

The IBM RS/6000 SP at the University of Michigan's Center for Parallel Computing (CPC), one of NPACI's resource partners, has been upgraded to 96 processors with 1 GB of memory on each of 48 processors.

The CPC SP was upgraded from 64 to 96 processors, now configured as two 48-processor machines. The new SP has 48 thin nodes with a 160-MHz POWER2 Super Chip processor and 1 GB of memory each, for a total memory of 48 GB and a peak performance of 31 Gflops. Each node has 8 GB of local scratch space.

The CPC SP is available to NPACI users through the normal allocation process; 50 percent of the time on the machine is allocated through NPACI. Along with the hardware upgrades, the new SP at the CPC has been updated with the latest versions of key software and compilers.

The CPC's original SP has 48 thin nodes with 66-MHz POWER2 chips. Thirty-two nodes have 256 MB of memory, and 16 nodes have 128 MB for a total of 10 GB and peak performance of 13 Gflops. (v3.5)

NPACI Hosts Successful Second Annual All-hands Meeting at UCSD

More than 350 participants from 60 institutions convened at SDSC and the UC San Diego campus for the second annual NPACI All-hands Meeting, as well as several meetings held prior to the NPACI event.

"The All-hands Meeting is designed to catalyze partner activity and collaborations," said Sid Karin, NPACI director. "The number of attendees and the number of sites represented attests to the broad interest in NPACI and the success of the partnership."

The theme for the meeting was NPACI in 2002, the five-year point of the partnership. Sessions focused on integrating NPACI partners, resources, software, and education and outreach in the coming years. The complete agenda, the collected presentations, and meeting summary are available at the All-hands Meeting Web site. (v3.3)

MIT Researchers Use NPACI Resources to Design "Perfect Mirror"

A team of researchers from MIT reported in the November 27, 1998, issue of Science that they have made an important new advance in an age-old device--the mirror. Calculations that led to the discovery of their "perfect mirror," which reflects all light of a certain wavelength without regard to its reflection angle or its polarization, were performed on SDSC's CRAY computers.

"We've discovered an important aspect of mirrors that was apparently overlooked," said Yoel Fink, a graduate student at MIT's Plasma Fusion Science Center and one of the authors of the article.

Ordinary metallic mirrors are omnidirectional, reflecting light from all angles but absorbing a significant portion of the light in the process due to the interaction of light's electromagnetic waves with the electrically conductive metal. The dielectric mirrors studied by the MIT group are made of non-conducting materials and can reflect light more efficiently.

According to John D. Joannopoulos, a leader of the research team and Francis Wright Davis Professor of Physics at MIT, "Computation has played a dominant role in the study of photonic crystals." The discovery was an outgrowth of his research into ab initio simulations of the properties of dielectric materials, an effort that Joannopoulos has pursued with the assitance of SDSC's computers for the past several years. (v3.1)