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InTheLoop | 09.18.2006

The weekly electronic newsletter for Berkeley Lab Computing Sciences employees

September 18, 2006

Director's Review of CRD Scheduled for Thursday and Friday, Sept. 21-22

The annual director's review of Computing Sciences, to be held Thursday and Friday, will focus this year on program in the Computational Research Division. The review, to be held in Perseverance Hall, will feature a series of presentations which are open to interested staff.

Thursday presentations:

10:15 a.m.: Scientific Data Management Group, Arie Shoshani
11 a.m.: Overview of SDM Research Program, Doron Rotem
11:30 a.m.: FastBit, John Wu
1 p.m.: Scientific Visualization and Analytics, Wes Bethel
2 p.m.: Overview of High Energy and Nuclear Physics Computing, Craig Tull
3 p.m.: Biological Data Management and Technology Center, Victor Markowitz
3:45 p.m.: Production Biological Data Management and Integration, Krishna Palaniappan

Friday presentations:

8 a.m.: Distributed Systems Department, Deb Agarwal
8:40 a.m.: IceCube, Chuck McParland
9 a.m.: PyGridware and CEDS, Keith Jackson
9:20 a.m.: Cryptography Research, Olivier Chevassut
9:40 a.m. Cybersecurity, Brian Tierney

Review panel members are Rick Stevens, Argonne National Lab; Deborah Frincke, PNNL; Prof. Satoshi Matsuoka, Tokyo Institute of Technology; Prof. Tekin Ozsoyoglu, Case Western Reserve University; Prof. John van Rosendale, College of William and Mary; Vicki White, Fermilab; and Prof. John Wooley, UC San Diego.

ESnet's Joe Metzger Co-Authors Best Paper at International Conference

ESnet's Joe Metzger, along with collaborators in five other countries, received the award for best paper at the International Conference on Internet Surveillance and Protection (ICISP) held last month in France. Other authors of the paper entitled “Complementary Visualization of perfSONAR Network Performance Measurements” are Andreas Hanemann, German Research Network; Vedrin Jeliazkov, Institute for Parallel Processing (Bulgaria); Olav Kvittem, Norwegian Research Network; Luis Marta, Fundacao para a Computaao Cient?fica Nacional (Portugual); and Igor Velimirovic, Croatian Academic and Research Network.

Here is the abstract from the paper:
“Research backbone networks are currently used by a variety of scientists and research projects interested in maximizing the benefit they receive in using the networks. Therefore, it is highly desirable for them to get access to network performance monitoring data which is prepared to serve their needs.

“The perfSONAR measurement framework, which is jointly developed by the EU-funded GN2 JRA1 project, Internet2, and ESnet, has developed a prototype for measuring a variety of network performance metrics such as utilization, one-way delay, one-way delay variation, packet loss, available bandwidth, and others. Corresponding measurements are currently carried out in the contributing research networks in a prototypical manner and will be installed on a regular basis in the future.

“For the visualization of measurements a set of tools is under development which is in the focus of this paper. The design of the tools is carried out to serve the interests of the broad user community and uses best practices gained from a survey of visualization possibilities.”

The full paper can be read at http://wiki.perfsonar.net/jra1-wiki/images/b/b1/Icisp2006.pdf.

Alvarez Fellow Joshua Schrier's Talk Wins Award at ACS Meeting

Joshua Schrier, a postdoc in the Scientific Computing Group and a Computing Sciences Alvarez Fellow, was honored at the American Chemical Society's (ACS) 232nd national meeting last week. Joshua's talk, "Applications of the charge patching approach to individually heterostructured semiconductor nanocrystals," won the "Emerging technologies in Computational Chemistry" award. The talk, which described Joshua's work with Lin-Wang Wang in the Scientific Computing Group, was one of 20 submitted and six selected to be presented. The award was given by the ACS Division of Computational Chemistry, and was funded by Schrodinger, Inc. The panel of judges consisted of members of academia and industry. The talks were judged on the basis of the novelty and widepsread applicability of the method in question.

An article about Joshua's research can be found at http://crd.lbl.gov/html/news/CRDreport0905.pdf.

Two “New” Staffers Join BDMTC

Amy Chen and Ken Chu joined the Biological Data Management and Technology Center (BDMTC) of CRD on Sept. 1. Amy and Ken are software engineers who will be responsible for developing data management systems and bioinformatics software tools for BDMTC.

Both come from Gene Logic, which recently closed its Berkeley office in a restructuring exercise. At Gene Logic, they worked with BDMTC Head Victor Markowitz during his tenure as CIO and Senior VP of Data Management Systems.

Amy is a returning Lab employee, who also worked under Victor in the Scientific Data Management Group during the early 90s, developing data management tools applied to biological databases. Ken, prior to joining Gene Logic, worked for Atomic Energy of Canada Ltd. in Toronto.

Deb Agarwal to Give Sept . 20 Talk on Prototype Server for Sharing Environmental Data

Deb Agarwal, head of the Distributed Systems Department and a researcher with the Berkeley Water Center at Cal, will give a joint presentation on "Early Experience Prototyping a Science Data Server for Environmental Data" at 12 p.m. Wednesday, Sept. 20, in 540 Cory Hall, UC Berkeley. Deb will be joined by Catharine van Ingen of Microsoft Research and the Berkeley Water Center. Their talk, which is open to the public, is part of the CITRIS Research Exchange series and will be broadcast live online at mms://media.citris.berkeley.edu/webcast.

Here's the abstract:
“At the Berkeley Water Center, we are using data from the Oak Ridge National Laboratory Ameriflux carbon flux measurement towers to develop and prototype a new server for use by a collaborating group to jointly analyze data across sites. Working with data and metadata from the Ameriflux data repository, we are developing a scientific data server. This prototype server provides a framework to allow easy data download, quality checking, cleaning, and storage. The server also includes scientifically important metadata such as site biome or climate along with the actual data. The prototype is designed to allow data from other related data sets to be included as needed.”

Cal's CITRIS to Host Google's Peter Norvig in Sept. 25 Talk

Peter Norvig, director of Machine Learning, Search Quality and Research at Google, will be the next speaker in the Distinguished Speaker Series hosted by the Center for Information Technology Research in the Interest of Society (CITRIS) at UC Berkeley. Norvig will give his talk on “Theorizing from Data: Avoiding the Capital Mistake” starting at 4 p.m. Monday, Sept. 25, in the HP Auditorium, 306 Soda Hall on the UC Berkeley campus. The talk, which is free and open to the public, will also be broadcast live online at mms://media.citris.berkeley.edu/webcast.

Here is the talk abstract:

"'It is a capital mistake to theorize before one has data.' Sir Arthur Conan Doyle's words from 1891 remain true today. Researchers in computational linguistics and information retrieval now have a million times more data than was available 30 years ago. This talk explores what this data can do for problems in language understanding, translation, information extraction, and inference, and extrapolates to what more data may bring in the future.”

Peter Norvig has been at Google Inc. since 2001 as the Director of Machine Learning, Search Quality, and Research. He is a Fellow of the American Association for Artificial Intelligence and co-author of “Artificial Intelligence: A Modern Approach,” the leading textbook in the field.

University of Oklahoma Hosting Oct. 4 Supercomputing Symposium

The University of Oklahoma, Norman campus, is hosting the 2006 Oklahoma Supercomputing Symposium from 8 a.m. to 5:30 p.m. Wednesday, Oct. 4. A reception and poster session will be held from 5:30-7 p.m. Tuesday, Oct. 3. There is no charge to attend, but registration is required. Details can be found at http://symposium2006.oscer.ou.edu/.

The keynote speaker will be Dan Atkins, new head of the National Science Foundation's Office of Cyberinfrastructure. Other speakers include Stephen Wheat, Intel's Director of High Performance Computing, and Prof. Miron Livny of the University of Wisconsin.

About Computing Sciences at Berkeley Lab

The Lawrence Berkeley National Laboratory (Berkeley Lab) Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy's research missions: developing new energy sources, improving energy efficiency, developing new materials and increasing our understanding of ourselves, our world and our universe.

ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 7,000-plus scientists at national laboratories and universities, including those at Berkeley Lab's Computational Research Division (CRD). CRD conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. NERSC and ESnet are Department of Energy Office of Science User Facilities.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.