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InTheLoop | 01.07.2008

The weekly newsletter for Berkeley Lab Computing Sciences

January 7, 2008

BDMTC Helps Organize Microbial Genomics and Metagenomics Workshops


The Biological Data Management and Technology Center (BDMTC) will take part in three Microbial Genomics and Metagenomics Workshops this year at the DOE Joint Genome Institute (JGI). The five-day workshops will provide training in microbial genome and metagenome analysis.

The workshops will offer two days of intensive seminars and three days of hands-on tutorials on a variety of data analysis tools, in particular the tools provided by the Integrated Microbial Genomes (IMG) family of systems developed by BDMTC in collaboration with the Genome Biology Program (GBP) at JGI. Nikos Kyrpides, head of GBP, David Gilbert, head of public relations for JGI, and Victor Markowitz, head of the BDMTC, are the workshop organizers.

The first workshop begins today and will end Friday (January 7–11). Markowitz is scheduled to speak about the IMG-Expert Review (IMG-ER) and IMG-Educational (IMG-EDU), two recently released systems from the IMG family. Krishna Palaniappan of BDMTC will speak about the challenges of integrating different types of genomic data for comparative analyses.

The same material will be covered in workshops on May 19–23 and September 15–19, 2008. Find out more about the workshops at http://www.jgi.doe.gov/meetings/mgm.


Seminar to Discuss Fast Pointing Expansion for CMB Experiments Today


Theodore S. Kisner will present a seminar titled “Fast Pointing Expansion for CMB Experiments” today (Monday, January 7) from 1:00 to 1:30 pm in the 50F-1647 Conference Room. Here is the abstract:

“Current and planned experiments which measure the Cosmic Microwave Background have hundreds to thousands of individual microwave detectors which are sampled at several hundred hertz. Analysis of the resulting data time streams requires accurate knowledge of each detector’s pointing and orientation on the sky at each sample. Saving this information for each detector for the entire length of a mission requires tens of terabytes of storage space. On the other hand, computing this information at run time can potentially dominate the computational cost of the analysis. A highly tuned library for on-the-fly pointing decompression will be presented.”


International Supercomputing Conference Issues Call for Papers for 2008 Event


ISC’08, the 23rd meeting of the International Supercomputing Conference, is seeking papers from researchers in computing and scientific disciplines reporting original work in theoretical, experimental and industrial research and development. The deadline for submissions is Tuesday, February 19.

ISC’08, the premier supercomputing event in Europe, will be held June 17–20 in Dresden, Germany. Selected papers will be presented on June 17 as part of Scientific Day, an open forum for engineers and scientists in academia, industry, and government to present and discuss issues and trends that will shape the future of high performance computing and networking.

The conference seeks papers reporting original work in theoretical, experimental, and industrial research and development on the following topics:

  • Advances in very large-scale applications of science and engineering modeling, simulation and design
  • Successful implementation and deployment of large-scale grid-enabled systems
  • Computation pipelines and workflows for life sciences, especially computational biology and biological data integration
  • High performance computer architectures
  • Data-intensive and I/O computing
  • Scalable tools for performance analysis and tuning for hundreds and thousands of PEs
  • High-speed system area networks for large computer system architectures
  • Measurement and modeling of grid middleware and applications

Two papers will be selected for awards. Authors of the winning papers will each receive a high-end workstation based on the latest Intel® Xeon® processor or Intel® Core™2 Quad processor. The conference also plans to publish selected papers in a special issue of Concurrency and Computation: Practice and Experience.

Papers should be submitted in English. Extended abstracts of not less than four pages but not more than 6,000 words should be submitted in electronic form (pdf or doc) to cfp@supercomp.de by February 19. Abstracts should clearly describe the contents, relevance, and originality of the contribution. The topic area should be indicated, and important references must be included. All papers will be refereed, and authors will receive notification of acceptance by May 1.

For more information about the conference, please see ISC.


The December Issue of CRD Report Is Now Online


The December issue of the CRD Report is now online at http://crd.lbl.gov/html/news/CRDreport1207.pdf. Highlights of this issue include:

  • Research on microbes inside termites’ hindguts relies on the IMG/M system for managing and analyzing data.
  • A paper showing how zinc oxide can be a good alternative for building photovoltaic devices was popular among readers of Nano Letters.
  • CRD researchers made a significant contribution to the latest Cyberinfrastructure Technology Watch, which features various SciDAC projects.
  • A paper on the use of a “trust region” and the direct minimization algorithm for solving the Kohn-Sham equation was published in the SIAM Journal on Scientific Computing.

Actor Alan Alda to Discuss M*A*T*H in January 17 Berkeley Talk


The Mathematical Sciences Research Institute (MSRI) is sponsoring “M*A*T*H: Alan Alda in conversation with Bob Osserman” on Thursday, January 17, at the Berkeley Rep’s Roda Theater in downtown Berkeley. Alda, probably best known for his role as Hawkeye Pierce on the TV show M*A*S*H, is an Emmy award-winning actor, director, writer for film and television, and author of bestselling books. He will talk with mathematician Osserman about his lifelong interest in science, which led Alda to become the host of Scientific American Frontiers on PBS for 11 years. Tickets are available online (with a $7 service fee) at Berkeley Repertory Theatre or from the Berkeley Rep box office (no fee) at 2015 Addison St.


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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 6,000 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 DOE 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.