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InTheLoop | 03.19.2007

The weekly newsletter for Berkeley Lab Computing Sciences

March 19, 2007

Updated Version of Integrated Microbial Genomes System Is Released

The Joint Genome Institute and CRD’s Biological Data Management and Technology Center have released an updated version of the Integrated Microbial Genomes (IMG) data management system. IMG 2.1, released on the second anniversary of its launch, includes microbial genomes from the latest release of the National Center for Biotechnology Information’s Reference Sequence collection. Other new features include model eukaryotic genomes and plasmids, all of which will enable scientists to carry out more extensive genome analysis. The new version of IMG would not have been possible without the Biological Data Management and Technology Center, headed by Victor Markowitz, who also is the system development lead for IMG. You can check out IMG at http://img.jgi.doe.gov.

Seaborg Fellowship Candidate to Give March 26 Seminar

Kevin Chu, a candidate for the Lab’s Seaborg fellowship, will present a seminar at 9:30 a.m. Monday, March 26, in Bldg. 50B-4205. Chu, of Princeton University, will give a talk on “Recent Applications of Level Set Methods in Material Science: Dislocation Models of Grain Boundaries and Equilibrium Microstructures.” All interested staff are invited to attend.

Here’s the abstract:
“The level set method continues to be a popular computational and analytical tool for studying many interesting problems in material science and engineering. In this seminar, we discuss recent applications of level set methods to two longstanding problems in material science. First, we present a level set formalism for describing dislocation models of low-angle grain boundaries. Using a dislocation dynamics simulation based on this formalism, we examine the microstructure of equilibrium grain boundaries and investigate the motion of grain boundaries under applied stresses. Next, we present a variational level set approach to theoretically and computationally study triply periodic, two-phase equilibrium microstructures. Here we focus on systems where only the interfacial energy between the two phases contributes to the free energy and where the volume fraction of the two phases is constrained. We demonstrate, theoretically, that equilibrium microstructures are those where the interface between the phases possesses a constant mean curvature. We then computationally study the stability of microstructures whose phases are separated by well-known minimal surfaces and explore the properties of equilibrium microstructures when the volume fractions are unequal.”

March 28 Scientific Computing Workshop Schedule Set

A one-day Workshop on Scientific Computing organized by CRD’s Scientific Computing Group for Wednesday, March 28, will feature nine talks by Lab staff and visitors from research institutions and universities in the U.S., Asia and Europe. The workshop will be held in Perseverance Hall next to the Lab cafeteria. Here’s the schedule of talks:

For more information, contact Sandi Fischer (SKFischer@lbl.gov), Parry Husbands (PJRHusbands@lbl.gov), or Esmond G. Ng (EGNg@lbl.gov).

Osni Marques Invited to Speak at ICCM 2007 Conference in Hiroshima

Osni Marques of CRD’s Scientific Computing Group has been invited to give one of four “semi-plenary” lectures at the International Conference on Computational Methods (ICCM 2007), to be held in Hiroshima, Japan, April 4-6, 2007. His topic will be “Rewards of software reuse and an outlook on scientific software libraries.” Osni and Tony Drummond provide maintenance, outreach and training for the ACTS Collection of DOE-developed software tools.

The ICCM 2007 conference provides an international forum for the presentation and showcase of recent advances in various aspects of computational methods. It will reflect the state of the art of the computational methods involving theory, algorithm, programming, coding, numerical simulation, error and uncertainty analysis and/or the novel application of computational techniques to problems in engineering, science, and other disciplines related to computations. More information can be found at http://home.hiroshima-u.ac.jp/iccm2007/.

Reminder: March 30 Deadline for Tech Program Submissions to 2007 Tapia Conference

The deadline for submissions for papers, panels, workshops for the 2007 Richard Tapia Celebration of Diversity in Computing Conference is Friday, March 30. Tapia 2007, the fourth in the series, will be held Oct. 14-17, 2007, in Orlando under the theme “Passion in Computing — Diversity in Innovation.” While the program will cover technical areas, the conference is aimed at providing a supportive networking environment for under-represented groups across the broad range of computing and information technology, from science to business to the arts to infrastructure. Organized by the Coalition to Diversify Computing, Tapia 2007 is co-sponsored by the Association for Computing Machinery and the IEEE Computer Society, in cooperation with the Computing Research Association.

Researchers are invited to submit papers to Tapia 2007 in the following areas of interest:
* Information Security
* Intelligent Systems
* Human Centered Computing
* Computational Math and Science

Papers on other areas of research will also be considered. Prospective authors are invited to submit extended abstracts of no more than four pages, single-spaced in 12-point type size, including results, figures and references. All papers must be submitted electronically.

Proposals are also invited for panels focusing on technical areas or issues related to increasing diversity in the field of computing. Panel proposals should be no more than one page, single-spaced in 12-point type size.

Finally, proposals are invited for workshops focusing on issues related to increasing diversity in the field of computing. Workshop proposals should be no more than two pages, single-spaced in 12-point type size.

Details can be found on the conference Web site at http://www.richardtapia.org/Participating.html. Extended abstracts should be submitted by Friday, March 30. Authors will be notified of acceptance decisions by June 15, 2007.

For the first time in the history of the Tapia conference, the 2007 meeting will be co-located with the Grace Hopper Celebration of Women in Computing conference, to be held Oct. 17-20, 2007, in Orlando.

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.