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InTheLoop | 06.05.2006

The weekly electronic newsletter for Berkeley Lab Computing Sciences employees

June 5, 2006

ESnet's Long Island Metropolitan Area Network Boosts BNL Connectivity Eightfold

ESnet continues to roll out its next-generation architecture on schedule with the recent completion of the Long Island Metropolitan Area Network, connecting Brookhaven National Laboratory to the ESnet point of presence (POP) 60 miles away in New York City. The new design is built on a diversely routed dual 10 Gb/s Dense Wave Division Multiplexed (DWDM) ring that connects the DOE Office of Science laboratory to both the ESnet IP core and the new Science Data Network (SDN) for high-throughput science data and collaboration.

This service upgrade provides BNL with a fully usable aggregate bandwidth of 20 Gb/s, an eightfold increase over the lab's previous 2.4 Gb/s link to Manhattan. This architecture is designed to be easily expanded to eight waves supplying 80 Gb/s to the lab. BNL is the largest tier one data distribution site for the ATLAS experiment at CERN and requires this next-generation network to support its ATLAS mission.

One of these two 10 Gb/s lambdas in place at BNL will access the ESnet SDN and be provisioned primarily for dedicated circuits scaling to support the demands of petabyte data transfers, such as those required by ATLAS. The data will be generated by the ATLAS experiment to be conducted on the Large Hadron Collider (LHC) currently under construction at CERN. This data will be carried from CERN to New York City by USLHCnet.

BDMTC's Microbial Database Work Cited in Genome Technology Magazine

The June issue of Genome Technology magazine includes an article on the IMG/M, an experimental metagenome data management and analysis system created jointly by CRD's Biological Data Management and Technology Center and the Joint Genome Institute.

Here's a short excerpt from the article: “IMG/M … builds on JGI's integrated microbial genomes (IMG) system and extends its comparative tools to metagenome data. The IMG system, built through a collaboration with Lawrence Berkeley National Lab, is updated quarterly and contains both draft and complete JGI genomes, in addition to other publicly available microbial genomes. Researchers interested in analysis, as opposed to just browsing the bank, can navigate the samples by phenotypes, ecotype, disease, and relevance.

“According to Victor Markowitz, head of Lawrence Berkeley National Laboratory's Biological Data Management and Technology Center and the system's chief architect, the idea was always to broaden IMG's remit. ‘Once we had IMG, we asked what it would take to extend [the system] to metagenomes,' Markowitz says. It took a lot, especially in terms of conceptual organization of the raw data. Whereas IMG charts isolate genomes for which assembly and gene prediction is done, IMG/M must contend with data from entire microbial communities for which assembly scaffolds come from different organisms.

“Given those complexities, the LBNL team forged ahead to create a repository capable of evolving with its diverse data sets. Working on the system mostly on weekends, the group built IMG/M over a period of five months, and a preliminary version was distributed for expert testing at the end of last year. One of the early users, JGI's Phil Hugenholtz, test drove the system to analyze enhanced biological phosphorus removing (EBPR) sewage sludge metagenomes, which yielded results slated to appear in an upcoming paper.”

The June issue of Genome Technology can be downloaded from http://qmags.com/gt/download_gt_jun.asp.

EH&S Ergonomic Equipment Display Moves to Bldg. 75B

The Lab's display of ergonomic equipment, such as chairs and computer accessories, has moved from Health Services in Bldg. 26 to Bldg. 75B room 110B. The display center is open from 8 a.m. to 5 p.m. Monday through Friday. No appointment is needed, but can be arranged by calling Edith Perry at x7170, if desired.

At the center, employees can:
* See and try out ergonomic furniture and accessories
* Participate in the chair loaner program
* Review educational material (videos, brochures, posters)

Job Opening: Librarian-Archivist

The IT Division has posted a job opening for a Librarian-Archivist. Position duties including staffing the Reference Desk of the central Lab library and assisting in the archiving of historical photographs and digital images in a central electronic repository. The complete job posting can be found at http://jobs.lbl.gov/LBNLCareers/details.asp?jid=19081&p=1.

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.