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InTheLoop | 11.26.2007

The weekly newsletter for Berkeley Lab Computing Sciences

November 26, 2007

BDMTC’s Ernest Szeto Co-Authors Metagenomic Analysis of Termite Gut Microbes


Ernest Szeto of CRD’s Biological Data Management and Technology Center (BDMTC) contributed to a groundbreaking metagenomic analysis of termite gut microbes published in the November 22, 2007 issue of Nature (F. Warnecke et al., “Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite,” Nature 450, 560–565). The genomic sequencing and analysis of the termite gut microbes was carried out by the Department of Energy Joint Genome Institute (DOE JGI) and several research partners.

Termites — notorious for their voracious appetite for wood, rendering houses to dust and causing billions of dollars in damage per year — may provide the biochemical means to a greener biofuel future. The bellies of these tiny beasts actually harbor a gold mine of microbes that have now been tapped as a rich source of enzymes for improving the conversion of wood or waste biomass to valuable biofuels. “The data set provided by Warnecke et al. is a treasure trove for researchers,” wrote Andreas Brune in a separate article commenting on the research in the same issue of Nature.

The termite gut metagenome dataset will become publicly available in the next version of DOE JGI’s metagenome data management and analysis system, IMG/M (http://img.jgi.doe.gov/m), scheduled for release in January 2008. Szeto was responsible for data processing and loading the dataset into IMG/M.

For more information and to view a video about this research, go to http://www.jgi.doe.gov/News/news_11_21_07.html.


David Patterson Is Named AAAS Fellow


David Patterson, a member of Berkeley Lab’s Computational Research Division and holder of the E.H. and M.E. Pardee Chair of Computer Science at UC Berkeley, has been named a 2007 Fellow of the American Association for the Advancement of Science (AAAS). The new Fellows will be recognized for their contributions to science and technology at the Fellows Forum to be held on February 16, 2008 during the AAAS Annual Meeting in Boston, where each will receive a certificate and a blue and gold rosette as a symbol of their distinguished accomplishments.

Patterson is also a member of the National Academy of Sciences and the National Academy of Engineering. He led the design and implementation of RISC I, the first VLSI Reduced Instruction Set Computer, and he shared the 2000 IEEE von Neumann medal and IEEE’s 1999 Reynold Johnson Information Storage Award. He is currently building novel microprocessors using Intelligent DRAM for use in portable multimedia devices, and is a member of the ROC project, for Recovery Oriented Computing.


Reminder: CS Staff Asked to Review Property Lists by November 30


In preparation for the Labwide property inventory early next year, Computing Sciences is asking all staff to log into the inventory database and review items in their name. All laptop computers and all assets over $1 million will have to be scanned with a bar code reader during the inventory. CS Facilities would appreciate staff assistance in identifying any potential problem assets or items that may be difficult to scan before Friday, November 30.

Please take a look at the property that is currently in your name by completing the three steps below.

Step 1: Go to http://warrior.lbl.gov:7777/pls/snflwr_report_amsprd/amsadm.as_owa_user_defined.form_1?p_application_name=Sunflower+Assets+-+Production+3.7.0.0&p_return_to_name=User+Defined+Reports&p_return_to_procedure=amsadm.as_owa_user_defined.main.

Step 2: Enter your employee ID number in the “Identifier” field on the “Custodian” line.

Step 3: Click on “Submit” at the bottom of the page, and on the next page that appears, select “Acrobat” and hit “eXecute.”

The computer will then generate the Property Verification by Signature Report, listing all the property that is currently in your custodianship. Review this list and if everything is correct, please sign, date and mail a hardcopy to your division representative. If the list contains incorrect info, please make corrections. CS and CRD employees should send the report to Parisa Farvid, x4965, PFarvid@lbl.gov, MS50A-1148. NERSC employees should contact Suzanne Stevenson, x6190, SMStevenson@lbl.gov, MS943-256.


Leah Gutierrez Joins the Computing Sciences Administrative Staff


Leah Gutierrez has joined the Computing Sciences administrative staff to assist Kathy Yelick and the NERSC Division. Leah came to the Lab in May 2006 to work in the Director’s front office, and has worked in office and operations management for several Bay Area professional and financial services companies.

Zaida McCunney is still located in the CS suite and will now be assisting the CRD department heads, Juan Meza, Deb Agarwal and Victor Markowitz.


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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.