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InTheLoop | 12.03.2007

The weekly newsletter for Berkeley Lab Computing Sciences

December 3, 2007

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 next 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 will be held on January 7–11, 2008. Markowitz is featured 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.


“Democracy Defeats Meritocracy” in Machine Learning Seminar Wednesday


“The Counter-Intuitive Properties of Ensembles for Machine Learning, or, Democracy Defeats Meritocracy” will be the topic of a Scientific Computing Seminar Wednesday, December 5, from 1:00 to 2:30 pm in the Building 50B, 2222 Conference Room. The speaker will be Philip Kelgemeyer of Sandia National Laboratories, Livermore.

Here is the abstract:
“Machine learning is the process of using past experience to predict the future. There are many machine learning methods: neural nets, support vector machines, decision trees. The design trade-offs in optimizing them are a tricky business, still more art than science.

“‘Ensembles’ are a machine-learning meta-method that can be applied to most machine learning algorithms. Ensembles generally greatly improve accuracy, provably do no harm, reduce or remove most of the design issues, are admirably suited to parallel and distributed computation, and are delightfully weird and counter-intuitive.

“This talk will provide a terse introduction to machine learning and then discuss the properties of ensembles; what they are, various theories on why they work, and how they can be simply applied to improve existing machine learning code in situ.”


Reminder: Pay Attention to Ergonomics When Using Laptops


As more employees opt for laptops for both their office and travel computers, the Lab’s EH&S Division offers several tips for preventing injuries while using and carrying your laptop.

In the office, use an external keyboard, mouse and monitor. The laptop’s attached screen and keyboard mean you can’t align the display with your eyes or the keyboard and mouse with your hand and arms. While a laptop and wireless connection allows you to be connected on the bed or a comfy chair, this can also lead to painful posture, such as bending over too far to read the screen. A better way is to use a cushion on your lap to support the computer and pillows to support your arms.

When traveling, take care to avoid injury from lugging your laptop by using a shoulder bag with a wide, well-padded strap (and frequently switch shoulders) or distribute the weight evenly by using a backpack. Better yet, get a case with wheels and let the rollers carry the load.


Employee Concerns and Whistleblower Protection at LBNL


Employees have the right — and the responsibility — to identify and report improper governmental activities and environment, health and safety concerns and to do so without fear of reprisal. Employees are encouraged to discuss concerns with their immediate supervisor, any level of management, or their human resources representative. In cases where employees or others are unable or do not wish to raise issues to management, including retaliation, alternative mechanisms for reporting are available. In all cases, employees have the right to a respectful, prompt and effective response to their concerns.

In addition to the 24 hour anonymous hotline number (800-403-4744), other internal and external resources are listed at http://www.lbl.gov/CS/staff/concerns.html.


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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.