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InTheLoop | 02.05.2007

The weekly newsletter for Berkeley Lab Computing Sciences

February 5, 2007

Juan Meza to Lead MSRI Undergraduate Program This Summer

Juan Meza, head of CRD’s High Performance Computing Research Department, will direct the research of twelve undergraduate students in the 2007 Mathematical Sciences Research Institute Undergraduate Program (MSRI-UP). The MSRI-UP is a comprehensive program for undergraduates that aims at increasing the number of students from underrepresented groups in mathematics graduate programs. MSRI-UP includes summer research opportunities, mentoring, workshops on the graduate school application process, and follow-up support.

Under the general topic “Computational Science and Mathematics,” student research topics may include:

  • nonlinear eigenvalue algorithms for material sciences
  • optimization methods for nanoscience simulations
  • machine learning algorithms for feature detection in supernova searches and hurricanes
  • studies of climate change
  • combinatorial algorithms for detecting vulnerabilities in power grid networks
  • partial differential equations for combustion and supernova simulations
  • fast algorithms for data mining in large scientific data sets

MSRI-UP will run from June 17 to July 29, 2007. Students who will finish their sophomore or junior year in 2007 can apply for this program at http://www.msri.org/up/intropage. African American, Latino and Native American students are especially sought. Due to funding restrictions, only U.S. citizens and permanent residents are eligible to apply. Each student will receive room and board, a $3,000 summer stipend, transportation to and from Berkeley, and funding to attend a national conference.

For further information, see the description/requirements page at http://www.msri.org/up/description.

Metagenomics Data Management and Analysis System Is Upgraded

On the one-year anniversary of the launch of the experimental metagenome data management and analysis system, IMG/M, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has released the latest upgrade. IMG/M, accessible to the public at http://img.jgi.doe.gov/m, is the result of a collaboration between JGI and CRD’s Biological Data Management and Technology Center (BDMTC).

Targeting DOE JGI’s expanding user base, IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence, in the context of reference isolate genomes, using a variety of public functional and pathway resources. The enhanced version of IMG/M now offers aggregate genome (metagenome) data generated from microbial community samples that have been the subject of recently published studies. These include samples from biological phosphorus removing sludge (Nature Biotechnology Volume 24, Number 10, October 2006), human distal gut (Science 312: 1355-1359, 2 June 2006), a gutless marine worm (Nature 443, 950-955, 26 October 2006), and obese and lean mouse gut (Nature 444, 1027-131, 21 December 2006). In addition, IMG/M includes three of the simulated metagenome data sets employed for benchmarking several assembly, gene prediction, and binning methods http://fames.jgi-psf.org/.

IMG/M’s reference isolate genomes were included from version 2.0 of JGI’s Integrated Microbial Genomes (IMG) system, a total of 2,301 isolate genomes consisting of 595 bacterial, 32 archaeal, 13 eukaryotic, and 1,661 virus genomes.

IMG/M will be demonstrated at a workshop on March 28, as part of the DOE JGI Second Annual User Meeting http://www.jgi.doe.gov/meetings/usermtg07/.

Investment Offer Prompts Reminder on Conflicts of Interest

Last week, NERSC Center General Manager Bill Kramer sent a message to all NERSC staff about several emails and phone calls by representatives claiming to be from Credit-Suisse Bank and offering him presales for an IPO. Apparently a vendor to the Lab had referred Bill’s name to the investment firm. As Bill noted to the staff, “Such special deals are not appropriate since this vendor is actively soliciting future business with NERSC and LBNL. Further, since part of all our duties is to periodically serve on selection teams, taking part in such an offer is a conflict of interest for NERSC-related staff.”

The Lab’s Regulations and Procedures Manual (RPM) has a section on conflict of interest at http://www.lbl.gov/Workplace/RPM/R10.01.html. Additionally, clause 1.66 of the Lab contract defines organizational conflicts of interest, stating “The purpose of this clause is to ensure that the Contractor (1) is not biased because of its financial, contractual, organizational, or other interests which relate to the work under this contract…”

Employees who are contacted with investment offers which pose a potential conflict of interest should decline the offer, document the fact, and notify your supervisor.

Proposals Sought for Mentoring Workshops to Reach Underrepresented Groups

The Committee on the Status of Women in Computing Research (CRA-W) and the Coalition to Diversify Computing (CDC) are jointly soliciting proposals for discipline-specific mentoring workshops in the broad field of computing. The goal of these workshops is to increase participation of members of underrepresented groups within a specific research area by providing mentoring advice and discipline-specific overviews of past accomplishments and future research directions. Specifically, the workshop should focus on helping young researchers at the graduate or post-graduate level become interested in and knowledgeable about the research and research paradigms of a specific discipline.

Prospective workshop organizers are requested to submit a proposal at least nine months prior to the proposed workshop date. The format for workshop submissions is left unspecified, but organizers are encourage to include at least the following information:

  • Full contact information for the organizers. The team of organizers should include members of underrepresented groups.
  • Research focus area of the workshop
  • Proposed dates for the workshop
  • Proposed workshop agenda
  • Organizational time table, including arrangements for the venue, hotel, advertising, meals, panelist invitations, selection process, follow-up activities
  • Estimated number of workshop participants
  • Advertising plans, especially plans for reaching out to underrepresented groups
  • Proposed budget and requested support from CRA-W and CDC
  • Fundraising plans.

Proposals will be reviewed two times a year and should be submitted by March 1 or September 1 for consideration. The results of the review process will be made available by the end of March (for the March 1 deadline) or mid-September (for the September 1 deadline). For more information go to http://www.cra.org/Activities/craw/cdc/.

NERSC’s Seaborg Computer Draws Interest of Consulting Franchise Firm

With the arrival last month of the first production nodes of NERSC’s new Cray supercomputer, the center’s workhorse IBM supercomputer known as Seaborg may be wondering where its career path leads. Well, thanks to the initiative of one Pam Duskocy at the Schooley Mitchell Telecom Consultants, a new rewarding career as a franchised consultant might be in the cards. Last week, in an email addressed to “Seaborg Home Page” and titled “Regarding Your Resume,” Pam sent the system a “Dear Seaborg” pitch, noting that the company’s top 25 percent of employees “averaged $315,000 in revenue last year.”

“Have you considered owning your own professional business to provide advice to other business owners and executives? Consulting Business ownership opportunity with Schooley Mitchell Telecom Consultants — telecom background not required.” While this may sound too good to be true, Pam offers that the company’s success is due to “Providing business advice to more than 10,000 business owners and executives.”

And Seaborg would appear to meet their qualifications, having been a strong performer since 2000. Schooley Mitchell’s ideal candidate is described as “This person has a strong passion for customer success. We desire someone who has strong execution skills, is focused, responsible and accountable.” Check, check, check, check and check.

Best of all (thanks perhaps to email formatting glitches), the company isn’t so demanding in other areas, such as “Integrity and ethics are critical ?”

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 7,000-plus 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 Department of Energy 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.