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InTheLoop | 05.26.2009

The weekly newsletter for Berkeley Lab Computing Sciences

May 26, 2009

IMG Expert Review Goes Primetime

After a genome is sequenced and automatically annotated, researchers often manually review the predicted genes and their functions in order to improve accuracy and coverage across the vast genetic code of the particular target organism or community of organisms. These annotations drive the publication of high-profile science relevant to advancing bioenergy research and our understanding of biogeochemistry—the biological, chemical, physical, and geological processes that regulate our environment.

Scientists at the DOE Joint Genome Institute (JGI) and the Biological Data Management and Technology Center (BDMTC) in the Computational Research Division at Lawrence Berkeley National Laboratory have launched the Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system. IMG ER supports and enhances the review and revision of annotations for both publicly available genome datasets and those newly released from private institutions. Read more.


ESnet, NERSC Help Speed Up Data Transfers between DOE Facilities

With the installation and deployment of new dedicated data transfer nodes at NERSC and NCCS linked by ESnet, researchers are now able to move large data sets between each facility’s mass storage system at a rate of 200 megabytes per second (MB/sec). At this rate, 74 terabytes of information in the U.S. Library of Congress’ digital collection could be transferred in approximately four days. Read more.


This Week’s Computing Sciences Seminars

Collecting Trace Data for HPC Applications

Wednesday, May 27, 1:00–2:00 pm, 50F-1647
Noel Keen, Computational Research Division, LBNL

By intercepting calls to the system LIBC library, trace data was collected, specifically I/O and memory allocation operations. Functionality was extended to allow IPM (lightweight MPI profiling tool) to treat these intercepted LIBC calls in much the same way that IPM handles MPI calls. Intercepting calls to LIBC calls only requires that the application code be re-linked to a static library. A tool was written to post-process and visualize the trace data that can be used as an aid to performance profiling. Data was collected on Franklin (Cray XT at NERSC) using several codes, including I/O intensive applications (MADbench and Chombo-IO) and an astrophysics particle-in-cell (PIC) code named Charm that uses Chombo.

Extracting Multiscale Information from Time Series Characterizing Single-Molecule Systems under the Influence of Time Dependent External Forces

Friday, May 29, 10:30–11:30 am, 50B-4205
Christopher Calderon, Department of Computational and Applied Mathematics, Rice University

Single-molecule experiments and computer simulations have generated data sets containing useful information about the dynamics of complex biomolecules. However, the many degrees of freedom present, time dependent external forces, and multiple time-scale fluctuations inherent at this level of detail complicate the task of summarizing the interesting information in these dynamical systems. I demonstrate how a collection of surrogate processes, estimated from a relatively small number of non-equilibrium time series, can assist in characterizing these systems. Both thermodynamic (e.g., potential of mean force) and kinetic information (e.g., effective molecular friction) can be extracted using the collection of surrogate models. The methods are also useful when a good set of reaction coordinates is unknown or not experimentally accessible, e.g., a collection of surrogate models can also be used to infer information about slowly evolving degrees of freedom not directly monitored. Illustrative results obtained using various MD simulations and AFM experiments are presented. I also discuss new algorithms and computational techniques that were developed to assist in modeling the single-molecule time series data.


Link of the Week: Caltrans Eagle Cam Revisited

As reported in the March 30 InTheLoop, Caltrans installed a webcam above a bald eagle nest along the Sacramento River near Redding. The three chicks that hatched on March 17, 19, and 22 have grown to about 70% of their adult size. The parents will continue feeding the young but will have a decreased presence at the nest in the coming weeks. The eaglets are beginning to flap their wings and jump around in the nest. These behaviors will eventually develop into “branching,” as the eaglets periodically make their way out onto the cottonwood tree branches and return to the nest. The fledglings are expected to begin flying in mid-June.



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.