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InTheLoop | 11.12.2012

November 12, 2012

ACS Researchers Win Best Paper at SC12 Data Cloud Workshop

Scientific applications are increasingly using cloud resources for data analysis workflows. However, managing data effectively and efficiently over clouds is challenging due to the myriad storage choices with different performance and cost trade-offs, wide variety of application choices and the complexity associated with elasticity and failure rates in these environments.

Devarshi Ghoshal (a summer student) worked with Lavanya Ramakrishnan to explore a framework that uses different data partitioning and distribution strategies to balance application and resource characteristics in cloud environments. The paper describing the initial design and implementation of the FRIEDA framework  (Flexible Robust Intelligent Elastic Data Management) was awarded Best Paper at the Third International Workshop on Data Intensive Computing in the Clouds (DataCloud 2012). Ghoshal and Ramakrishnan also won the best paper at the workshop last year for their joint work with Shane Canon at NERSC on "I/O Performance of Virtualized Cloud Environments." More details on FRIEDA can be found on the website.

Berkeley Lab Contributes to SC12 Technical Program Sessions

Once again, scientists and engineers from Berkeley Lab are making significant contributions to the SC12 Technical Program, sharing their expertise and experience with thousands of attendees at the annual conference sponsored by the IEEE Computer Society and ACM SIGARCH. SC12 will be held Nov. 10-16 in Salt Lake City, Utah. Read more.

Modeling Feat Sheds Light on Protein Channel's Function

Using supercomputers at the Department of Energy's National Energy Research Scientific Computing Center (NERSC), chemists have managed, for the first time, to simulate the biological function of a channel called the Sec translocon, which allows specific proteins to pass through membranes. The model required bridging timescales from the realm of nanoseconds all the way up to full minutes, exceeding the scope of earlier simulation efforts by more than six orders of magnitude. The result is a detailed molecular understanding of how the translocon works. Read more.

Wehner Awarded INCITE Grant to Study Climate Change and Extreme Weather

In the wake of super storm Sandy and the record-breaking 2011 Texas drought, more people are asking,"is this climate change?" While it's practically impossible to give a straight yes or no answer to that question, Michael Wehner of the computational research division is working to understand how climate change influences the risks of such extreme weather events. To that end, he was recently awarded an INCITE grant of 150 million processor hours on Argonne National Laboratory's "Mira," an IBM Blue Gene/Q supercomputer. Wehner plans to use the award to run the super-high resolution (25 km CAM-5) atmospheric models he piloted at NERSC.

On a related note, Scientific Computing Group Staff Scientist Daithi Stone was quoted in the Science magazine article "Extremely Bad Weather" about the link between climate change and extreme weather events like droughts and super storms. Wehner also spoke on this topic on KPFA 94.1’s Terra Verde

The Microbiome: Dealing with the Data Deluge

Earlier this year, the Human Microbiome Project (HMP) Consortium published a slew of papers offering fresh insights into the role microbial communities play in the human body—including how changes in the vaginal bacteria of pregnant women affect the health of their babies, and how gut microbes influence inflammatory bowel disease. HMP participants sequenced thousands of metagenome samples—which contain genetic material from hundreds of diverse microbes—from up to 18 body sites in 242 healthy individuals.

Because the data are much more massive and messy, state-of-the-art tools for analyzing individual genomes aren’t well suited to analyzing metagenomes. So a team of researchers from the Department of Energy’s Joint Genome Initiative (JGI) joined forces with software engineers and computer scientists from the Biological Data Management and Technology Center (BDMTC) at Lawrence Berkeley National Laboratory to develop and maintain a suite of novel tools, including a quality control filter, a curation and annotation pipeline, and methods for analyzing and integrating the data. Read more.

Network Matters: Vote for ESnet5, a Good Steward of Petabytes

In this blog post for Network Matters, ESnet’s Inder Monga explains some innovative testing concepts that are currently being implemented by ESnet engineers to ensure that users experience little or no disruptions when the network switches its production traffic from ESnet4 to ESnet5. Read more.

In the News: Is Supercomputing the New Space Race?

Horst Simon, the Deputy Director of Lawrence Berkeley National Laboratory who helps run the Top500 supercomputer list is quoted in this Wired story entitled “Is Supercomputing the New Space Race?” In this story, reporter Mike Barton speculates about whether OakRidge’s Titan supercomputer will be the most powerful machine on the Top500 list.

The Top500 was published this morning. Read more.

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.