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New Microbial Metagenome Data Analysis System in Production

May 1, 2006

An experimental metagenomics data management and analysis system co-developed by the Biological Data Management and Technology Center (BDMTC) at Berkeley Lab with the Genome Biology Program and Microbial Ecology Program at DOE’s Joint Genome Institute and released earlier this year is also already helping produce scientific discoveries. Called IMG/M, the system extends the Integrated Microbial Genomes (IMG) system with the ability to integrate and analyze metagenome data, and has… Read More »

CRD’s PyGlobus Tools Proving Popular

January 1, 2006

CRD’s Distributed Systems Department (DSD), which has led the development of the de facto standard tools for developing Grid Services, applications and portals using the Python programming language, proved a popular draw at the LBNL booth at the SC05 conference in Seattle. Python is a high-level interpreted language that supports a rapid application development cycle. Python’s minimal syntax makes it an ideal language for use by non-computer scientists. It also easily supports… Read More »

CRD’s Chevassut Shares Expertise in Cryptography

January 1, 2006

Olivier Chevassut, who is the lead cryptographer for CRD, continues to build a reputation as an international expert on the theoretical and practical aspects of both cryptography and network security. In the first few months of 2006, Chevassut and several collaborators will have three conference papers and one journal article published. As part of his work in designing and analyzing novel complex cryptographic technologies, Chevassut has served as the lead of a project entitled… Read More »

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ViCE Helps Smooth Scientific Workflows

January 1, 2006

DSD’s work in higher-level interfaces to the Grid has led to the development of a visual programming tool, ViCE, that is used to collaboratively develop and execute complex scientific workflows. Scientific projects today are frequently large collaborations among geographically and organizationally distributed teams. ViCE is designed to support scientists collaborating over a visual description of their workflow. A workflow is represented as a set of nodes and links. The nodes… Read More »

Former DOE Fellow Returns to Berkeley

January 1, 2006

Jon Wilkening Jon Wilkening, who earned his Ph.D. in 2002 from UC Berkeley working with CRD Math Group Lead James Sethian, has returned to Berkeley as an assistant professor and collaborator with the Math Group. Wilkening accepted a DOE Computational Science Graduate Fellowship in 1997 (while declining an NSF fellowship) and was named a Fred A. Howes Scholar in Computational Science in 2003. As a DOE fellow, he worked as a research assistant in the Math Group from 1997 to 2002. His… Read More »

Bailey Co-Organizes Math Course

January 1, 2006

David H. Bailey, the Chief Technologist of the Computational Research Division, co-organized a two-day course entitled “Experimental Mathematics in Action” at the annual joint meeting of the American Mathematical Society and the Mathematical Association of America. The meeting was held January 10-15 in San Antonio, Texas. Approximately 80 people signed up for the course, which was organized in the spirit of the two recent books by Bailey and Jonathan Borwein, Mathematics by… Read More »

Berkeley Lab to Showcase HPC and Networking Leadership in Talks, Demos at SC05

November 8, 2005

Computing and networking experts from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory will share their leadership expertise via talks, technical papers and demonstrations at the SC05 conference to be held Nov. 12-18 in Seattle. Sidney Fernbach AwardJohn Bell, a senior staff mathematician and head of the Center for Computational Sciences and Engineering at LBNL, has been named as the recipient of the 2005 Sidney Fernbach Award. The Fernbach Award is given by the IEEE… Read More »

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Berkeley Lab’s John Bell Receives 2005 Sidney Fernbach Award

November 1, 2005

John Bell, a senior staff mathematician at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory, has been named as the recipient of the 2005 Sidney Fernbach Award. The Fernbach Award is given by the IEEE Computer Society for an outstanding contribution in the application of high performance computers using innovative approaches. The award was presented at the SC05 conference held Nov. 12- 18, 2005, in Seattle. “I am delighted to confirm that you have been selected to… Read More »

Journal Features Climate Modeling Articles by CRD’s Chris Ding, Helen He

November 1, 2005

The International Journal of High Performance Computing Applications (IJHPCA) has dedicated its Fall 2005 issue to climate modeling, especially on the software design of the Community Climate System Model Helen He (CCSM). Among the contributing authors are CRD's Helen He and Chris Ding, who wrote an article on “Coupling Multicomponent Models with MPH on Distributed Memory Computer Architectures” and contributed to another on “CPL6: The New Extensible, High Performance Parallel… Read More »

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CRD’s Brian Tierney Writes Article on Maximizing Network Throughput

November 1, 2005

Brian Tierney, a member of CRD’s Distributed Systems Department, has built a strong track record in analyzing the performance of networks and distributed computing systems. His Netlogger toolkit allows users of distributed systems to analyze performance and locate bottlenecks which hamper the overall performance of a system. He recently shared his expertise in an article he wrote for OnLAMP.com. LAMP, an acronym used in Germany to define how MySQL is used in conjunction with Linux, Apache and… Read More »