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SC06: High performance computing research highlights from PNNL

November 10, 2006 Share This!

RICHLAND, Wash. – Pacific Northwest National Laboratory will participate in the following activities at the international supercomputing SC06 conference November 11-17, 2006, in Tampa, Fla.

Finalist, HPC Analytics Challenge – PNNL is one of three finalists in this SC06 challenge. Researcher Chris Oehmen will present "High-throughput visual analytics for biological sciences: Turning data into knowledge." (See schedule below)

Finalist, Bandwidth Challenge – Scientist Tim Carlson will discuss PNNL’s Secure Collaboration Zone that, coupled with intrusion detection capabilities and tight system configuration management controls, eliminates the traditional firewall bottleneck and creates a layered security model for secure, scaleable data transfer. During the challenge, a computer cluster on the conference floor will access an information archive of high throughput biological spectral data located at PNNL in Richland, Wash. Tuesday, November 14, 4:00 - 4:10 p.m., Rooms 24-25.

Tutorial, Global Arrays Parallel Software Development Toolkit – Laboratory Fellow Jarek Nieplocha will present an overview on how the Global Array toolkit provides a "shared-memory" programming interface that greatly simplifies the development of programs on modern high performance computer architectures, even ones with distributed-memory computers. Monday, November 13, 1:30 - 5:00 p.m., Room 20

PNNL researchers also will demonstrate the following technologies in Booth 321.

Tuesday, November 14

High-throughput BLAST calculations on a cluster, 11:00 a.m. - 12:00 noon

ScalaBLAST is a high-throughput sequence alignment tool for performing genome-scale and multiple genome-scale BLAST searches. ScalaBLAST uses a powerful combination of new and original features of the Global Array toolkit – process groups and nonblocking memory access – to get 'hardware shared memory' performance on clusters through a 'software shared memory' interface. This unlocks the potential of clusters to be on the leading edge of sequence data analysis for biological research.

Network Infrastructure Protection, 2:00 - 3:00 p.m.

SCinet is the most advanced technology network built on site to enable world-class demonstrations and support the annual SC conference. The infrastructure protection program uses a variety of sensors, automated analysis methods, visualization tools and architecture to pass information between the various components to help SCinet Security Personnel recognize and mitigate attacks against the SCinet infrastructure. Critical features include visualization and analysis of streaming transactions and threaded dialogue analysis.

Wednesday, November 15

Bioinformatics Resource Manager, 11:00 a.m. - 12:00 Noon

Bioinformatics Resource Manager is a problem-solving environment providing data retrieval, management, analysis and visualization through all aspects of a biological study. BRM provides users with the ability to integrate their experimentally derived data with other publicly available heterogeneous data sources. Designed in collaboration with biologists, BRM simplifies the merging of microarray and proteomic data across platforms with other publicly available data sources, thereby facilitating the integration of heterogeneous data from various high-throughput technologies.

Thermal Management, 2:30 - 3:30 p.m.

PNNL is working closely with industry to resolve cooling issues associated with high performance computing. The thermal management demonstration provides a viewable explanation of two cooling solutions. The SprayCool acrylic enclosure shows a 6-slot VME card cage using liquid evaporation, or phase change, to cool the electronics. The SprayCool M-Series Rack is designed to address the needs of rack-mounted systems in data center environments.

Thursday, November 16

Network Infrastructure Protection, 10:00 - 11:00 a.m.

See Tuesday, 2:00 - 3:00 p.m.

InfoStar, 11:30 a.m. - 12:30 p.m.

InfoStar is an information system that supports the SC06 conference. It combines multiple data sources, collaboration capabilities and an innovative data clustering and visualization technology to provide conference attendees with real-time access to SC conference information on any device with internet capabilities. With an updated schedule of events, maps, search capabilities, visual explorations, web cameras, photo galleries, forums and more, InfoStar is the most complete information source about SC06.

Analytics Challenge – High-throughput visual analytics for biological sciences: turning data into knowledge, 1:00 - 2:00 p.m.

High-throughput experimental facilities are fast becoming the norm in biological research. Keeping up with this data avalanche can become its own 'grand challenge'. PNNL will demonstrate a modular workflow for harnessing the power of supercomputing hardware in an end-to-end data analysis pipeline that takes high-throughput data all the way to a browsable representation. PNNL's Bioinformatics Resource Manager brings together advanced high-performance peptide applications such as Polygraph, dataset viewers like PQuad, and web-based tools allowing users to create their own problem-specific workflow.

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Interdisciplinary teams at Pacific Northwest National Laboratory address many of America's most pressing issues in energy, the environment and national security through advances in basic and applied science. Founded in 1965, PNNL employs 4,300 staff and has an annual budget of about $950 million. It is managed by Battelle for the U.S. Department of Energy. For more information, visit the PNNL News Center, or follow PNNL on Facebook, Google+, LinkedIn and Twitter.

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