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SGI Solutions to Help NCI Solve Demanding Biological Research Problems

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Silicon Graphics and SCICOR, an authorized SGI Solution Provider have announced that the National Cancer Institute's Advanced Biomedical Computing Center (ABCC) in Frederick, Md., has purchased from SCICOR a broad range of SGI® high-performance computing, visualization, and data storage solutions to help solve some of the most demanding biological research problems, including bioinformatics, proteomics, imaging, and computational biology and chemistry.

ABCC supports National Cancer Institute (NCI) and National Institutes of Health (NIH) research in such areas as deciphering the human genome, understanding structure-function relations of biological molecules, and the development of therapeutics for numerous diseases, particularly AIDS and cancer.

Scientists at NCI, NIH, and extramural biomedical researchers can now match their specific problem needs to the appropriate SGI hardware platforms.

Such a diversity of SGI systems at ABCC allows applications to be configured for the appropriate machine in terms of utility and efficiency.

“NCI's supercomputing center is a world-class bioinformatics resource for molecular biologists, providing computational tools for a complete range of biological research problems, from primary sequence determinate to molecular modeling and gene linkage analysis,” said Frank Meier, president of SCICOR.

“The combination of SGI's high-performance computing, advanced visualization and data storage solutions will prove to be an invaluable and integrated resource for performing a diverse set of very complex research tasks.”

“Together, these SGI solutions represent a dynamic analysis environment designed to tackle some of the most compute-intensive biomedical research problems and to provide the breakthroughs that NCI scientists have been working towards for years.”

The dramatic growth of its databases has forced ABCC to address increasingly complex user queries, which have required additional processor power, memory, and data storage capacity.

In order to address these growing demands, ABCC has purchased an SGI® Altix® 3700 supercomputer, powered by 256 Intel® Itanium® 2 processors and running the open-source Linux® operating system, which will serve as an important scientific computational resource that is part of a growing list of SGI servers at the center.

ABCC researchers depend on the Altix systems' scalability and their ability to handle large memory problems, such as modeling anti-cancer drug interactions with known tumor targets or analyzing genomic/proteomic data.

To increase its data storage capacity, ABCC has purchased a 50TB SGI® InfiniteStorage Total Performance 9700 (TP9700) RAID storage array, the Fibre Channel storage array equipped with 4Gb/second interfaces, to operate with SGI® InfiniteStorage CXFS™ shared filesystem and SGI® InfiniteStorage Data Migration Facility (DMF).

ABCC had already been using CXFS to share data within its Storage Area Network, enhancing workflow and reducing costs by eliminating file duplication and the time it takes to move large files over the network.

Manipulation of larger and larger DNA sequences and sets of DNA sequences is a growing requirement at ABCC.

To bolster its visualization capabilities that are so critical to its data analysis, ABCC will convert an existing 64-processor SGI Altix server into a 64-processor Silicon Graphics Prism™.

With the help of an existing Silicon Graphics Prism visualization system, ABCC recently won a “Best Practices Award for Knowledge Management” from Bio-IT World.

ABCC's Silicon Graphics Prism visualization system accelerated the efficiency and workflow for microscopy scientists, providing efficient analysis of large datasets, and presenting results of several test cases on microscopy samples provided by NCI for evaluation.

On the software visualization front, ABCC uses MineSet™ to perform genome sequence comparisons.

Introduced by SGI in 1999, MineSet is a suite of powerful software tools for Visual Data Mining and Data Visualization.

It distils complex information into accessible and easily understood interactive 3D real-time graphics to help users quickly identify trends and patterns in their data.

Purple Insight has licensed development, support and distribution rights for MineSet from SGI.

ABCC has also purchased an SGI® Reality Center®, an immersive visualization environment ideally suited for cross functional teams like those at NCI and NIH that need to collaborate, enabling project teams to take a multi-disciplinary approach to their biomedical research.

The Reality Center was chosen for its high-performance graphics and stereoscopic visualization capabilities, which will allow a high level of interactivity with very large visual data sets, such as large molecules, and will enhance the speed of the decision-making process between cross-collaborative scientific teams.