Breakthrough BLAST-n Solution From SGI and Mitrionics Speeds Query Performance by Up to 16 Times

BOSTON, April 30 /PRNewswire-FirstCall/ -- BIO-IT WORLD -- SGI (Nasdaq: SGIC) and Mitrionics(TM), Inc., today unveiled the world's first turnkey bioinformatics appliance based on Field Programmable Gate Array (FPGA) technology and open source software. This solution is designed to break through query logjams that result from next-generation sequencing instruments and multiple genome studies using NCBI BLAST-n.

BOSTON, April 30 /PRNewswire-FirstCall/ — BIO-IT WORLD — SGI (Nasdaq: SGIC) and Mitrionics(TM), Inc., today unveiled the world's first turnkey bioinformatics appliance based on Field Programmable Gate Array (FPGA) technology and open source software. This solution is designed to break through query logjams that result from next-generation sequencing instruments and multiple genome studies using NCBI BLAST-n.

The new SGI(R) RASC(TM) Appliance for Bioinformatics – Featuring Mitrion(TM)-Accelerated BLAST-n achieves faster query times by combining SGI RASC (Reconfigurable Application-Specific Computing) technology, an accelerated version of BLAST-n software developed by Mitrionics, and the acclaimed SGI(R) Altix(R) server platform.

Leveraging powerful and energy-efficient FPGA technology and the Mitrion Virtual processor, the new appliance completes complex BLAST-n queries up to 16 times faster than a standard server based on Intel(R) Itanium(R) 2 processors, and 10 times faster than a server based on AMD Opteron(TM) processors(1). BLAST-n (Basic Local Alignment Search Tool for nucleotides) is the world's most widely used bioinformatics application.

SGI is demonstrating capabilities of the new solution this week in Booth 405 at the Bio-IT World Conference and Expo through May 2 at the World Trade Center in Boston.

Unlike other FPGA offerings that require extensive end-user optimization, the SGI RASC Appliance for Bioinformatics is a pre-configured solution that dramatically simplifies the deployment of a platform for running nucleotide sequence queries using BLAST-n. The industrial-scale appliance addresses productivity problems in a range of bioinformatics environments – from those that serve thousands of users running BLAST queries against a single database, to others with smaller numbers of users running complex queries against databases that are hundreds of Gigabytes in size.

Using Mitrionics software and FPGA technology specifically optimized for BLAST-n, the SGI RASC Appliance for BioInformatics offloads workloads from typical Linux clusters. The SGI RASC appliance further increases throughput by executing multiple BLAST-n queries in parallel on multiple FPGAs.

"The accelerating pace of genomics research means scientists are running more and larger nucleotide sequence queries," said Michael Brown, sciences segment manager, SGI. "As traditional servers fail to keep up, SGI and Mitrionics have developed a turnkey BLAST appliance that transforms long- running batch jobs into interactive scientific investigation. We believe that the combination of higher performance, simplified system management, and as little as one-tenth the power consumption per BLAST-n query will drive wide adoption throughout the scientific community."

Available to customers starting at $39,950 US, the new appliance is far more cost- and energy- efficient than traditional rack server deployments, because it relies on FPGA technology for the bulk of BLAST-n query processing. In fact, the SGI RASC Appliance for BLAST consumes up to 90 percent less power than an Opteron- or Xeon-based rack system. This equates to lower cost of ownership and longer asset life.

BLAST Optimization via the Mitrion Virtual Processor

The fine-grained, massively parallel Mitrion Virtual Processor is the core of the Mitrion Platform and a vital component of the new SGI RASC Appliance for BLAST. It runs software written in the Mitrion-C parallel programming language in FPGAs and completely eliminates the need for the programmer to master hardware design. The Mitrion Virtual Processor has a unique architecture that lets it be adapted to each program it is running in order to maximize performance. This dramatically reduces the total development costs for FPGA-based software acceleration, and more importantly, enables the whole supercomputing industry to benefit from FPGA application acceleration.

"This is an exciting time for Mitrionics and SGI as we demonstrate how the Mitrion Virtual Processor and SGI RASC platform are able to accelerate computationally intensive portions of the code by up to 100x, resulting in an application speed-up of up to 16x," said Anders Dellson, CEO of Mitrionics, Inc. "We look forward to our continued strong collaboration with SGI in delivering BLASTn and additional turnkey bioinformatics applications. As we work together, we plan to accelerate applications in other industries, such as financial, imaging, seismology, and encryption – all of which can benefit from similarly dramatic productivity gains."

The SGI RASC Appliance for BLAST is available today from SGI in two pre- configured blade packages: a single-blade version suitable for most environments serving internal BLAST users, and a dual-blade configuration for environments that serve hundreds or thousands of BLAST users. The appliance features an SGI Altix 450 server installed in a single SGI(R) Altix(R) 450 IRU with 8GB to 72GB of memory. (Users can also upgrade the appliance to a general-purpose server powered by up to 68 processor cores and more than 400GB of memory.) The appliance features one or two SGI(R) RASC(TM) RC100 blades powered by dual Xilinx Virtex(TM) 4 LX200 FPGAs with Mitrion(TM) Virtual Processors. The solution also includes a single SAS disk, DVD drive, Novell SUSE Linux Enterprise Server 10, and SGI's RASC library, RASClib 2.1

For users already outfitted with SGI(R) Altix(R) 450 or SGI(R) Alti(R)x 4700 systems, and who have an available blade slot in their system, SGI also is offering an SGI RASC Appliance for BLAST-n Upgrade. With customer pricing starting at $29,950 US, the upgrade package includes an SGI RASC blade, Mitrion Virtual Processor and bioinformatics software, and RASClib 2.1.

About Mitrionics

Founded in 2001, Mitrionics, Inc. is the technology leader in the exciting new field of FPGA Supercomputing which provides higher processing power and lower energy consumption than clusters of computer systems. The company's Mitrion Virtual Processor and Mitrion Software Development Kit provide cost effective FPGA Supercomputing power to organizations for their most critical applications. The Mitrion Platform is unique from any other FPGA programming solution, because it eliminates the need for circuit design skills, thus making FPGA Supercomputing performance accessible to an entire new market of scientists and developers. Mitrionics has key industry relationships with Cray, Nallatech, and Silicon Graphics. For more information, visit the company Web site at www.mitrionics.com, or call 310-558-9495, or email: info@mitrionics.com.

SGI | Innovation for Results(TM)

SGI (Nasdaq: SGIC) is a leader in high-performance computing. SGI delivers a complete range of high-performance server and storage solutions along with industry-leading professional services and support that enable its customers to overcome the challenges of complex data-intensive workflows and accelerate breakthrough discoveries, innovation and information transformation. SGI solutions help customers solve their computing challenges whether it's enhancing the quality of life through drug research, designing and manufacturing safer and more efficient cars and airplanes, studying global climate, providing technologies for homeland security and defense, or helping enterprises manage large data. With offices worldwide, the company is headquartered in Sunnyvale, Calif., and can be found on the Web at www.sgi.com.

SGI, Altix, the SGI cube and the SGI logo are registered trademarks, and RASC and NUMAflex are trademarks of SGI in the United States and/or other countries worldwide. Linux is a registered trademark of Linus Torvalds in several countries. Intel, Xeon and Itanium are trademarks or registered trademarks of Intel Corporation or its subsidiaries in the United States and other countries. AMD Opteron is a trademark of Advanced Micro Devices, Inc. Novell is a registered trademark, and SUSE is a trademark of Novell, Inc. in the United States and other countries. All other trademarks mentioned herein are the property of their respective owners

This news release contains forward-looking statements regarding SGI technologies and third-party technologies that are subject to risks and uncertainties. These risks and uncertainties could cause actual results to differ materially from those described in such statements. The reader is cautioned not to rely unduly on these forward-looking statements, which are not a guarantee of future or current performance. Such risks and uncertainties include long-term program commitments, the performance of third parties, the sustained performance of current and future products, financing risks, the ability to integrate and support a complex technology solution involving multiple providers and users, and other risks detailed from time to time in the company's most recent SEC reports, including its reports on Form 10-K and Form 10-Q.

Editor's note

(1) In internal tests, dual-blade SGI RASC Appliance for Bioinformatics – Featuring Mitrion-Accelerated BLAST-n completed complex BLASTn queries faster than several standard servers, all running Linux.

— 16 times faster than a server powered by a single Itanium 2 processor core at 1.4GHz, with 8GB of memory per execution thread. — 10 times faster than a four-core AMD Opteron server at 2.8GHz with 8GB of memory per execution thread. — 4 times faster than a four-core Intel Xeon server at 3GHz with 8GB of memory per execution thread.


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