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News

SGI and Mitrionics helps Chinese National Human Genome Center accelerate blood fluke research

SGI : 24 July, 2007  (New Product)
Researchers at the China National Human Genome Center (CHGC) in Shanghai are using SGI compute technology running a Mitrion-accelerated bioinformatics application to improve early disease diagnosis and discover new drugs to effectively treat disease caused by the Schistosoma japonicum parasite or blood fluke.
The blood fluke is one of the major infectious parasites to a wide range of hosts including primates, rodents, carnivores, and humans.

Blood fluke has evolved for thousands of years. Currently, existing drugs target disease caused by blood fluke found in South America. In the past few years the Schistosoma japonicum has been re-found in some lakes and rivers in the east and south China area. To study the parasite evolution, improve disease diagnosis in the very early stages, and develop more effective drugs to treat disease, Chinese bioscientists decided to discover the secrets of the blood fluke genome.

CHGC implemented the first phase of blood fluke genomics sequencing using the new SGI RASC Appliance and SGI InfiniteStorage 350 storage solution, installed in February 2007. CHGC bioscientists achieved faster query times - up to 10 times faster - with the combination of SGI RASC (Reconfigurable Application-Specific Computing) technology, an accelerated version of BLAST-n software developed by Mitrionics, and the acclaimed SGI Altix server platform.

SGI InfiniteStorage 350 ensures that the data generated by the CHGC research is both protected and available to maximise analysis. A cost effective solution, the initial purchase of 8TB allows plenty of capacity for future expansion as the need arises. With integrated controllers, the density of the SGI InfiniteStorage 350 contributes to the mobility of Bioinformatics solution.

'Shortened time to results is critical to our success. With the blood fluke genome research, we have 300 million base pairs to study, and have 6-7 times more calculations in each step. The large shared memory and ease-of-use with the SGI RASC Appliance for BioInformatics enables our scientists to focus on achieving results faster and not spending valuable time on computer science,' said Dr Zhou, deputy director of bioinformatics department, CHGC.

The SGI RASC Appliance for Bioinformatics is a pre-configured solution that dramatically simplifies 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 an accelerated version of NCBI BLAST-n, the SGI RASC Appliance for BioInformatics offloads genome sequencing workloads that typically run on Linux clusters. The Mitrion accelerated BLAST-n running on the SGI RASC Appliance for BioInformatics runs large queries up to 15 times faster than a single-core r nodes powered by AMD Opteron 8820 SE processors, and production runs of thousands of smaller queries by up to 60 times faster.

The SGI RASC Appliance for BioInformatics further increases throughput by executing multiple BLAST-n queries in parallel on multiple FPGAs. With up to 16 FPGAs in a single SGI RASC Appliance for BioInformatics, customers can achieve throughput equal to between 240 and 960 AMD Opteron cores without the solution complexity and system management overhead.

'The accelerating pace of genomics research means scientists are running more and larger sequence queries. The turnkey solution SGI and Mitrionics have developed makes the genomics sequencing faster and easier, and the power consumption per BLAST-n query is as little as one-tenth,' said Alex Lee, country manager of SGI Greater China Region. 'CHGC's successful implementation of this solution is tantamount to their leadership position in China and the world.'

'This turnkey accelerated BLAST solution from Mitrionics and SGI represents a significant HPC industry milestone by establishing new performance levels for processing power and reduced power consumption,' stated Anders Dellson, CEO of Mitrionics. 'Bioinformatics and genomics are among the areas in the life sciences industry where several of the most widely-used applications are ideally suited for FPGA acceleration. We're extremely excited to be working with both SGI and CHGC as they are leading their respective industries in delivering and utilizing accelerated computing technologies.'

The CHGC also recognised that the research into the genome of the blood fluke would require them to run much more than BLAST-n. The scalable, general purpose nature of the SGI RASC Appliance for BioInformatics supported that capability by enabling the system to be upgraded to a total of 48-cores of Intel Itanium 2 processors, 128GB of shared memory and an InfiniteStorage 350 with 8TB of disk storage. The system's ease-of-use and portability of open source software running in the shared memory environment have proved crucial for the second phase of their research. The SGI RASC Appliance for BioInformatics is running Novell's SUSE Linux Enterprise Server 10. A CHGC research paper is scheduled to be published in July 2007.

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