Chinese National Human Genome Center at Shanghai leverages accelerated bioinformatics solution from SGI and Mitrionics for faster time to insight

Shanghai 24 July 2007To help extinguish effects of the ancient parasite, the Schistosoma japonicum or blood fluke - one of the major infectious parasites to a wide range of hosts including primates, rodents, carnivores, and humans - Chinese Scientists 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 this parasite.


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. CHGC bioscientists achieved faster query times - up to 10 times faster - with the combination of SGI Reconfigurable Application-Specific Computing (RASC) 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 maximize 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 the 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", stated Dr. Zhou, Deputy Director of the 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", stated 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 Inc. "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 recognized 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.

The Chinese National Human Genome Center at Shanghai, a new research unit organized by the institutes from the related fields in Shanghai for fulfilling the national scientific projects of human genome research and its application and development, was established on October 29th,1998 on the basis of its former Shanghai Human Genome Center founded in Shanghai Pudong Zhang-Jiang High-tech Park on March 4th, 1998.

The founding members of CHGC include the National Center for Biotechnology Development affiliated to the Chinese Ministry of Science and Technology, the Shanghai New Drug Research and Development Center, Pudong Technical Venture Capital Company, the Shanghai Branch of the Chinese Academy of Sciences, Fudan University, Ruijin Hospital affiliated to the Shanghai Second Medical University, the Shanghai Institute of Cancer Research, Shanghai Medical University, Shanghai Second Military Medical University, and the Shanghai Zhang-jiang Hi-Tech Park Development Company.

Mitrionics AB, developer of the Mitrion Software Acceleration Platform and the Mitrion Virtual Processor, together with SGI, developer of the SGI RASC RC100 and SGI BLAST accelerator, have been demonstrating the latest open source, FPGA-accelerated bioinformatics applications at the 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB) held in July 2007 in Vienna, Austria. Located in the SGI booth, Mitrionics has been featuring its Mitrion Development Platform, the Mitrion Virtual Processor, and the recently released Mitrion-accelerated NCBI BLAST-n bioinformatics application. Leveraging powerful and energy-efficient FPGAs from Xilinx, the ultra-fast memory subsystem in SGI Altix servers and the Mitrion Virtual Processor, the Mitrion Accelerated NCBI BLAST is able to run 60 times faster in sustained operation on one FPGA as compared to running on one core of a 2.8GHz Dual Core AMD Opteron Processor 8220 SE.

Additionally, Mitrionics' Senior Software Engineer Henrik Abelsson, the company's lead developer of the Mitrion-accelerated BLAST application, has spoken at the Bioinformatics Open Source Conference (BOSC 2007) taking place as one of several Special Interest Group (SIG) meetings occurring in conjunction with ISMB. Mr. Abelsson spoke about the open source Mitrion-accelerated BLAST application and the Mitrion-C Open Bio Project, where open source applications are developed and contributed to the bioinformatics community.

"Mitrionics' open source accelerated BLAST application running on SGI's turnkey RASC system is currently in use at multiple customer sites and gaining significant interest and traction in the bioinformatics industry", stated Anders Dellson. "Our combined solution sets a new industry benchmark for pure processing power and very low electrical consumption that can immediately benefit genomics researchers at institutions and pharmaceutical companies worldwide."

"Speed-ups of up to 60x with Mitrion accelerated BLAST-n running on the SGI RASC Appliance for Bioinformatics show the enormous benefits that can be obtained through the use of modern software development environments with FPGA technology", stated Michael Brown, sciences segment manager, SGI. "These results were achieved by changing only 0,2 percent of the original BLAST-n source code, which shows how easily this breakthrough technology can be applied to new compute intensive applications. The use of FPGAs has the potential for revolutionizing the entire bioinformatics work flow."

The fine-grained, massively parallel Mitrion Virtual Processor (MVP) is the core of the Mitrion Platform and a vital component of the new accelerated Mitrion-BLAST. The MVP runs software written in the software-centric, Mitrion-C parallel programming language for 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 programme 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.

Founded in 2001, Mitrionics Inc. is a technology expert 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 organisations 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. More company news can be found in the VMW July 2006 article Mitrionics develops turnkey BLAST/Bioinformatics application for instant FPGA Supercomputing performance acceleration.

Leslie Versweyveld

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