APPLICATIONS

BLAST, Smith-Waterman, & Hidden Markov Models to Be Accelerated and Contributed to Open Source Community: Mitrionics, Inc., developer of the Mitrion Virtual Processor and software-centric Mitrion-C programming language for FPGA Supercomputing acceleration, announced the Mitrion-C Open Bio Project, where the company will actively participate in developing FPGA Supercomputing applications such as: BLAST, Smith-Waterman, and Hidden Markov Models for the bioinformatics industry. Applications completed under the Mitrion-C Open Bio Project will run on the Mitrion Virtual Processor (including the Mitrion-accelerated version of the NCBI BLAST application) and be contributed as open source applications to the bioinformatics community. Scientists and developers can download the Mitrion-accelerated NCBI BLAST application and the Mitrion Software Development Kit -- Personal Edition at no charge from its Web site and use them to participate in the Mitrion-C Open Bio Project to create new applications or work on refining the BLAST application. The Mitrion-C Open Bio Project is designed to provide a development foundation for a wide range of FPGA Supercomputing bioinformatics applications and also to initiate an open source developer's community to promote future FPGA-accelerated applications for the Mitrion Virtual Processor. Currently, the Mitrion-accelerated BLAST program is being tested for use with the Mitrion Virtual Processor on the SGI RASC RC100 computation blade for the SGI Altix family servers. Mitrionics intends to support all FPGA-based computer systems from major vendors that are capable of running supercomputing applications. "Bioinformatics is one of the most exciting fields in the entire high performance computing market, with many terabytes of sequence data being generated per day," said Michael Brown, sciences segment manager for SGI. "Mitrionics' Open Bio Project, including the development of open source FPGA accelerated versions of BLASTN and other key algorithms, will give bioscientists more powerful tools with which to analyze the data deluge. The rapid analysis of these massive amounts of data will result in a better scientific understanding of fundamental biological processes and genetic factors that lead to disease." The Mitrion Open Bio Project The Mitrion Bio Project is a new program from Mitrionics where the company will actively participate in the Development of FPGA accelerated key bioinformatics applications such as various BLAST versions, Smith-Waterman, and Hidden Markov Models. BLAST with an accelerated BLASTN program is the first FPGA Supercomputing application developed under this project. As they are developed, the Mitrion-accelerated applications under the Mitrion-C Open Bio Project will be available to Mitrionics and SGI customers at no charge and also will be contributed to the bioinformatics community as open source through the web site: sourceforge.net. The open source Mitrion port of NCBI BLAST can be modified and refined by scientists and developers by using the Mitrion Software Development Kit (SDK) Personal Edition -- also available at no charge from www.mitrionics.com. A commercial version of the Mitrion SDK is available separately and customers have numerous support and training options available from Mitrionics as well. The Mitrion-Accelerated BLAST Application Mitrionics chose to use the NCBI BLAST source code and ported key computationally intensive portions of the BLASTN program for nucleotide searches utilizing the Mitrion-C programming language. The result is an accelerated NCBI BLAST with identical user interface, file formats, and output options, making it easy for anyone familiar with NCBI BLAST to get started immediately. The first version of Mitrion-Accelerated BLAST BLASTN searches shows a 20x faster total run time, wall clock time, per chip compared to a traditional processor. And the performance of the accelerated parts of the search, operating on the FPGA, is 35x faster. Mitrion BLAST is designed to run on the Mitrion Virtual Processor operating in FPGA (Field Programmable Gate Array)-based computer systems including the SGI RASC RC100 computation blade in SGI Altix family servers, built with dual Xilinx Virtex-4 FPGAs. The turnkey BLAST application provides instant FPGA Supercomputing performance acceleration without requiring any development costs, time, or risks by the customer.