Mitrionics develops turnkey BLAST/Bioinformatics application for instant FPGA Supercomputing performance acceleration

Los Angeles 30 May 2006Mitrionics Inc., developer of the Mitrion Virtual Processor and software-centric Mitrion-C programming language for FPGA Supercomputing acceleration, has launched a development project for the BLAST bioinformatics application. BLAST is used by scientists and researchers worldwide for similarity searches for genes and proteins and is the main tool for data mining in large databases in molecular biology.


Scheduled for release in Q3 of 2006, the Mitrionics developed and certified BLAST application is designed to run on the Mitrion Virtual Processor operating in Field Programmable Gate Array (FPGA)-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 will provide instant FPGA Supercomputing performance acceleration without requiring any development costs, time, or risks by the customer. Mitrionics will distribute and license the BLAST application to customers of its Mitrion Virtual Processor.

"Our turnkey version of BLAST will enable scientists and researchers in the bioinformatics industry to immediately realize the tremendous benefits of performance acceleration and lower power requirements made possible with the Mitrion Virtual Processor", stated Anders Dellson, CEO of Mitrionics Inc. "We've taken these steps to benefit our potential customers and also to create optimal conditions for the increased growth of FPGA Supercomputing."

Scientists and researchers strive to improve productivity by achieving faster performance in their supercomputing applications and lower power consumption in their systems. By rewriting the computationally-intensive portions of the BLAST application to run on the Mitrion Virtual Processor, Mitrionics expects to achieve a performance increase in the range of 10-100 times over that of traditional processors. The bioinformatics industry utilizes several versions of the BLAST application, each designed for specific and different purposes. Mitrionics chose the open source NCBI BLAST and re-wrote key portions of the application utilizing the Mitrion-C programming language.

With current revenues at around $840 million, the bioinformatics market is forecasted to become more dominant and increase to around $1,82 billion by 2007, and with a CAGR of about 15 percent up until 2010. (Source: Scope Ltd., BCC Inc.) Over the past years, bioinformatics has gained acceptance among a number of markets especially in pharmaceutical, biotechnology, industrial biotechnology and agricultural biotechnology (agbiotech). The bioinformatics industry is one of the largest segments within supercomputing and stands to benefit significantly from FPGA-based application acceleration.

Bioinformatics is the science of recording, annotation, storage, analysis, and searching/retrieval of molecular information such as gene sequences, protein sequences and structures genetic variation, and cell activity. This includes databases of the sequences and structural information as well methods to access, search, visualize and retrieve the information. Bioinformatics concern the creation and maintenance of databases of biological information whereby researchers can both access existing information and submit new entries.

Basic Local Alignment Search Tool (BLAST) is the primary tool for sequence comparisons in bioinformatics and contains several subprogrammes for different computational problems. These subprogrammes all use a heuristic search algorithm designed to speed up computations while retaining sensitivity. The amount of sequence data in public databases has been growing faster than CPU speed, making speed a fundamental problem in bioinformatics data mining.

The Mitrionics Virtual Processor is a software-created abstract machine that resides between the application and the hardware. The fine-grain, massively parallel Mitrion Virtual Processor in the FPGA makes it possible to program a processor instead of designing a circuit. Together with the Mitrion Software Development Kit, they offer a unique solution for developing supercomputing applications for FPGAs on a true software level. 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.

Leslie Versweyveld

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