Mitrionics, which develops virtual processor and programming software for Field Programmable Gate Array (FPGA) supercomputing acceleration, announced the Mitrion-C Open Bio Project.

The project is an effort by Mitrionics to get its products better known within the life sciences community. At the same time, programs developed as part of the project will be available as open source tools that any researcher can use.

Currently, the company offers a virtual processor and C-like programming language for FPGAs. Essentially, the software permits researchers to tap the processing power of FPGAs by making C-like calls within an application. This contrasts to the traditional method of FPGA programming that relies on writing instructions in the less commonly known Hardware Description Language (HDL). (For a more detailed description about how the Mitrionics tools work, go here.)

With the Open Bio Project, Mitrionics will help make bioinformatics applications such as BLAST, Smith-Waterman, and Hidden Markov Models run faster using FPGAs. Applications developed through the project will run on the Mitrion Virtual Processor and will be contributed as open source applications for researchers in the bioinformatics community.

Mitrionics will develop some programs itself and it will rely on researchers who want to develop Mitrion-C bioinformatics applications on their own. To participate in the project, researchers can download the Mitrion Software Development Kit – Personal Edition (and a copy of a Mitrion-accelerated version of NCBI BLAST) at no charge from the Mitrionics website.

Currently, an accelerated BLAST program is being tested for use with the Mitrion Virtual Processor on the FPGA-based SGI RASC RC100 computation blade. The RASC blade works in SGI’s Altix line of servers. Mitrionics says it intends to support all FPGA-based computer systems from major vendors that are capable of running supercomputing applications.

Email Salvatore Salamone.

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