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Looking to Build FPGA 'Ecosystem,' Mitrionics Launches Open Source Accelerated Blast, Free SDK

FPGA supercomputing shop Mitrionics is actively courting the bioinformatics market as part of its strategy to build a community of developers and third-party vendors around its field-programmable gate-array technology.   
This week, the company launched Mitrion Blast, an open source implementation of NCBI Blast that runs on the Mitrion Virtual Processor — technology that works alongside an FPGA to allow users to develop new accelerated applications without having to know hardware design, usually a prerequisite for FPGA programming.
In addition, the company released a free version of its software-development kit, called Mitrion SDK Personal Edition, to encourage developers to port their own applications to the platform. 
The two releases form the basis for Mitrionics’ Mitrion-C Open Bio Project, an initiative to create a “development foundation” for FPGA-enabled bioinformatics applications in the short term, and a broader FPGA development “ecosystem” in the longer term, according to Anders Dellson, CEO of Mitrionics.
Mitrionics is targeting several high-performance computing markets for its technology — including the intelligence community, geoscience, and financial services — but Dellson told BioInform that the bioinformatics sector is particularly attractive because its strong open source roots “make it one of the first verticals that can quickly benefit from FPGAs.”
In bioinformatics, Dellson said, “all the software is very accessible, and in most industries that’s not the case.”
As a result, Mitrionics decided to make its own tools openly available. Mitrion SDK PE and Mitrion Blast can be downloaded for free from Mitrionics’ website, and the Mitrion-C Open Bio Project is hosted by SourceForge. All applications developed under the project will be released under an open source license.
“We’ve seen how this market works and we realize we provide the most value by being as open as possible,” Dellson said.  
The goals of the Open Bio Project are two-fold. First, the company hopes to attract end-user customers for Mitrion Blast, which Dellson described as a “turnkey” accelerated implementation of NCBI Blast. Secondly, the company hopes to drive adoption of its platform among academic and commercial software developers interested in tweaking Mitrion Blast or in writing new accelerated applications.
Mitrion expects that this programming ability will give it an advantage in the FPGA-accelerated bioinformatics market, where dedicated systems like TimeLogic’s DeCypher have dominated. Even newer players in the market, like CLC Bio, are marketing appliances that run a predefined set of algorithms.
“The prime goal is to make this technology available for that market without being a black-box canned solution,” Dellson said.
Mitrion Blast currently runs with the Mitrion Virtual Processor on SGI’s RASC (Reconfigurable Application-Specific Computing) RC100 blade, but the company eventually intends to support all standard FPGA-based hardware. So far, Mitrionics has disclosed partnerships with Cray and Nallatech in addition to SGI.

“We’ve seen how this market works and we realize we provide the most value by being as open as possible.”

In benchmarks, the FPGA-enabled Mitrion BlastN ran 20 times faster than a traditional processor. Dellson noted that the company expects to continue improving the application, and expects the speedup to grow “significantly” over the next six months — especially if external developers lend a hand as anticipated.
Future accelerated applications planned under the Open Bio Project include “other Blast flavors,” as well as the Smith-Waterman algorithm and hidden Markov models, Dellson said, though he noted that future development will largely depend on community interest.     
Mitrion SDK PE, meanwhile, is expected to appeal to developers who are curious about the potential performance gains of FPGAs, but reluctant to spend thousands of dollars on hardware just to find out whether their application runs any better on the platform. Unlike the company’s standard SDK, which includes a processor design license, SDK PE allows developers to program and debug their applications and then simulate how they would run on the hardware.
The “key question” among many developers, Dellson said, is “can my application run successfully on an FPGA?” Acknowledging that not all applications run faster on the technology, he said that the free version of the SDK should help lower the barrier to entry for many developers.    
Eventually, Dellson said, Mitrionics hopes to foster a community of academic and commercial application developers as well as a set of “computer vendors and systems integrators that will be able to deliver solutions based on that source code.”

The company will be demonstrating Mitrion Blast with SGI at Supercomputing 2006 next week in Tampa, Fla.

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