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Following Roll-out of High-Speed Blast Service, MPT Adds Gromacs, Readies Cluster Version


Massively Parallel Technologies, a high-performance computing firm specializing in software-enabled parallel processing, is getting ready to launch its second life science product in April — a web-based service that will speed molecular dynamics algorithms like Gromacs.

In December, the company officially released Blast VPC, a high-speed version of NCBI Blast that runs on its in-house 255-processor Dell cluster and is accessible via a web-based interface. MPT's implementation of Blast, called Blast PbH (Powered by HOWARD), runs on the company's HOWARD middleware, which was developed to speed communication between processors. MPT claims that its software-based approach can reduce the number of cross-communication steps in parallel processing to improve scalability without high-speed connectivity.

MPT developed the technology over six years with funding from the Defense Advanced Research Projects Agency, and has taken a cautious approach to the marketplace as well. The company began an "extensive" beta-testing program for Blast VPC last summer [BioInform 07-11-05], and didn't release the full commercial version of the service until December.

MPT claims that its software-based approach can reduce the number of cross-communication steps in parallel processing to improve scalability without high-speed connectivity.

Kevin Howard, MPT's president and CEO, told BioInform that around 60 to 65 organizations participated in the beta program.

Howard said that the company is now preparing to launch a version of the on-demand system that will run Gromacs and two other molecular dynamics algorithms that he declined to disclose.

In addition, MPT is readying a version of Blast PbH that customers will be able to install on their own clusters. The tentative launch date for that product is mid-year, Howard said. The company's marketing team is currently determining the price for the cluster version of the technology, "and we are very close to being able to do that," he said.

One of MPT's "concerns" about selling an off-the-shelf version of its technology, Howard said, was "protecting our IP, but being able to deploy out into the world, and we finally found a way to do that. So it should be here soon."

The commercial version of Blast VPC includes a Matlab plug-in that allows users to run Blast queries on MPT's cluster as part of their Matlab workflows. A similar feature for Python scripts will be available in around a month, Howard said.

Howard said that the company has also added a status bar to the interface so that users know how quickly their job is being processed, and will soon add another feature that will calculate the cost difference for different query sizes at different speeds.

"The amount of compute effort is strongly related to the query length, coupled with the database size," Howard said. "So we've been able to profile all of that and come up with a strong curve so we can calculate that on the fly. Given a query or group of queries and the databases they're using, we know exactly how much compute effort that is."

The company does not provide pricing information for the service, but Howard told BioInform last year that it would run a typical lab around $100 per month.

Howard declined to provide much detail on the company's customers so far, but he did note that one customer — the Barbara Davis Center for Diabetes Research at the University of Colorado Health Science Center — has used MPT's technology to enhance its GeneSpeed database of PFAM protein domains in Unigene.

According to the GeneSpeed website, the MPT system "enabled us to utilize the complete set of PFAM domains, currently approaching 8,000 individual domains. Due to the efficiency of MPT's HOWARD technology, we were also able to expand our coverage beyond that of M. musculus to also include H. sapiens, C. elegans, and D. melanogaster."

MPT is mainly targeting academic groups that can't afford departmental clusters, Howard said. The firm had "low expectations" for the bioinformatics market, he noted, "but I would say that the community has really reached out and embraced a lot of what we're doing."

— Bernadette Toner ([email protected])

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