Edinburgh Biocomputing Systems has found the first customer for its MPSRCH 4 sequence analysis system. The company recently finished installing a full system at the European Bioinformatics Institute in Hinxton, UK.
MPSRCH 4 is the first commercial offering from EBS, a spinoff from the Biocomputing Research Unit of the University of Edinburgh. The company’s founders transferred techniques they developed in the 1980s to implement the Smith-Waterman algorithm on massively parallel supercomputers to off-the-shelf 64-bit machines.
This “microparallelism” behind MPSRCH 4 can run the Smith-Waterman algorithm on a $5,000 Compaq Alpha system just as well as previous versions of MPSRCH could run it on million-dollar MasPar supercomputers, said EBS CEO Shane Sturrock.
“The performance on those machines is every bit as good as it was on the supercomputers in the past,” Sturrock said. “In fact, when you look at the price performance now that we can deliver, the hardware solutions that are out there implementing Smith-Waterman are actually looking quite comparable with what we get in pure software on a general-purpose computing platform.”
In addition to their lower cost compared to parallel supercomputers, the general-purpose machines are capable of running the algorithm along with other bioinformatics applications without a drop in performance, Sturrock said. He added that this gives MPSRCH 4 an advantage over dedicated hardware boxes such as Paracel’s GeneMatcher Plus, which only runs a limited number of applications and can cost over $100,000.
Sturrock said that MPSRCH 4 would take around 15 seconds to perform a search against Swiss-Prot, compared to 10 to 15 minutes for SSearch, a common Smith-Waterman software implementation.
The EBI’s Rodrigo Lopez said that MPSRCH 4 supports the lab’s web-based BLITZ service, which offers scientists a choice of Smith-Waterman implementations. He said the service began 10 years ago at EMBL in Heidelberg using MPSRCH running on a MasPar computer. However, the MasPar was decommissioned and they turned to Compugen Biocellerators as a replacement.
“Now that MPSRCH is back and being received positively by our users there is, in my humble opinion, the knowledge that we are providing a very accurate and fast tool for searching our protein databases,” said Lopez.
The EBI now has MPSRCH 4 running on two Compaq ES40s with four Alpha processors in each. Sturrock said that the EBI server could now run eight separate job queues rather than the two offered by the Biocellerators. In addition, the general-purpose machines can run multiple searches on a single processor.
Many companies would be able to run the software without any further investment in hardware. EBS is in the process of installing a one-month demo system for a company on a cluster of 64 processors that is currently running Blast. “Because MPSRCH 4 can co-exist with Blast on the same pieces of equipment, it’s a great boon to them,” Sturrock said.
The supported software for a basic system starts at $15,000. Sturrock said that EBS has seen “a good degree of interest” from prospective clients.