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Southwest Parallel Shifts From Software Development Into Consulting Services


BELLEVUE, Wash.--Following two years of product development, Southwest Parallel Software, a bioinformatics company here, is adding consulting to its repertoire.

Southwest's initial mission was to produce high-performance application software on general-purpose computer systems, according to Daniel Joy, president. But after building a client list that includes Lawrence Livermore National Laboratory, Incyte Pharmaceuticals, Schering-Plough, Zeneca, and the Genetics Institute division of American Home Products, consulting, he said, is "the next logical step." Joy said he hopes now to work with pharmaceutical and biotech companies needing improved software performance.

Joy launched the company in Dallas, Texas, in January 1997, but moved to this town nearby Seattle a year later. "Now we're Southwest in the Northwest," he remarked. Joy has established relationships with hardware companies and distributors including Compaq/DEC, Silicon Graphics, and Sun. After securing a license to distribute University of Washington researcher Phil Green's application software Phrap, SWAT, and Cross_Match, Joy began coordinating on the development and testing of parallel versions with Gary Montry, whom he met in Dallas two years ago.

The mantra of the partners, who both hold computing degrees, is speedy output. "Our company is unique because we concentrate on making software run fast. We do not develop algorithms, but we do optimize existing algorithms," Joy said. This includes improving the flow of data through the algorithm, parallel porting, and better memory management.

Montry, vice-president, said speed comes from parallel systems. Last year Joy reported that Southwest's systems ran at three times the pace per CPU of all Smith-Waterman algorithms on general-purpose computer systems. "Our product gets large jobs completed more quickly. We allow researchers to get answers a lot faster," said Montry.

While Southwest competes with the serial version of Phrap distributed by the University of Washington, Joy said he believes his company has found a niche in the market. "We're the only company doing a parallel portion of Phrap," which took two years to develop, he said. "It was an incredibly difficult project," he added, crediting Montry with its success.

Client expansion has been challenging with a staff of two , Joy admitted, but added, "as a small company we can have a big presence with a web page." Southwest's address online is

Joy's short-term goal is to identify pharmaceutical and biotech companies that need better software performance. "Optimizing and parallel porting of applications can be challenging work," he said. "It makes good sense to use experienced software engineers who can do the work well and on time."

--Amy E. Nevala

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