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Paracel Reinvents Itself, Modifies Its Product Lineup for Mass Market Bioinformatics


If you ask Joe Borkowski, Paracel’s director of product development, about the company’s traditional customer base, he sums it up in three simple words: “hardcore bioinformatics types.” But although the ten-year old company claims an enviable following among researchers working at the bleeding edge of the field, Borkowski said the Celera subsidiary is expanding its reach beyond the accelerated bioinformatics hardware that made its name.

“The bioinformatics market has been evolving for a period of time now. It’s moving more towards average biologists making full use of this technology,” Borkowski said. “There are [perhaps] hundreds of thousands of biological researchers worldwide. And as the genomes become a routine part of their research, they’re going to be making use of computational tools a lot more routinely.”

Armed with this vision for the future of the bioinformatics market, the company has taken a number of steps over the past year to cultivate a broader market presence. Jason Molle, a Celera VP who served as general manager of the company’s online business, moved to Pasadena to head up operations at Paracel in September. The company is currently expanding its sales team as well as its R&D staff, Borkowski said, and has launched an all-out marketing blitz around the recent release of its expanded line of GeneMatcher and BlastMachine bioinformatics hardware systems.

This week, Paracel will expand its product line even further with the launch of a new desktop software package called PathWorks, a pathway drawing program that is geared specifically toward the bench biologist. PathWorks will be marketed along the same lines as Adobe Acrobat, Borkowski said: A PathWorks reader will be available for free so that anyone can view images created with the package. The software provides a graphical system that researchers can use to store, organize, and share DNA and protein sequence information, Blast results, microarray data, or even PDFs related to biological pathways, according to Borkowski. In addition, he said, “Anything that you draw could be output as a print-quality tiff [file] for publications.”

Make New Friends, but Keep the Old

Borkowski noted that despite its plans to expand its user base, Paracel doesn’t intend to abandon its loyal base of bioinformatics heavy-hitters. Of the three new GeneMatcher models, for example, only two — GeneMatcher2 CD (Chip Design) and GeneMatcher2 GA (Gene Annotation) — are geared toward laboratory biologists. The third, GeneMatcher2 Bfx, is an updated version of the company’s traditional GeneMatcher for bioinformatics, Borkowski said.

The three models all rely on the same custom ASIC and Linux cluster shared by the original GeneMatcher, but are optimized to run different types of algorithms. The CD model is tailored for Smith-Waterman analysis, which Borkowski said is in high demand at oligo and chip-design companies. The GA model, meanwhile, is optimized for hidden Markov models and gene prediction algorithms, while Bfx “is designed for all-around bioinformatics computing tasks,” he said.

In another sign that Paracel is comporting itself more like a mass-market software provider, the company is unabashedly open about its pricing: GeneMatcher2 starts at $79,000 for the CD model, $89,000 for GA, and $99,000 for Bfx, Borkowski said. BlastMachine, a turnkey Linux cluster that comes with the parallelized Paracel Blast installed and ready to run, starts at $34,000 for an 8-CPU configuration. And in a bid to attract as broad a user base as possible for its newest software tool, the company has made PathWorks available for $495 for commercial users and $295 for academic users.

Borkowski said the company is hoping to move away from the standard bioinformatics sales model, in which “people come out and consult with you for a long period of time before you finally get your infrastructure in place.” The company has found “that there’s a tremendous market pull for something where they can just call us up, we send them something, and it’s like setting up a centrifuge: You plug it in, turn it on, and you’re ready to go.”

Of course, for those still looking to push the envelope of bioinformatics, Paracel is more than happy to oblige. The company has a 221,000-processor in-house system dubbed “GeneMatcher Ultra” that Borkowski said the company could easily build for interested users.

With Celera’s blessing to run itself as a standalone software company, Paracel has a number of advantages over its competitors in the quickly evolving bioinformatics sector. It can operate in lean-and-agile startup mode to keep pace with the market’s demands, yet it has the formidable financial stability of the Applera behemoth behind it. Of course, Paracel’s bet that the market is ready for mainstream bioinformatics software could be viewed as either ahead of the curve or as premature, but Borkowski harbors no doubts about the timing of the move. “A lot of people don’t realize that Paracel has been around for over 10 years now, so we have a lot more experience in selling to people than a lot of the newer companies,” he said. “We’re just responding to the way that our customers want to buy things.”

Borkowski also dismissed the possibility that the company’s history of catering to the hardcore bioinformatics crowd will limit its success in the nascent mainstream market: “What we’re finding is that a lot of the bench biologists don’t really have a clear idea of how bioinformatics can help their research, so to the hundreds of thousands of biomedical researchers worldwide, we are a new company.”

— BT


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