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Sequence Bioinformatics Puts a Friendly Face on Open Source


Just five people strong, Sequence Bioinformatics knows it has some formidable opposition from larger bioinformatics vendors, but the Montreal-based company is counting on two things to guide it through the competitive terrain. The first is a one-on-one, personalized approach to winning — and keeping — clients in its very targeted market of small biotechs and academic users. The second is a low-cost bioinformatics environment built upon readily available open source standbys.

Shibl Mourad is well-practiced at answering the obvious question: How does the year-old company convince researchers to pay for tools they can easily download for free off the web? “What we’re doing could be done in house, but we figure we’re reducing the time. We’re not improving on the application itself, but we are providing an environment where you can track what’s happening, it provides security for you, it provides support, so if something goes wrong we can help you, and it provides a layer of unification — all these things are unified on one interface.”

The company’s flagship software package, called OpenGene, includes the GenBank, Ensembl, and Swiss-Prot databases, along with over 250 applications such as Primer3, TACG, ClustalW, several versions of Blast, and all the Emboss tools. Licenses for the package, which places all these tools behind a single, intuitive interface, start at Can$5,000 (US$ 3,200) per seat for a shrink-wrapped CD and can range as high as Can$25,000 for more customized installations.

This Red Hat-style model for commercializing open source bioinformatics software is beginning to gain ground in the sector, but few companies have been at it long enough to prove its success. South Africa’s Electric Genetics is setting out on a similar path with an upcoming suite of open source tools, while Iobion has carved out a comfy niche in the academic market for its GeneTraffic gene expression analysis platform, which uses some open source components.

Mourad said Sequence opted for its open source building blocks for several reasons, including the lower price point and the flexibility it offers end-users who often appreciate the ability to modify certain aspects of their research software. But the biggest factor, he said, “is the quality of the open source software that’s out there. There’s so much science that’s embedded in that software, that if any single company wants to go and rebuild it themselves, it’s possible, but it requires a lot of funding and then you’d end up with the same problem that the industry faced in the last three years.”

Sequence is not venture backed, preferring to run its business the old fashioned way: It relies solely on cash flow from its current customer base to keep going. The company is currently engaged in several projects with researchers at McGill University and counts local biotech firm Galileo Genomics among its key customers. Several other clients are in the pipeline, Mourad said. With a small but steady revenue stream balanced against its low overhead, the company is aiming for profitability in six to 12 months.

Right now, Sequence is alpha testing the newest component of its OpenGene platform, a bioinformatics programming language called Seq that biologists with little or no programming experience can use to automate their bioinformatics pipeline. The syntax for the scripting language is “very simple,” Mourad said, permitting users to link several related tasks with a simple command. Eventually, the company plans to build a visual interface that can generate scripts on top of the scripting language, which should be available in around two months.

Assessing the recent history of the sector in which it hopes to become a success, Mourad said, “The lesson that we’ve learned from what’s happened to the whole industry is that it’s very hard at this stage to build a product that will serve everybody’s needs. …The mistake is to say, ‘Let’s build it and they will come.’ It’s more, ‘Let’s go and build it with the clients.’ It’s a high client interaction and service approach.”

— BT

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