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From Humble Bioinformatics Beginnings, Eolas Lands in the Microsoft Antitrust Spotlight


Budding bioinformaticists take note: You never know where today’s development efforts may lead you. In the case of Mike Doyle, founder and CEO of tiny R&D firm Eolas, it’s brought him face-to-face with Microsoft in a patent infringement trial to be held this July.

Eolas, based outside of Chicago, is suing Microsoft for infringement of US patent 5,838,906, which protects Java-like applet technology that Doyle invented in the early 90s to solve a biomedical informatics problem.

The David-versus-Goliath case has brought Eolas a mountain of publicity in the IT press, but has overshadowed a key aspect of Doyle’s original mission: to develop useful informatics tools for biomedical and genomics research. In the case of the patent under dispute, Doyle developed the plug-in-capable web browser technology to enable collaboration among a team of distributed researchers working on the Visible Embryo Project, a massive collection of digitized images depicting the earliest stages of human development. “The Web browser work was a spin-off from the Visible Embryo Project, back around 1993, when I was the director of the University of California San Francisco’s Center for Knowledge Management,” Doyle told BioInform. “It’s kind of like back in the 60s when you had the space program spinning off things that later became ubiquitous, like Tang,” he mused.

After filing the patent, Doyle founded Eolas, an acronym for “Embedded Objects Linked Across Systems,” in 1994.

Since then, the company has stayed close to its life science beginnings. Eolas recently filed a patent on a technology to support what Doyle describes as “spatial genomics.” In a nutshell, the technology builds a 3D rendering of a biological sample using tissue microdissection images, and then maps gene expression data from microarray experiments onto the 3D reconstruction. The technology, called SAGA (Spatial Analysis of Genomic Activity) “is sort of like doing a very large number of microarray analyses where each analysis corresponds to only a small little voxel, or volume element, of tissue,” according to Doyle. “And that then gives you a three-dimensional context for what’s going on in terms of the genome activity.”

Eolas is using pieces of the SAGA technology as well as other tools in its ongoing work with the Visible Embryo Project, which is funded through the National Library of Medicine as part of its Next-Generation Internet Initiative. The fully functional Visible Embryo is expected to come online within three years, Doyle estimated.

Whatever the outcome of the Microsoft patent trial, “I’m always going to be doing informatics projects,” said Doyle. However, the company’s future direction is closely tied to the outcome of the impending suit, in which Eolas is seeking a permanent injunction to force Microsoft to cease the manufacturing, use, and sale of all infringing products, including Microsoft Windows. One option, Doyle said, would be to launch a new company around the web technology if the outcome is favorable. However, if it’s not, he can always go back to the bioinformatics drawing board, which he described as the perfect “testbed” for developing technologies that are generally applicable on a wider scope: “It’s such a complex problem domain, that if you solve major problems in this space, the technologies that provide those solutions just tend to be useful for many, many more simple things,” he said. “The web technology is a perfect example of that. That’s something we developed to solve some problems in the informatics space and suddenly now virtually every person who uses the web sees it.”

— BT


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