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PATENT WATCH: Sep 21, 2001 (rev. 1)


If you’ve got deep pockets, there are several fine software suites you can buy to do your microarray data analysis, said Stephen Sharp of Iobion Informatics. But bench scientists aren’t often in that position. So his company is aiming to fill the gap with a robust database, analysis, and visualization package at a price that isn’t out of reach.

With Genetraffic 1.0, released in August, Iobion has kept the costs down by building on open source software, including the PostgreSQL relational database, the R statistical language, and the Apache Web server. A relatively bare-bones client, implemented using Macromedia Flash accessed via Microsoft Internet Explorer, also helps keep the costs low. “The user gets a fully interactive client, but it’s really running off the server,” Sharp said. The tradeoff, however, “is it limits what you can do as far as complex visualization.”

Genetraffic’s biggest strength, said Sharp, is the use of the relational database, since most other microarray data analysis packages use flat files. “Try handling a million data points in Microsoft Excel. It’s really not the best way to do it,” Sharp said. Iobion has filed two US patent applications on its database schemas and applications.

The focus of Iobion’s product differs enough from other microarray data analysis packages to make it complementary as well as competitive, according to Sharp. “Some sites are exporting saved data out of Genetraffic and doing their visualization using GeneSpring or Spotfire,” he said.

Iobion, although an independent company, is the “brainchild” of Stratagene, the company’s primary investor. Stratagene CEO Joseph Sorge serves as acting head of Iobion as well. Sharp, previously at MSI (now Accelerys) runs marketing and business development for Iobion from La Jolla, Calif.

Iobion’s CSO, Jason Goncalves, is finishing up his graduate work at the University of Toronto, and Iobion is opening a Toronto office where software development will continue. At present the company has eight employees, with plans to hire more as revenues allow.

Terry Gaasterland of Rockefeller University is a key scientific consultant. Many of the ideas embodied in her lab’s TANGO (Transcriptome Analysis of Genomes) software were incorporated into Genetraffic, but none of the code, Sharp said. “Terry’s MAGPIE [Multipurpose Automated Genome Project Investigation Environment] program also has a lot of nice ideas, in terms of bringing in genomic information,” he added, and that will be an area of future development for Iobion.

Also under consideration is porting the software to a larger Unix server to accommodate corporate enterprise solutions and handle microarray data with more than two million spots. An add-on module slated for release later in the year will accommodate single-color microarray experiments along with Genetraffic’s current two-color capabilities.

The price structure for Genetraffic is two-tiered, with academic users getting the software at half price. Commercial customers pay $8,000 for the first user, and $4,000 for subsequent users. The package also requires a dedicated computer running the Linux operating system.

Sharp stressed that Iobion’s philosophy is to get its software into the hands of the individual biologists doing microarray experiments, regardless of the size of their organizations or budgets. So far, Genetraffic has been made available to a dozen early adopters. Only half were beta testers, he added; the others just couldn’t wait for the official release.


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