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Affymetrix Set to Host Internet Bake-off Comparison For Array Software Developers

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Affymetrix plans to host the bioinformatics community’s first “bake-off” style software comparison via a series of webcast presentations scheduled for Feb. 9-19.

Such comparisons are common in the consumer applications market, but they are rare in the scientific computing world. Affymetrix, however, saw an opportunity within the growing microarray analysis sector to “both help our customers find an appropriate tool for their needs, and help the software vendors get some exposure to our customers,” said Scott Jokerst, senior product manager for data management products and head of Affy’s external developers’ program.

The event is an outgrowth of the company’s ongoing effort to encourage software developers to write tools that analyze data produced on the Affymetrix platform, Jokerst said. “We now have several commercial software providers who are in one stage or another of building in integration into the Affy system,” he said. So, late last year, the company invited a number of them to analyze [a] data set, “and told them to show off the best parts of their tools.”

Each company pre-recorded a 30-45 minute presentation based on its analysis, and these sessions will be broadcast one per day over a two-week period. A live Q&A session between viewers and vendors will follow each presentation.

Software firms that will participate in the webcast include: Spotfire, VizX, Silicon Genetics, Infor-sense, Iobion, BioDiscovery, Insightful, and Strand Genomics. They will each analyze data from a time-course experiment performed at the Fred Hutchinson Cancer Research Center to study the progression of granulocyte differentiation following retinoic acid simulation in a model cancer cell line.

But unlike software benchmarks that occur in the consumer market, Affymetrix isn’t planning to declare a victor among the eight participants. Due to the inherent variability of microarray analysis, which is still as much of an art as it is a science, “they may come up with slightly different gene lists and that type of thing,” Jokerst said. “Actually, I think that’s going to be one of the interesting parts to the webinar, seeing what things do some of the vendors uncover that others don’t, and what are some of the common themes that vendors uncover.”

— Bernadette Toner, editor, BioInform

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