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Affy, Bioinformatics Companies Seek to Profit From New GeneChip-Compatible Program

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BOSTON —Affymetrix this week launched a program to identify informatics packages that can be integrated with the GeneChip platform and named 19 software providers whose products will now bear the mark "GeneChip-compatible."

The new GeneChip-compatible applications program is an extension of the Affymetrix Developers Network, which the company described in a statement as "a forum through which Affymetrix actively supports its ADN participants and customers." With the new program, designated software providers can market their products to Affymetrix users, as well as take advantage of co-marketing opportunities with the microarray manufacturer.

"This recognition will be a reassurance to all our existing and potential customers," S. Sowmyanarayan, manager of business and development and alliances at Strand Life Sciences, told BioArray News this week. "This will also help our channel partners market the software aggressively since most of our distributors in Asia Pacific are distributors of Affymetrix systems," he said. Strand, which sells the Avadis microarray analysis software, is one of the initial 19 program members.

The most obvious symbol of program membership will be the GeneChip compatible logo, which Mike Lelivelt, the senior manager of the program at Affymetrix, said in a statement would show the software has "a unified workflow and direct data exchange with the Affymetrix GeneChip platform."


"We believe that this certification allows us access to a large customer base that Affy currently addresses."

Somewhat less obvious are the co-marketing opportunities members stand to gain from the program.

According to Affymetrix's Steve Lincoln, vice president of informatics, program members will not only benefit from appearing to be Affy approved, but also from "referencing products on each other's web sites, educational joint webinar presentations, and other activities we plan for the future."

Lincoln told BioArray News via e-mail this week that members should also benefit from scientific collaboration with Affy, as well as Affy's help in integrating their software with the GeneChip platform.

"[Our] scientists work closely with software providers to create case studies, algorithms, and tools for current as well as new applications of Affymetrix GeneChip technology. Many of our current customers use technologies, chip designs, and approaches developed by these collaborations," Lincoln explained.

"Affymetrix [will also] provide the necessary tools and technical support for integration with the GeneChip platform," he said. "This includes copies of development software to create testing environments and the appropriate licenses to Affymetrix development tools for commercial software applications."

"Over the last few years Genedata and Affymetrix have been in constant direct contacts on all levels from sales reps to management," Michael Brueckmann, Genedata's head of marketing communications, wrote in an e-mail to BioArray News this week.

Brueckmann said that membership in the new program "did not come as a surprise" for his company, which sells its Expressionist software primarily to labs involved in biomarker discovery.

"The tight integration between the Affymetrix technology and Genedata Expressionist has always been a natural requirement for us, rather than having been triggered by this specific program," Brueckmann said.

Becoming — and Staying —
GeneChip-Compatible

According to Affymetrix, the 19 first GeneChip-compatible software providers are Biocomputing Platforms, BioDiscovery, Biotique Systems, Genedata, GeneGo, Gene-IT, Genomatix Software, Golden Helix, IMC, Ingenuity Systems, Insightful, Ocimum Biosolutions, Partek, Progeny Software, Rosetta Biosoftware, Strand Life Sciences, Stratagene, Teneo Sciences, and VizX Labs.

But if you are not among the initial 19, how do you become GeneChip-compatible?

According to Affy's Lincoln, all software providers of GeneChip-compatible applications must agree to meet a set of specifications that help ensure integration between the application and the Affymetrix microarray platform.

The specific requirements vary depending on the type of application, Lincoln said, "but in general they include reading and writing native versions of Affymetrix binary data files, consistently accessing sample attribute information to aid biological interpretation of the analysis, and having access to the most current NetAffx annotations for microarray content."

Because Affy's platform is updated on a regular basis, Lincoln said that current members will also benefit from "a provision that the requirements will be updated as the Affymetrix platform continues to evolve."

Current program members told BioArray News that they would also take advantage of Affy users to improve the quality of their software.

"We have had very close interactions with the Partek users at Affymetrix who have given us great feedback that have helped us tune Partek's [software] to work very well for [the] analysis [of] GeneChip studies," Tom Downey, president of program member Partek, told BioArray News this week.

Other program members see the ability to stand side-by-side with Affy in the marketplace as one of the primary benefits of the program.

"Affy is the market leader in arrays," Ocimum Biosolution's CEO Anuradha Acharya told BioArray News this week. "We believe that this certification allows us access to a large customer base that Affy currently addresses."

— Justin Petrone ([email protected])

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