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Affy Formalizes Software Compatibility Specs, Lends Logo and Marketing Muscle to Partners


Affymetrix is literally placing its stamp of approval on certain bioinformatics software packages that are compatible with its GeneChip microarray platform.

Under the new GeneChip-Compatible Applications Program, which Affy kicked off last week, the microarray giant is allowing software firms who meet a certain set of specifications to bear a new "GeneChip Compatible" logo on their products and marketing materials. These companies are also entitled to other co-marketing and co-promotion activities, and are listed in Affy's web-based software catalog.

The program is an outgrowth of the Affymetrix Developers Network, a web-based forum through which the company provides third-party software developers with file formats, software development kits, and other tools.

The GeneChip-Compatible initiative is essentially a more formal version of this resource, Steve Lincoln, Affy's vice president of informatics, told BioInform last week via e-mail. The program "is an evolution, and perhaps slight formalization" of the ADN and other initiatives that Affymetrix has launched to ensure that its customers have access to software that is tightly integrated with the GeneChip platform, he said.

As the company prepares to roll out its next-generation chips, which will have higher densities and work in many new application areas, it wants to work more closely with developers to ensure that the software keeps pace. "We're looking to build better relationships with our [software] partners because we're not going to be able to provide all products for all use cases," Lincoln said.

The move mirrors the strategy of hardware providers in the general-purpose IT market, who take pains to build strong ties with independent software vendors. "Apple's relationships with Adobe, Microsoft, and the KDE/BSD/GNU freeware communities are great examples of these collaborations," Lincoln noted. "The ISVs leverage the platform vendor to create new opportunities for themselves and to track the evolution of the platform." The platform vendor, meanwhile, keeps its customers happy by expanding the number of available software options.

Affymetrix previously listed a number of software packages on its website as "Affymetrix Premier Applications," but these packages were not subject to any stringent requirements and the list carried a disclaimer that Affymetrix did not guarantee their performance. Now, the company has outlined a clear set of specifications for 10 different application areas that serves as a compatibility checklist (see chart, below).

Affymetrix Compatibility Requirements
for Software Application Classes
(Complete specs available here)
Application Class
File Specification
Annotation Specification
Sample Attributes
Expression read CHP files NetAffx support read
XML file
Genomic Tiling read BAR and BMP files NetAffx support read
XML file
Statistical Analysis read CHP files NetAffx support read
XML file
SNP Analysis read CHP files NetAffx support read XML file
Chromosomal Copy Number read CHP files NetAffx support read
XML file
DNA Sequence Analysis read FASTA files NetAffx support read
XML file
Pathway/Network Analysis None NetAffx support read
XML file
Data Management read CHP files NetAffx support read and write XML file
Laboratory Management read CHP files NetAffx support read and write XML file
SOURCE: Affymetrix

In addition, Affymetrix is providing software, development tools, and technical support for software companies in the program. "This includes copies of development software to create testing environments and the appropriate licenses to Affymetrix development tools for commercial software applications," Lincoln said.

The initial rollout of the program is focused on commercial developers, but the company is considering extending it to academic packages as well. "Academic software plays a critical role for us, for our industry, and for our commercial software partners," said Lincoln. "Now that the program has officially been launched, we look forward to talking with various groups about where we should go from here. The issues are a little different with academics, but the shared goals are clear."

Who's In?

Affymetrix announced last week that 19 companies had already met the requirements for GeneChip Compatibility: 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.

Spotfire is also a member of the program, but did not join until after the announcement was finalized.

Several companies, including Agilent, Corimbia, InforSense, OmniViz, and Inpharmatica, were previously listed as "Premier Applications" on Affy's website, but were not included among the GeneChip Compatible partners.

Lincoln said that the initial members were made aware of the GeneChip Compatible program "by word of mouth only," and that Affy expects "that other providers will also want to participate or will want to talk with us about other areas of mutual interest" now that the initiative has seen its official launch.

What is GeneChip Compatibility?

Affymetrix outlines the requirements for its new GeneChip Compatibility program on its website (

"To participate, a partner needs to commit to integrating with the Affymetrix platform according to specifications provided by Affymetrix. If and when the integrated application is available, the partner will receive rights to use the GeneChip Compatible logo, and will receive space in the web-based GeneChip Compatible solutions catalog. Affymetrix will license at no cost various software and development tools for this purpose to the partner, and the partner agrees to license back to Affymetrix the compatible application (for internal use only) and the descriptive and training materials for inclusion in the catalog."

Jordan Stockton, informatics marketing manager at Agilent, told BioInform that "it's not in our plans" to join the GeneChip compatible program. He noted that the company, which sells the GeneSpring, SigNet, and Varia software packages — as well as its own line of microarrays — is "committed to servicing all of the hardware platforms that Affymetrix is going forward with."

Stockton declined to comment on Agilent's reasons for not participating in the program, but said that the company licenses all the necessary tools to ensure that its software is integrated with Affy's platform. "Our products going forward will continue to add more and more functionality to support the Affymetrix hardware platform, both in gene expression and genotyping," he said.

Some software vendors who did opt to join the program jumped at the chance to align themselves with Affymetrix.

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

Others, such as Genedata, viewed it as a natural development in an ongoing relationship. "Over the last few years Genedata and Affymetrix have been in constant direct contact on all levels from sales reps to management," Michael Brueckmann, Genedata's head of marketing communications, told BioArray News, so membership in the new program "did not come as a surprise."

For Gene-IT, the program is a sign that the bioinformatics market is beginning to mature. Ron Ranauro, CEO of Gene-IT, echoed Lincoln's suggestion that the model is a familiar one in the mainstream computer market. In the early days of the computer industry, Ranauro said, "everybody had their own operating system, their own database, their own compilers, and their own applications, and computer companies realized that the way to grow the market was to get the development community to actively develop for the platform. This is really, to me, a similar model."

Ranauro said that Gene-IT had previously integrated its GenomeQuest sequence-analysis platform with Affy's annotations through an "informal alliance" based on the NetAffx developer kit. "We were basically accessing the data as any other Affymetrix end-user customer lab would, and now they've really done a great job of formalizing the process so that customers can really be sure that all the players are committed," he said.

For a company like Gene-IT, which isn't widely known in the microarray analysis community, the alliance with Affymetrix poses a promising market opportunity. Ranauro estimated that Affymetrix has something somewhere between 1,200 and 2,000 core lab installations worldwide, "and each one of those would be a target for us if they're looking for a very reliable and up-to-date reference annotation set," he said.

"We're still of the view that this market is still in the early adopter phase and it's going to get very large," he said.

— Bernadette Toner ([email protected])

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