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In Wake of Dispute with Ariadne, Stratagene Inks Bioinformatics Software Deal with Strand

Following a dispute with bioinformatics partner Ariadne, Stratagene said last week that it would collaborate with Strand Life Sciences to develop bioinformatics software to analyze biological pathways and Affymetrix's new GeneChip microarrays.

Terms of the agreement call for the companies to co-design and co-develop software based on Strand's Avadis technology. Stratagene will exclusively market and sell the two products "shortly," the companies said.

The collaboration expands upon an ongoing collaboration between Stratagene and Affymetrix. Most recently, in February, Affymetrix — the dominant player in the microarray market — said it would use Stratagene software for GeneChip data analysis. As part of that non-exclusive license, Stratagene is developing a new software package, called ArrayAssist Lite, which will be offered as a free statistical analysis tool for Affy array customers.

Joe Sorge, chairman and CEO of Stratagene, said at the time that the pact with Affymetrix would provide "the opportunity to position our technology as a standard for expression analysis."

The agreement with Strand marks the end of a three-year pathway informatics collaboration, which Stratagene chose not to renew, with Ariadne Genomics.

Stratagene began distributing Ariadne's PathwayAssist three years ago, but the companies had a falling out over the terms of the agreement, a dispute that led to arbitration proceedings in the fall.


"We have gone through arbitration with Ariadne. The arbitrator has reached decisions there and they are now being formalized, but that situation is totally under control."

In Stratagene's quarterly report for the period ended June 30, the company said it had filed a request for arbitration in March "for declaratory relief and damages" related to the marketing and distribution agreement that the firms signed in 2002. In particular, Stratagene sought "to confirm that it holds the exclusive right to market, sell, and distribute the software products covered by the agreement and all upgrades thereof in any country or territory in the world, except Japan, for the duration of the term of the agreement."

Under the terms of the 2002 marketing agreement, Stratagene had agreed to pay Ariadne an up-front fee of $20,000 and 50 percent of net software revenues in exchange for exclusive rights to distribute Pathway Assist. Stratagene stated in the court records that sales of Ariadne's products generated more than $1 million of its total revenues of $80 million in 2004, and that "the opportunity and ability of Stratagene to receive further profits from the sale of the products is a substantial prospective economic advantage for Stratagene with which Ariadne seeks to interfere and disrupt, and has already done so, and will continue to do so unless enjoined, thereby causing irreparable harm to Stratagene."

"We have gone through arbitration with Ariadne," David Weber, senior vice president of marketing at Stratagene, told BioCommerce Week sister publication BioInform last week (BioInform 12/12/2005). "The arbitrator has reached decisions there and they are now being formalized, but that situation is totally under control."

The Strand Collaboration

The first products from the collaboration — PathwayArchitect and ArrayAssist Exon — are scheduled for release "directly after the new year," Weber said. Additional ArrayAssist modules for tiling arrays, 500K SNP arrays, and other upcoming Affymetrix arrays will roll out in "the early part" of 2006, he added.

PathwayArchitect, which enables researchers to build and analyze biological pathways and networks, will replace Ariadne's PathwayAssist in Stratagene's product lineup. "Beginning in January, as far as Stratagene's portfolio is concerned, PathwayArchitect will be the sole pathway product that we're going to run with," Weber said.

He said that Stratagene has "a plan in place" to encourage Stratagene's PathwayAssist customers to migrate to PathwayArchitect, but did not provide further details.

ArrayAssist Exon will be the first of several modules that Stratagene will add to its ArrayAssist product line, which currently analyzes only gene-expression data.

The two product lines represent the "two fastest-growing areas in informatics," Jason Goncalves, general manager of software development at Stratagene, told BioInform. Both will be built upon Strand's Avadis data-mining technology, which Goncalves described as "extremely flexible and scalable."

Goncalves noted that Avadis is a multi-platform technology, which will enable Stratagene to support the Mac platform for the first time, in addition to Windows and Linux. "We've had a lot of requests for support for Mac," he said, "and we're pleased now that we're able to offer that."

— Bernadette Toner ([email protected])

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