Stratagene officials said last week that the company will not renew a three-year distribution agreement for Ariadne Genomics' PathwayAssist software that began in 2002.
Instead, Stratagene has aligned with Strand Life Sciences to co-develop a new line of pathway-analysis software as well as a suite of tools for Affymetrix' next-generation 5-micron GeneChips.
The first products from the collaboration PathwayArchitect and ArrayAssist Exon are scheduled for release "directly after the new year," David Weber, senior vice president of marketing at Stratagene, told BioInform last week. Additional ArrayAssist modules for tiling arrays, 500K SNP arrays, and other upcoming Affymetrix arrays will roll out in "the early part" of 2006, he said.
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.
"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."
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," according to Jason Goncalves, general manager of software development at Stratagene. 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."
Avadis is also able to work with "tremendous data sets," Goncalves said a key factor in analyzing the 5-micron GeneChips, which generate about five times as much data per chip as Affy's previous 11-micron arrays.
In order to ensure that ArrayAssist supports Affy's current expression arrays as well as the next-generation chips, Goncalves said that Stratagene plans to build the product line as a series of modules.
The first of these, ArrayAssist Exon, wlll be designed to process the chip's 1.4 million data points and include several new algorithms designed to derive the so-called "splice index," which calculates the probability of alternative splicing, Goncalves said.
S. Sowmyanarayan, senior manager of business development and alliances at Strand, explained in an e-mail to BioInform that Avadis "has specific workflows to address Affymetrix data analysis. We just need to add a few specific analysis algorithms to enable exon analysis."
Sowmyanarayan said that Avadis also "has the ability to support pathways analysis. … All the pathway-specific components would be built on top of the platform."
Goncalves said that Avadis will serve as the foundation for a "user-defined workflow" feature in PathwayArchitect that will allow users to create a series of network-analysis steps that can be shared with colleagues.
He added that Stratagene has also developed what it terms "relevance statistics" for the PathwayArchitect product.
"Right now a lot of the pathway software really works by just looking at relationships, and unfortunately, it doesn't really take a statistical consideration as to the relevance of any connections that you see," he said. "What we're doing is now introducing methods that will allow us to measure the significance of any pathway connection and use that to help build networks that are optimized to be the most statistically relevant."
PathwayArchitect also features a database of "hundreds of thousands" of biological interactions that Strand mined from the biological literature using its text-mining software. PathwayArchitect can import gene lists from microarray experiments, protein lists from yeast-two-hybrid experiments, or lists of other biological concepts, such as disease terms. It also works with tabular data, "so it can actually import an entire microarray experiment and build these relevance networks," Goncalves said.
He added that PathwayArchitect has an open database structure that allows users to choose between Oracle or MySQL, and the software can be run on a local desktop or in an enterprise environment.
Weber said that Stratagene has "a plan in place" to encourage Stratagene's PathwayAssist customers to migrate to PathwayArchitect, but did not provide further details.
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. [BioInform 10-24-05]
"We have gone through arbitration with Ariadne," Weber said. "The arbitrator has reached decisions there and they are now being formalized, but that situation is totally under control."
The original distribution agreement with Ariadne was scheduled to expire on Dec. 12. According to court documents filed prior to the arbitration proceedings, PathwayAssist contributed more than $1 million to Stratagene's total revenues of $80 million in 2004.
Officials from Ariadne declined to comment on the company's plans for marketing PathwayAssist following the expiration of the agreement with Stratagene.
Bernadette Toner ([email protected])