This article has been updated from a previous version to correct the name of Stratagene's pathway analysis software.
Using developers from Strand Life Sciences, Agilent is merging the ArrayAssist microarray analysis software it picked up as part of its acquisition of Stratagene earlier this year with its GeneSpring array analysis platform. The latter was part of the cache from its purchase of Silicon Genetics three years ago.
The next version of GeneSpring, version 9.0, will include features of both products and is slated for release this fall.
In line with the development plans, “less than a handful” of bioinformatics developers have been let go from Agilent’s Pleasanton, Calif., facility. Developers from Strand, which is based in Bangalore, India, are carrying out the redesign. The company was not at liberty to disclose further details regarding the layoffs, said spokesperson Stuart Matlow.
Enhancements to GeneSpring will include tools for analyzing splice variation, copy number variation, and comparative genomic hybridization, according to Agilent’s director of software solutions, David Edwards. All of the new features will come from ArrayAssist.
Edwards added: “We are also enhancing the project-based functionality that is available in the current version of GeneSpring to make it easier to use and able to support analyses across multiple experiments, such as from different arrays.” He said that GeneSpring 9.0 will support the Affymetrix array platform.
“This is an expansion of the existing partnership between Stratagene and Strand, and working with Strand gives us an opportunity to become more competitive within the bioinformatics market than we’ve been in the last couple years,” Edwards told BioInform this week.
The upgrade stems in part from a well-entrenched relationship between Stratagene and Strand, Edwards said of the relationship that began in December, 2005 when Stratagene hired Strand to develop its ArrayAssist and PathwayArchitect products.
It’s likely that financial considerations played a part in the agreement as well.
However, according to Strand marketing executive Thiru Reddy, money is not the factor at play. He noted that there are facets to the deal that are not readily apparent.
“I don’t think … the Indian cost angle/benefit is something that is [a factor] anymore. We are also facing huge increases in salaries,” Reddy said. “Strand is made up of people who have come back from US and Europe,” he added.
According to one source familiar with software developers’ salaries in India, pay scales are somewhat lower than in the U.S., but are creeping up. “It used to be that the differential was 70 to 80 percent, but now it may be around 30 to 40 percent, which is still good, but when you factor in the cost of program management and so on from there, it quickly goes down to 10 to 15 percent.”
“There are two angles [to] this,” Reddy said. “One is what we’ve been doing for the last five years, the software we’ve been building in this space.” He said that Strand’s Avadis software platform allows the company’s developers to build products for any data analysis application very quickly because of its extensibility. GeneSpring 9.0 is also being built on this platform, Reddy said.
The other aspect, he said, comes from Strand’s success in assembling a “truly interdisciplinary R&D team” of more than 50 computer scientists and 20 life scientists.
Strand’s original agreement with Stratagene called for Strand to rebuild the company’s ArrayAssist line on top of the Avadis architecture.
Now, Strand will be merging that project into GeneSpring 9.0. “We will be the sole company building it, and it will be built on our platform with our IT,” Reddy said.
Features of the new GeneSpring include what Reddy calls a “very rich graphical user interface,” an algorithmic engine, and an automation engine to enable analytical workflows within the product.
As to why Strand was chosen over Agilent’s in-house developers – resulting in the layoffs – Reddy said Strand has the advantage of being able to “spit out” data analysis software products in a very short period of time.
Strand currently markets four software products, all of which are built upon Avadis, with applications ranging from research biology to computational chemistry. Reddy said these are ArrayAssist, PathwayArchitect, Sarchitect Designer, and Sarchitect Miner. The first two are marketed by Stratagene and the last two by Strand.
“This is an expansion of the existing partnership between Stratagene and Strand, and working with Strand gives us an opportunity to become more competitive within the bioinformatics market than we’ve been in the last couple years.”
Reddy added that GeneSpring 9.0 took Strand’s developers less than three months to develop and manufacture, “which is a testament to the fact that the [Avadis] platform allows us to build these sorts of products.”
Best of Both Worlds?
Jim Woodgett, director of the University of Toronto's University Health Network microarray core facility, uses both GeneSpring and ArrayAssist. He told BioInform via e-mail this week that while he hasn’t yet tried GeneSpring 9.0, he can “see advantages of incorporating the best features of ArrayAssist into it and hence broaden[ing] the types of analysis that can be done in one package.”
He noted that GeneSpring is more complex than ArrayAssist and has a steeper learning curve for more “casual users.”
One downside to the integration, however, is that “ArrayAssist was fairly cheap and likely achieved good sales for individual users, [and] because of that there were various versions available as well as site licenses,” Woodgett wrote. “For many occasional users, the ability to run ArrayAssist off their desktop rather than in a core lab was a big advantage.”
In an interview with BioInform’s sister publication BioArray News in April, Woodgett said that ArrayAssist costs $1,500 for a single academic license, while a single GeneSpring license cost around $3,400 per year. [BioArray News 04-10-07]
This week, Woodgett wrote that he’s not surprised by the consolidation of products, given the current climate of acquisitions and the “maturity of the market (and development tools).”
He added that “something has been lost as Stratagene had something to prove and was price-aggressive.”