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Agilent to Release Intermediate Upgrade of GeneSpring to Address ‘Omissions’ in GX 9.0

Agilent Technologies is preparing to release an “intermediate” upgrade for its GeneSpring GX 9.0 microarray analysis software in the next few weeks that will include a number of features that were available in previous versions of the software, but were sidelined in the most recent release.
GX 9.0, which the company released in February, was the first version of GeneSpring to include features from ArrayAssist, the microarray-analysis software package that the firm gained through last year’s acquisition of Stratagene.
Last summer, Agilent, which had been supporting both packages, decided to abandon that strategy and hired Strand Life Sciences to redesign an entirely new product based on Strand’s Avadis platform that would bear the GeneSpring name [BioInform 08-17-07].
GeneSpring has been a staple of the microarray-analysis toolkit since Silicon Genetics first launched the software in the late 1990s, “but it was old code and we wanted to prepare it for the future,” Thon de Boer, product marketing manager for bioinformatics at Agilent, told BioInform. Agilent has marketed GeneSpring since it acquired Silicon Genetics in 2004.
“Since we built it on the new platform, we basically had to re-implement every single feature of GeneSpring, and we wanted to do this really fast,” he said. One problem with this approach, he said, was that “because we had to re-implement every single feature that we had in GX 7 for version 9 … we decided to drop a number of features that we at that point felt were either power-user tools or were no longer necessary because there were other ways of doing things, and also sometimes because we just didn’t have the time to get it in.”
The upshot, he said, is that “some people feel — and they are correct — that there are some … very important features that were left out.”
Indeed, in a thread on the Gene-Arrays listserv several weeks ago, a number of dissatisfied GeneSpring customers bemoaned the changes in the software and shared options for alternative packages. The thread prompted a response from de Boer and another Agilent product manager that outlined the company’s plans to address these issues.
De Boer told BioInform that while the next formal release of GeneSpring — version 10.0 — isn’t scheduled to appear until late summer or early fall, the company plans to soon release an intermediate version — 9.0.5 — “that is going to have some smaller additions, some very glaring omissions that people” were calling to have reinstalled.
Two key “omissions” include the ability to import a gene list from an Excel file or another source, rather than relying on lists created within the product, and the ability to update array annotations from external sources. The release will also restore some normalization and visualization options that were available in previous versions of GeneSpring.
The company is also allowing customers to keep GX 7 and GX 9 running at the same time in order to help them adjust to the new version. “We know that this was such a big change and we realize that people don’t want to necessarily move immediately,” de Boer said. Users will be able to use GX 7 until the end of the year, “and when they are ready for it they can migrate into 9,” he said.
Fear of Switching
At least one customer is taking advantage of that option. Jiri Zavadil, an assistant professor in the department of pathology at the New York University Medical Center said he’s been using GeneSpring since 1999 and never had a problem with previous upgrades.
However, he said that GX 9 did away with the “interactive interface” that he had grown accustomed to, so he is sticking with GX 7 until it expires, at which point he’ll determine whether to move to GX 9 or something else, such as BioConductor.
“I really hate the change,” said Zavadil, who is also assistant director of the NYU Cancer Institute’s genomics facility. “I think GeneSpring hit it right from the beginning — with the graphics, with the ways that it could visualize data. I think that was its strongest point.”
The interface for GX 9, he said, resembles ArrayAssist more than GeneSpring. “It’s more static, and it forces you to go through [the analysis] a certain way.”
Indeed, the new release of the software includes “guided workflows” that are designed to appeal to more inexperienced microarray users.

“Some people feel — and they are correct — that there are some … very important features that were left out.”

Agilent’s De Boer said that while GeneSpring’s core customer base has always been “the expert market,” the company determined that the gene-expression sector has matured to the point where there are many more potential users for the software. “So what we wanted to do with GeneSpring was make it much easier to get started with, make it much easier to use for those new users.”
In line with this decision, “we gave it a guided workflow interface for people who chose to use that, and that is quite different from the way things were done in the past,” he said.
“For some people, the change was just too big,” de Boer acknowledged, but added that “we also have a whole slew of people who definitely see the benefit.”
He said that in the last two months, more than 650 people have downloaded and activated a demonstration copy of the software, “and the vast majority of them are completely new to GeneSpring … so it’s showing us that there’s a much larger market out there than just the market that we’ve been addressing over the last 10 years.”
And not all experienced users are dissatisfied with GX 9. Jenny Xiang, director of the microarray core facility at the Weill Medical College of Cornell University and a GeneSpring user since 2001, said that it’s just a question of getting used to the change.
“It takes time to get familiar with the new version,” she said. “You just need to play with the new version and you will find out it’s better.”
She added that the new version is particularly good for inexperienced microarray users because the guided workflow allows them to analyze the data themselves immediately without a training course. It also includes a number of new functional analysis tools and quality control features, she said.
However, she suggested that it might be helpful if Agilent provided more training to help familiarize people with GX 9. “Now many people are used to the older version and they don’t want to switch, but actually they just need time,” she said.
Moving in on the Market
In the meantime, some of Agilent’s competitors in the microarray-analysis software sector consider the latest release of GeneSpring a market opportunity.
“We have seen a definite pickup in business after the new GeneSpring,” Anu Acharya, CEO of Ocimum Biosolutions, told BioInform via e-mail.
Ocimum this week launched version 4.0 of its Genowiz software for gene-expression analysis. “We believe that we have a much better product which is very easy to use and priced right for the market,” Acharya said.
Nevertheless, she noted that GeneSpring is still the “key competitor” in a market that includes other key contenders such as Rosetta Biosoftware, Partek, SAS subsidiary JMP Genomics, and VizX Labs. She said that Ocimum plans to differentiate itself by targeting its software to experimental biologists through “a perpetual license with probably the most competitive price” on the market, though she did not provide pricing details.
Partek is also seeing a “steady transition within the marketplace to Partek Genomics Suite away from GeneSpring,” Michael Lelivelt, vice president of genomics at the company, told BioInform via e-mail, though he added that this is part of a trend away from “other genomics software, both commercial and freeware.”
He said that the company views its software’s advanced statistical capability as a key advantage in the marketplace, as well as its “comprehensive support and integrated analysis of multiple genomic assays from a variety of assay providers.”
Another possible reason for the transition Partek is seeing, Lelivelt suggested, is that users may “find comfort in using software from a privately owned, independent company that is free to support genomic assays from any provider.”
Other GeneSpring customers may stray from the software not so much because of shortcomings in the new release or support issues, but because of recent advances in publicly available options. “For us, the real issue is not so much GX 7 vs. GX 9, it’s whether GeneSpring is worth the nearly $4,000-per-year price tag,” Kate McInnerney, a research associate in the Montana State University Functional Genomics Core Facility, told BioInform via e-mail.
“GeneSpring was never that easy to use, and now that microarrays are less novel, there is also less need for publication-quality graphics,” she said. Meanwhile, “open-source software has improved greatly in terms of its user interface and graphics.”
McInnerney said that she has been testing her lab’s data on several different software packages and is currently “leaning toward” FlexArray from McGill University and the TM4 suite from the Dana-Farber Cancer Institute.
The GeneSpring of the Future
Agilent’s De Boer said that the firm hasn’t seen a drop-off in software sales since launching GX 9.0. He noted that a certain amount of customer dissatisfaction was to be expected in the wake of a major product overhaul, and was the price the company had to pay in order to make the necessary changes to the platform.
“We had been the big gorilla in the area, so for us, growth was difficult to come by. Single-digit growth over the last couple of years is good, but we can do much better than that. And that’s why we made this decision” to re-engineer the software, he said.
“It was a hard decision because we knew that we’d be disappointing some of the users who are just happily using GeneSpring as it is today, but this is the GeneSpring of the future, rather than the GeneSpring of the past, and there are different markets out there now,” de Boer said.
GeneSpring, he noted, “was always focused on the gene-expression market and the whole code was built around that premise,” but Agilent — and the microarray research community — has moved beyond expression in recent years. Future versions of the software, built upon the “more flexible” Avadis platform, will be targeted toward “systems biology” rather than gene expression or other niche applications, he said.
In line with that approach, version 10.0 of the software will be completely integrated with Stratagene’s Pathway Architect software, he said, which will allow users to create new pathways and new networks based on information in the literature.
Future development plans also call for support for a wide selection of array applications, including comparative genomic hybridization, copy number variation, and microRNA analysis.
De Boer also stressed the fact that GeneSpring will continue to support microarray platforms from other vendors. “We definitely won’t be an Agilent-only shop as far as GeneSpring is concerned,” he said.

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