Around a year and a half ago, Nonlinear Dynamics began overhauling its entire product-development process to comply with so-called "agile" software-development practices. Last week, a company official said that step has paid off in the form of two new software products that it launched at the Human Proteome Organization World Congress in late August • along with an upgrade of its Progenesis line of 2D gel analysis software and a preview of an image-warping application it plans to launch this fall.
The company embarked on the new product-development strategy as part of a broader mission to expand its reach in the proteomics software market beyond its historical role as a provider of 1D and 2D gel analysis tools.
"We're known in the marketplace, and we've got a very good reputation, as a gel analysis company," said John Spreadbury, group sales and marketing director and CEO of the firm's US subsidiary. "We are a gel analysis company, but that's not all we do. We have fantastic data-mining tools, query tools, we have tools for databasing as well, [and] mass spec modules.
"We're really looking at supplying our users and other people's users out in the marketplace with more tools, and better quality tools to ensure statistically correct results," he continued. "But to do that, we had to go back and change the way we develop products so that we can make products better."
"We're known in the marketplace, and we've got a very good reputation, as a gel analysis company. We are a gel analysis company, but that's not all we do."
Nonlinear conducted a "massive" market survey of customers and prospects over the last year to ensure that its new and upcoming products will meet user needs, and also re-branded nearly every product in its lineup to accommodate this expanding suite of applications (see box, below). "We changed everything," Spreadbury said.
Under the revamped product-development strategy, the company broke down each of its product lines into components so that smaller development teams could focus on writing better quality code. In the case of 2D gel analysis, for example, teams with only a handful of developers would focus on writing separate modules for spot detection, warping and matching, and other features, Spreadbury explained. The result, he said, is production-ready code at almost any time so that small software modules can be released more often in order to keep up with customer needs.
This approach is a drastic shift from the company's previous development cycle, which focused on annual releases and was plagued by "feature shift," Spreadbury said, "so that 12 months becomes 13 and then 14 and then 15."
The new modular focus is evident across the company's expanded product line. One of its new products, called Modas (for multiple omics analysis system), is a three-tier, client-server system for integrated analysis of 2D gels and mass spec data. Additional modules that will enable researchers to analyze other types of data are planned for release "on a regular basis," Spreadbury said, noting that this would most likely be around every two months.
Nonlinear also released the first of a planned suite of biomarker analysis products. The software, called Progenesis PG600, was developed in collaboration with PerkinElmer, but Spreadbury stressed that it will analyze mass spec traces from any platform. A number of mass spec vendors are developing their own biomarker software packages to run on their instruments [BioInform 6-13-05], but Spreadbury said Nonlinear's platform independence should give it an edge in this increasingly competitive segment of the proteomics software market.
"If you go to ABI or to Thermo or to Bruker, they have their own software, but it will only work with their own mass spec," he said. "We're creating a generic product that will work with any hardware, and customers want this."
Nonlinear also expanded its Progenesis 2D gel analysis line to three products by incorporating features of the former Phoretix 2D gel line, and adding a number of new features. Dubbed the PG200, PG220, and PG240, the applications range in price and functionality from entry-level to advanced. Nonlinear has not yet disclosed pricing for any of its new products, but Spreadbury said that the company has "priced our products accordingly so that everybody in the market at any level can afford to invest in our products." This pricing structure, again, stems from the firm's new modular development approach, he added. "You can have one of each module for a very low fee, and then you can scale up when required, so if your workload increases for a small period, you can ramp up during that period with extra tools."
Tiger on the Horizon
Nonlinear Rebrands its Product Lineup
|Phoretix 1D Pro||TL120 DM|
|Phoretix 2D Expression||PG200|
|Phoretix 2D Evolution||PG220|
Nonlinear also showcased a prototype for an upcoming software product at HUPO that is based on an image-analysis technology it has code-named "Tiger" • not in emulation of Apple's latest OS X release, Spreadbury said, but because the method "doesn't use spots," which differentiates it from other pattern-recognition algorithms.
The first product to use the Tiger technology, a warping tool for aligning 2D gel images called TT900 STS (for spot-to-spot), is slated for release in November, Spreadbury said. This application, which will provide image alignment "that was just not possible before," will be a "generic product that will work with any third-party image-analysis software."
Nonlinear also plans to release software based on the Tiger technology for other types of data analysis, and intends to incorporate the technology in future releases in its biomarker software line as well, Spreadbury said. The method has been tested on LC/MS and "other data streams," he noted, "and it works very well."
In the long term, the 70-person company is looking to expand its product portfolio into a number of other new areas, such as chip analysis, HPLC, and other proteomic data sets. "I wouldn't put it past us maybe to have something looking at the diagnostic market in the near future," he said.
• Bernadette Toner ([email protected])
For Nonlinear, New Partners, Standards Expected to Drive Growth
Nonlinear announced two new strategic partners at HUPO: Invitrogen and Waters. This adds to the firm's current stable of instrumentation and software partners, which includes PerkinElmer, Shimadzu, Sigma-Aldrich, and Matrix Science.
Under the Invitrogen partnership, Nonlinear will ensure that its software products are optimized to work with Invitrogen's SILAC labeling technology and other proteomics reagents, Spreadbury said.
In the Waters deal, Nonlinear will integrate its Progenesis 2D gel line with Waters' ProteinLynx Global Server 2.2.5 mass spec informatics system.
Spreadbury said that as an independent software company, Nonlinear must partner with as many industry players as possible. However, he noted, "We're not looking for people to resell our products." Rather, he said, the company seeks partners that will help ensure that its software products are fully integrated with instruments and other products that its customers are using.
Nonlinear is also keeping an eye on various data standards emerging from HUPO's Proteomics Standards Initiative. "I think the commonality between hardware and reagents will only happen with software," he said. "If we can make software a standard item • standard user interface, standard results, standard calibration, very reproducible • then that is the way forward. I truly believe that we can take that variability out, model the noise, and we can get much more consistent results."
The company is "open to adopt" and "will endorse" any standards that come out of the PSI effort, Spreadbury said.