Integromics of Grenada, Spain, is planning to roll out a new biomarker-discovery software package that will take a “guided workflow” approach to analysis that the company expects will give it an edge in a competitive marketplace.
The software, called Integromics Biomarker Discovery, or IBD, was developed in collaboration with Tibco Spotfire, and is targeted for release next month.
Imad Yassin, commercial director for Integromics, said that IBD draws upon the visualization capabilities of Spotfire’s DecisionSite analytical software and the statistical rigor of the open source Bioconductor package.
IBD, which is Integromics’ second software tool for biomarker analysis, adds a “guided step-by-step workflow” as a front end to these tools, which allows users to address “key scientific questions without needing to learn the R programming language nor become an expert biostatistician,” Yassin explained to BioInform via e-mail.
IBD is compatible with Affymetrix data as well as data from two-channel platforms such as Agilent. It walks users through experimental design, quality control, filtering, normalization, and differential expression analysis.
Its analytical features include SAM, eBayes-moderated t-statistic, and false discovery rate, as well as a number of clustering algorithms and tools for comparative genomic hybridization analysis.
The IBD license includes “all the needed software, including the Spotfire license, required to run the application,” Yassin said.
He noted that usability will be a “key differentiator” for IBD in the marketplace, which is quickly growing crowded with software tools from companies that have identified biomarker research as a growth area.
A number of players are marketing software tools for biomarker discovery, including microarray analysis software firms like Rosetta Biosoftware and Genedata; statistical software shops like Partek and SAS’s JMP subsidiary; pathway informatics firms like Ingenuity and GeneGo; and proteomics software providers like Nonlinear Dynamics.
“Why is it [that] when it comes to science the user experience is neglected, yet … everything else from using your phone to navigating the web is getting easier?”
But Yassin noted that most bioinformatics firms tend to overlook ease-of-use when they develop new tools — a fact that could give Integromics a competitive edge.
“Why is it [that] when it comes to science the user experience is neglected, yet … everything else, from using your phone to navigating the web, is getting easier?” he said. “This is the key differentiator of what IBD can offer: a guided workflow that is transparent that can help the researcher arrive at the desired answers from his data.”
Yassin added that Integromics has worked “closely with Spotfire and key microarray users” in developing IBD to ensure that researchers “will be able to [visualize] and analyze their data in a way that was not possible previously within one package.”
In addition, he said, the company can use its experience in the research market to its advantage.
“Over the past 10 years we have seen magnificent analysis tools appear and disappear,” he told BioInform’s sister publication BioArray News last week. “Having come from the research side of the market, we are able to take what is relevant to researchers and give them a package that is well supported and well built that they can use themselves. So far it has been quite a healthy market for us.”
New Partner, New Tool
IBD is Integromics’ second software tool for biomarker analysis. The company’s Real-Time StatMiner software, developed in collaboration with Applied Biosystems and Novartis and launched in July, performs data visualization, statistical analysis, and data mining on real-time PCR data from ABI’s TaqMan platform.
“IBD’s focus is microarray data analysis, while the StatMiner analyzes qPCR data,” Yassin said. “Both are complementary to one another but developed as separate projects with two different partners, Applied Biosystems and Spotfire.”
Yassin noted that IBD also complements Integromics’ other software tools, which include a laboratory information-management system called ArrayHub, and ArrayUnlock, “an extension to IBD and StatMiner” that performs secondary analysis for functional annotation, he said.
Both IBD and StatMiner were developed as “plug-ins” for the Spotfire platform, and Integromics is also using Spotfire’s software for a project to build an interactive bioinformatics platform for the region of Andalusia in southern Spain. [BioInform 02-22-08]
“We have worked pretty closely with Spotfire and we have seen that the new functionality of this platform is exciting for our customers,” Yassin told BioArray News. “Spotfire has invested a lot in bringing their new technology online and we have extended and built new algorithms and guided workflows. From the visualization point of view alone, it makes sense for [customers] to upgrade” to IBD.
Integromics plans to release follow-on upgrades to IBD. Early next year, the tool will be able to import data from other widely used microarray platforms, such as Illumina’s BeadArray platform, Yassin said.
The company is also thinking about developing a version of IBD for proteomics biomarker discovery, which, Yassin said, “could be an interesting area to develop in if we identify the right partner to work with.”