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Spotfire Improves Integration with Affy, But Sees Biggest Life Science Growth in Screening

Spotfire has just released version 9.0 of its DecisionSite data-analysis platform, which includes a number of usability enhancements as well as tighter integration with the Affymetrix NetAffx annotation portal.
Spotfire customers using DecisionSite for Functional Genomics and DecisionSite for Microarray Analysis can now synchronize with the NetAffx annotation library to search for annotation files that match the chip type they are analyzing. The tool enables users to automatically download the annotations and merge them with the expression data in DecisionSite.
While that feature is the only genomics-specific enhancement in the current release, the new version offers a number of other new capabilities that will be useful for life science researchers, Christian Marcazzo, senior director of life sciences at Spotfire, told BioInform.
Many of these enhancements should be of particular interest to researchers in high-throughout and high-content screening, Marcazzo said. Although screening is a relatively mature market for Spotfire, Marcazzo said that it is currently “the biggest growth area for us,” largely because many of Spotfire’s pharmaceutical customers are modernizing their screening infrastructures and their accompanying data-management tools.
“There are a lot of projects going on out there with customers to help them continue to evolve their [screening] systems,” Marcazzo said. Some customers are implementing “next-generation screening platforms,” he said, while others are scaling up their HTS capacity so that it’s “much more of a manufacturing operation” than a research activity.
“A lot of customers are looking to overhaul their screening infrastructure, from the point of view of data management, data analysis,” he said, “Whereas we don’t really see anything like that happening in genomics.”
In particular, high-content screening is “growing like mad,” Marcazzo said. “We’re seeing a lot of requests coming to help our customers work better both with Cellomics and GE [Healthcare] IN Cell data,” he said.
The company signed an agreement with GE Healthcare in July to bundle DecisionSite with GE's IN Cell Investigator 1.0 software [BioInform 07-07-06].
DecisionSite 9.0 was designed to help users manage and analyze the very large data sets typical in screening as well as genomics, Marcazzo said. One feature that has been “requested from customers for quite awhile” is improved color-management capabilities.
“In areas like high-throughput screening, you have this real cluster of data around no activity, and then these outliers with very high activity or, in some kinds of assays, a negative activity,” Marcazzo said. “Some of our customers using our software in screening were frustrated that the color schemes that DecisionSite gave them would allow one or two outliers to really bias the whole color scale,” making it difficult to see trends and correlations.
DecisionSite 9.0 includes a color template “that restricts the meaningful color transition to where most of the data is, thus resisting the distorting effects that outliers can have on your visualizations,” according to a company product sheet.
“This functionality allows the users to be really specific about determining the colors for certain kinds of outliers and defining where the gradients are,” Marcazzo said. “It makes it much more configurable to show color that’s intuitive and reflects well what someone may be looking for in that particular analysis. That’s relevant in screening and relevant in genomics.”

“A lot of customers are looking to overhaul their screening infrastructure, from the point of view of data management, data analysis. Whereas we don’t really see anything like that happening in genomics.”

Marcazzo said that many of Spotfire’s life science customers are starting to look at “really, really wide data sets with hundreds or thousands of columns, and the difficulty then becomes finding the column that has the data that you’re interested in plotting, or finding the column that you want to put into a table that you’re building.” DecisionSite now includes a column selector tool that enables users to enter free text that will automatically filter by column name.
Spotfire has also updated the Spotfire server so that it supports both the DecisionSite 9.0 client as well as the DXP client, an analytical software package targeted at business users that the company launched earlier this year.
“Our pharmaceutical customers are starting to use DXP to look at sales and marketing data and clinical trials … and our bioinformatics and cheminformatics customers continue to use DecisionSite because of some of the chemistry and genomics-specific functionality that we have there. But from an IT perspective, now, they have one server that supports all those different users,” Marcazzo said.
Another improvement targeted to the pharma IT department is support for Microsoft’s .NET 2.0 and Internet Explorer 7.0.
“Our APIs now support .NET 2.0 so our customers can build extensions in .NET that allow them to extend the functionality or provide integration with other things they’re building internally,” Marcazzo said. He added that .NET is currently more in use “in big pharma and in cheminformatics than in bioinformatics or smaller biotech companies.”

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