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Canary Awards $225K to help 15 Labs Adopt Open-Source CPAS; Labkey to Provide Support

Seattle-based Labkey sprung from the minds of former Microsoft developers, so it should come as no surprise that the open-source proteomics-analysis system they designed, CPAS, is being used for big things.
This week, the company said that the non-profit charitable organization Canary Foundation has awarded $225,000 under its so-called Bioinformatics Platform Dissemination Award program to support the implementation of CPAS at 15 labs in the US, Canada, Korea, and the UK, where it is expected to help standardize early cancer detection research.
LabKey said in a statement that “most of the award funds” will go toward LabKey’s design, development, integration, and support services.
CPAS, or computational proteomics analysis system, is based on the company’s Labkey Server data-integration platform and is freely available under an open-source license from the Labkey Software Foundation, a separate non-profit entity that owns and manages the software. LabKey said that it will contribute all software developed under the Canary grants to the open source project.
“We are the main experts in CPAS right now and most of the awardees will use our services to either support or help them adapt the CPAS system for their particular needs,” Peter Hussey, a founding partner of Labkey, told Bioinform. “This doesn’t apply to everyone, but for most it will take down a barrier for adoption – such as how do we get the thing up and running?”
Labkey is “essentially a consulting business,” Hussey said, “so we build and modify software on contracts to labs here in Seattle and other labs associated with Seattle projects.”
Hussey said that the consulting model has been successful for the firm, which spun out of the Fred Hutchinson Cancer Research Institute in 2005 [BioInform 10-03-05]. “As long as scientists have new things to build and need new features, which they seem to do on a regular basis, we think that’s a good model going forward,” Hussey said. “And we think that will sustain enough active development on the Labkey platform – both for CPAS proteomics applications and other application areas we’ve developed on the same core server.”
Martin McIntosh, a principal investigator at the Fred Hutchinson Cancer Research Institute, said that proteomics research is particularly powerful for early cancer detection. LabKey’s founders originally developed CPAS while working in McIntosh’s research group at the Hutch under a broader, $9.7-million grant for proteomics analysis from the National Cancer Institute.
Of that award, only a fraction ― “maybe $1 million” ― went toward software development, McIntosh said.
Now, the focus is entirely on software development, perhaps because Don Listwin, founder of the Canary Foundation and former Cisco executive vice president, is keen on the idea of using CPAS to drive cancer research.
“When key labs are using and building on the same software platform, they can focus their efforts on discovering biomarkers for cancer instead of reinventing the wheel,” he said in a statement. “We're betting that CPAS is going to be one of those platforms.”
According to McIntosh, who is also chair of the Canary Foundation award evaluation committee, the committee found the CPAS proposal particularly in keeping with Listwin’s vision and therefore appealing for its ability to mesh research ideas into the common platform model.
McIntosh told Bioinform that Listwin “decided he wanted to support Labkey because he is basically a big promoter of people supporting data [sharing], and helping people collaborate.”
This is not the Canary Foundation’s first involvement with CPAS. About a year and a half ago, the organization provided McIntosh’s group at the Hutch about half a million dollars to begin building an infrastructure for the user community that eventually became CPAS.

“We are the main experts in CPAS right now, and most of the awardees will use our services to either support or help them adapt the CPAS system for their particular needs. This doesn’t apply to everyone, but for most it will take down a barrier for adoption – such as, how do we get the thing up and running?”

It would appear that Labkey’s fairly lodged in Canary’s pockets, but Hussey said that the firm is not entirely dependent on the foundation’s largesse.
Hussey said that since LabKey’s genesis, the firm has added “smaller contracts” with the Hutch and the University of Washington, “and we’ve also had contributions from developers in Singapore and from the University of Kentucky.”
In addition to Labkey’s proteomics projects, “we’re doing work for some researchers associated with the Sharp organization, an HIV vaccine and clinical trials network,” McIntosh said. McIntosh added that the Canary awards should help build a larger user community around CPAS.
“This grant is the next step in the process to support the next group of people who want to enter, use, and develop the platform; it’s a second tier,” he said.
While the first Canary CPAS grant was for McIntosh and his group, this one, he explained “is going to everyone but me.”
The 15 grant recipients — which include the Institute for Systems Biology, the Broad Institute, and Korea’s KIST Functional Proteomics Center, among a dozen more — were chosen based on their willingness to install the CPAS system within their organizations, according to McIntosh.
McIntosh said the funders wanted to make sure that if, say, a $10,000 award went out that the recipients were putting in commensurate effort. “For example, the University of Texas was picked because of people’s willingness to install for a larger group of people,” he said. “If someone paints a house, they’re more invested in it.” 
Labkey sees this current partnership with Canary as a “nice win, and hopefully the beginning of an exciting adoption curve,” Hussey said.
 “We don’t have all our eggs in this basket, by any stretch. We see it as more of an opportunity to find some ongoing customers beyond this,” Hussey said. “These are relatively small contracts individually – small to medium contracts — and long term we would hope to establish our place as a development shop for Labkey applications, and as an incredibly useful platform.”

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