to keep paying attention, and keep asking hard questions about the progress Sage is making on its mission.
So when I spoke to Friend last week by phone, I asked him to list off two or three accomplishments Sage has made since the last Congress, and two or three items of unfinished business.
The first big accomplishment, he says, was in building a common computing platform known as Synapse. There has also been some progress to report on creating disease-specific consortiums for data sharing, including one announced this week to pool data for research into psychiatric disorders. Another key step came when Sage’s Jonathan Derry published “a coherent set of components and principles on working in an open space,” in the journal Nature Genetics.
At last year’s Congress, Sage didn’t really have a computing platform set up that researchers could efficiently dump data into and view it. There has been significant progress since then, with the Synapse system, according to Sage director John Wilbanks. “Synapse emerging from Sage (and thus from Merck/Rosetta) was not unlike Mozilla emerging from Netscape – a technology that had to be fundamentally turned around to be a public resource,” Wilbanks says. “And there’s remarkable work on doing collaborative computational science on the network that’s inside there, killer stuff around provenance tracking, group permissions, all the blocking and tackling you need to really work on big biological data with people in a distributed manner.”
Then there are the roadblocks. The first one Friend mentioned has occurred with the Sage Federation, in which the nonprofit agreed to get a handful of top biomedical researchers to agree to pool their experimental genomic data. Those scientists—including Atul Butte at Stanford University, Trey Ideker at UC San Diego, and Andrea Califano at Columbia University—agreed to join the Sage Federation, only to see legal adoption of the agreements at the various institutions take an additional six to 12 months. “Legal adoption has been slower than we thought,” Friend says.
The second speed bump came with what Friend calls the “non-responder” project in cancer, in which he has been trying to coax pharmaceutical companies to contribute detailed data from the control groups of big clinical trials. Friend, as a former pharmaceutical executive, figured this would be an innocuous way to get pharma companies to contribute some valuable data without divulging anything about proprietary compounds, but even so, he’s found it to be a hard sell. “It’s been very hard to identify individuals willing to fund those projects,” Friend says. “We’ve moved to other projects in fields like RA (rheumatoid arthritis), where there’s more interest in industry.”
The third item, which Sage hopes to present as a success story at this year’s Congress, is the development of a standardized patient consent form, in which patients grant researchers the right to analyze all kinds of genomic, proteomic and other data from their tissue samples, while protecting basic patient rights and privacy. Wilbanks, a director of Sage and a fellow at the Kauffman Foundation, has played a key role in this effort, which requires lots of careful, time-consuming legal and ethical review.
“Structurally, what we’re running is a clinical study that allows people to upload data that they already have about themselves into a technology that then syndicates the data into computational research environments like Sage’s Synapse,” Wilbanks says. “So we’ll show all the parameters, running software, and the consent form as submitted, but we won’t throw open the gates quite yet.” The consent system still needs to complete the review with the institutional review board that is the watchdog for patient safety and ethical concerns.
Sage clearly has a hard-core group of supporters—about 80 percent of the people who made videotaped commitments at last year’s event are coming back this year, Friend says. And there are some new groups getting interested that tend to have specific disease-related concerns, like a post-traumatic stress disorder research group called One Mind for Research, he says.
When asked if Sage is at the point where he thought it would be three years into a five-year plan, Friend said, “I do—I do feel it’s on track.” But a lot of what comes next will depend partly on what Sage does to clear the way, and what people in the biomedical research community choose to do with its platform. “Our mission is to develop flexible approaches that can be championed by others,” Friend says.
Wilbanks sees major progress in the growing number of champions for the cause. “The conversation around open biology is totally different than it was three years ago,” he says. “We started with hope, now we’re shipping code (both software and law) and people no longer think it’s an impossible dream. That’s not to say it’s going to be easy, but that sense of possibility is itself a real achievement.”
