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Collaborative genetics, part 2: Five Easy Pieces, Sage's Federation

Previous installment:
The ambitious goals of Sage Commons Congress

A pilot project was launched by Sage with four university partners under the moniker of the Federation, which sounds like something out of a spy thriller (or Star Trek, which was honored in stock photos in the PowerPoint presentation about this topic). Hopefully, the only thrill will be that expressed by the participants. Three of them presented the results of their research into aspects of aging and disease at the Congress.

The ultimate goal of the Federation is to bring together labs from different places to act like a single lab. Its current operation is more modest. As a pilot, the Federation received no independent funding. Each institution agreed simply to allow their researchers to collaborate with the other four institutions. Atul Butte of Stanford reported that the lack of explicit funding probably limited collaboration. In particular, the senior staff on each project did very little communication because their attention was always drawn to other tasks demanded by their institutions, such as writing grant proposals. Junior faculty did most of the actual collaboration.

As one audience member pointed out, “passion doesn’t scale.” But funding will change the Federation as well, skewing it toward whatever gets rewarded.

[Photo of audience and podium]

Audience and podium at Sage Commons Congress

When the Federation grows, the question it faces is whether to incorporate more institutions in a single entity under Sage’s benign tutelage or to spawn new Federations that co-exist in their own loose federation. But the issue of motivations and rewards has to be tackled.

Another organization launched by Sage is Arch2POCM, whose name requires a bit of elucidation. The “Arch” refers to “archipelago” as a metaphor for a loose association among collaborating organizations. POCM stands for Proof of Clinical Mechanism. The founders of Arch2POCM believe that if the trials leading to POCM (or the more familiar proof of concept, POC) were done by public/private partnerships free of intellectual property rights, companies could benefit from reduced redundancy while still finding plenty of opportunities to file patents on their proprietary variants.

Arch2POCM, which held its own summit with a range of stakeholders in conjunction with the larger Congress, seeks to establish shared, patent-free research on a firm financial basis, putting organizational processes in place to reward scientists for producing data and research that go into the commons. Arch2POCM’s reach is ambitious: to find new biological markers (substances or techniques for tracking what happens in genes), and even the compounds (core components of effective drugs) that treat diseases.

The pay-off for a successful Arch2POCM project is enticing. Not only could drugs be developed much more cheaply and quickly, but we might learn more about the precise ways they affect patients so that we can save patients from taking drugs that are ineffective in their individual cases, and eliminate adverse effects. To get there, incentives once again come to the fore. A related platform called Synapse hosts the data models, providing a place to pick targets and host the clinical data produced by the open-access clinical trials.

This posting is one of a five-part series. Next installment: Dividing the pie, from research to patents.

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  • http://www.selican.com Jack H. Pincus

    The Federation concept is interesting and mirrors some of the European Framework Programmes such as the Innovative Medicines Initiative. It would be interesting to hear the lessons learned form the pilot project. It would also be interesting to know how they managed communication, coordination, and data sharing in a multisite project with multiple teams.

  • http://www.sagebase.org Justin Guinney

    Jack, I am working on one of the Federation projects and can share some of the lessons learned. One important lesson was to make sure project workflows were done in parallel; sequential workflows can slow project momentum considerably. Regular, active engagement is another important factor. We have bi-weekly calls at the latest, and utilize different communication strategies including skype, whiteboard sharing technologies, and of course conference lines. Technology is critical to enable data and results sharing: this include source repositories for code sharing, and wikis for project coordination. We also use a technology called S-weave, which combines our computational analyses and project narrative into a single document. This assists with analytical transparency, and is also great for scientific reproducibility when it comes time to publish.