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GEN News Highlights : Feb 19, 2013
Sage Bionetworks Achieves DREAM of Collaborative Science
Sage Bionetworks will merge its efforts with the DREAM Project to run open science computational challenges to encourage broader collaboration within the research community. This partnership will pair Sage Bionetworks’ Synapse, an open compute platform that allows data to be shared and worked on collaboratively, with the DREAM Project’s experience from running 24 computational challenges over the last five years.
According to Sage Bionetworks and DREAM, the open computational challenges represent an innovative new method to rapidly share and evolve predictive disease models that would otherwise take years to produce using the usual siloed research paradigms.
“The traditional ways of doing science has researchers too focused on being the first to publish,” said Dr. Gustavo Stolovitzky, founder of the DREAM Project. “This has given rise to a culture of secrecy about scientific results and data. By refocusing our efforts on creating a collaborative research environment, we at DREAM and Sage Bionetworks can foster a complementary way of doing science, which will accelerate the pace of discovery with the goal of contributing to a faster reduction of suffering due to disease. This seems to me like an ethical imperative.”
Sage Bionetworks and DREAM’s merger builds off their recent 2012 Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge that, for the first time, allowed participants to share code in the context of a computational biology challenge. Participating teams were asked to submit their computational model to Synapse as open source code made viewable to all participants. Their models were assessed against a hidden dataset and their scores were reported on a real-time leaderboard. The combination of immediate feedback and code sharing allowed participants to improve their leaderboard ranking by adjusting their own models or by borrowing the code of others to forge new models.
Synapse is built to meet the needs of the data scientists that participate in DREAM’s challenges. It provides a repository of analysis-ready data that scientific teams can work on in an open, online form accessible through a collaborative web portal.
“With the growing affordability of genomic data and wide availability of cloud-based computing, we know it is timely for us to join our efforts to scale and dream beyond the great things that DREAM has already enabled,” Dr. Stephen Friend, president and founder of Sage Bionetworks. “We want to evolve challenges so that solutions from the last phase become the starting point for a new step towards meaningful validation, and where newly created datasets might allow the answering of important clinical questions. These are the approaches that will bring about the promises of Precision Medicine.”
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