SEATTLE–(BUSINESS WIRE)–The White House hosted an Open Science Champions of Change event on June 20 and honored Dr. Stephen Friend of Sage Bionetworks (www.sagebase.org) for Sage’s vanguard work building open biomedical data systems and organizing Big Data Health projects that spur citizens and researchers to share and develop ideas in real time, leading to spectacular examples of how to harness the power of many minds to accelerate scientific progress.
United States Chief Technology Officer, Todd Park, presided over the event and applauded Friend’s contributions to Open Science as well as the two Big Data Challenge projects that Friend announced to crowdsource important questions for arthritis and Alzheimer’s disease research. “These Challenges that Friend and Sage Bionetworks announced here today are truly awesome examples of what we at the White House want to highlight. It’s these types of open efforts that will help grow our economy and improve our world.”
“At the core of Sage Bionetworks is the idea of building a precompetitive commons where citizens and researchers can come, interact, give and take basic research and build on one another’s insights,” said Dr. Friend. “It’s a novel combination of two existing concepts. The first is the Commons, a community where information is shared in order to achieve greater social benefits. The second is a precompetitive space – the idea that there is a basic research foundation that informs all effort to improve the health of people and families.”
An Information Commons to accelerate medical progress
Dr. Friend co-founded Sage Bionetworks in 2009 out of the belief that biomedical research will be more successful and affordable if conducted from a layer of data and models within an open “information commons” that individuals and teams can access to make better, faster and more relevant discoveries.
Synapse (www.synapse.org) is Sage Bionetworks’ open compute platform and represents the type of open data system that can fuel a biomedical information commons where transformational new community efforts can run. Friend refers to Synapse as a “sandbox for geeks:” it is built to meet the needs of data scientists by providing an open, well-governed repository of analysis-ready data that scientific teams can work on in an open, online form that is accessible to all through a collaborative web portal equipped with engaging social media tools.
With the Synapse platform in place, Sage Bionetworks has initiated partnerships with innovative groups such as DREAM (http://www.the-dream-project.org/) to apply the tools of open science to solve big problems in health.
What Participation in an Information Commons Might Look Like
In 2012, Sage Bionetworks demonstrated the types of democratized projects that an open compute platform like Synapse enables. Partnering with DREAM (http://www.the-dream-project.org/), a visionary distributed systems biology group that has run 24 successful open computational challenges over the last five years, Sage Bionetworks ran the Breast Cancer Prognosis Challenge (BCC). The BCC invited citizens and scientists alike to try their hand at building a computational model that would accurately predict breast cancer survival: the Challenge ended up attracting 350 participants from more than 35 countries who submitted a total of 1,700 models over a three-month period of time. Remarked DREAM co-founder Gustavo Stolovitzky, “By running the BCC off of Synapse, we were able to engage our Challenge players in exciting new ways that increased the level of participation. Synapse made it possible to share breast cancer patient data with anyone who wanted to compete and to run a real-time leaderboard where participants could track their own progress and access the model code of others to forge new models.”
Friend and Stolovitzky recognized that the most powerful incentive to gather a crowd of data scientists might be scientific publication instead of cash, and they worked with the editors of the journal Science Translational Medicine to position an invited publication on the winning model as the Challenge’s top prize.
Based on the success of the BCC, Sage Bionetworks and DREAM merged earlier this year to run open science computational Challenges that foster the broader collaboration of the research community and that provide a meaningful impact to both discovery and clinical research. DREAM’s 8th season of Challenges started earlier this month with the launch of three DREAM8 Challenges that are open for participation through September 15, 2013 (https://www.synapse.org/#!Challenges:DREAM8). Quips Stolovitzky, “These are three great Challenges tackling important questions in breast cancer, environmental toxicology and basic biology. We really hope that Challenge participants will use Synapse’s leaderboards, code-sharing and provenance tools to start a real-time dialog that fosters rapid learning and better predictive models: Sage Bionetworks and DREAM will help get the ball rolling by sprinkling in a few fun rewards.”
Sage Bionetworks Announces Grand Challenges In Rheumatoid Arthritis and Alzheimer’s Disease
Dr. Friend also announced two further open science Challenges that Sage Bionetworks and DREAM have planned to improve scientists’ understanding of two debilitating diseases affecting our society: rheumatoid arthritis and Alzheimer’s disease. Accompanied by key leaders from the arthritis and Alzheimer’s communities, Friend referred to these as Grand Challenges “…that are already engaging diverse groups eager to leverage DREAM Challenges to advance biomedical research and solve problems that matter most for patients. We fully expect that these Challenges will generate winning models that then inform the design of new clinical trials or that spell out the patient data we most need to help improve treatment options for arthritis and Alzheimer’s disease.”
The Rheumatoid Arthritis Responder Challenge
“This Challenge represents a unique interaction among an international team of researchers from academics and industry who share a common goal: improve the lives of patients with a debilitating form of arthritis,” said Director of Genetics & Genomics at Brigham & Women’s Hospital Dr. Robert Plenge, who is also a leading organizer of the Rheumatoid Arthritis Responder Challenge. “For people with RA, strong immunosuppressive medications are administered in order to treat pain and inflammation; unfortunately the medication only works for 30% of patients and we don’t know why. We want to run this Challenge to make complex genetic and genomic patient data available and ask the crowd of Challenge participants to generate predictive models that will help doctors know which patients are most likely to respond to treatment.”
Indeed, the Rheumatoid Arthritis Responder Challenge has already received scientific support and funding from the Arthritis Foundation, the Consortium of Rheumatology Researchers of North America, Inc. (CORRONA), Merck, Novo Nordisk and likely additional pharmaceutical companies.
Accompanied by leaders from arthritis research and the Arthritis Foundation, Friend described the Rheumatoid Arthritis Responder Challenge as starting later this year and announced that the Challenge’s “winner” will get to see their winning classifier potentially drive a prospective clinical trial with an already existing registry of RA patients (the Arthritis Internet Registry).
“Innovative research collaborations like this are crucial to help answer key biologic questions as we work toward a goal of personalized medicine for rheumatoid arthritis,” said Arthritis Foundation Vice President of Research, John Vernachio, Ph.D. “We are excited about gaining genetic insight from the Rheumatoid Arthritis Responder Challenge and applying the findings to citizen scientists enrolled in the Arthritis Internet Registry.”
The Alzheimer’s Disease Big Data Challenge
With 5 million Americans and almost 40 million people worldwide currently afflicted with Alzheimer’s disease, the Global CEO Initiative on Alzheimer’s Disease (http://www.ceoalzheimersinitiative.org/) is joining with Sage Bionetworks/DREAM to co-lead this Challenge. The first partner for the Challenge is the national Alzheimer’s Association. The goal of this Challenge will be to respond to science and industry demands for accurate predictors of Alzheimer’s risk in pre-clinical populations. Dr. Robert C. Green of Brigham and Women’s Hospital and Harvard Medical School is co-chairing the scientific advisory board for this effort and remarked: “We hope that this first Big Data Challenge on Alzheimer’s disease will be part of a global approach to identify faster and more accurate predictive models to guide science and industry toward more effective treatment strategies.”
For the first Alzheimer’s disease Big Data Challenge, Sage Bionetworks/DREAM will utilize data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI, www.adni-info.org), already a leader in sharing data. The ADNI dataset consists of cognitive, imaging, biochemical, and whole genome sequencing data on cohorts of volunteers, who are cognitively normal, have mild cognitive impairment and have Alzheimer’s disease. The winning predictive model from the Challenge will be determined by evaluation against a similarly structured validation data set that is either newly generated for the Challenge or not yet released. The winning team will be featured as lead authors in a Challenge article in a prominent journal, to be announced.
Stated George Vradenburg, Convener of The Global CEO Initiative on Alzheimer’s Disease, “It’s time to disrupt ‘business-as-usual’ with innovative ‘big data’ techniques. And there is no more pressing a challenge on which to try this innovation than finding the best mix of predictors for Alzheimer’s. We are co-leading this Challenge to bring innovative approaches to the bedeviling challenges of Alzheimer’s.”
Excited by the impact of an Alzheimer’s Challenge, Friend reflected, “A DREAM Challenge for Alzheimer’s disease based on this ADNI cohort provides a unique opportunity to promote open science in the study of this terrible disease, and an opportunity for an even larger community to collectively develop an understanding in the integration of these complex data types. By engaging a diverse community of Challenge participants and letting them learn how to build predictive models driven by a variety of complex data, we set the stage for running Alzheimer’s Disease Challenges #2, #3 and so on.”
Dr. Michael Weiner, ADNI’s Principal Investigator, confirmed, “This innovative proposal by Stephen Friend at Sage Bionetworks to launch a Challenge using ADNI and other data from the Alzheimer’s field is expected to lead to new discoveries that will accelerate diagnosis and effective treatments and preventions of this terrible disorder which affects millions.”
Added Maria Carrillo, vice-president for medical and scientific relations of the national Alzheimer’s Association: “As a global leader in Alzheimer’s research, the Alzheimer’s Association applauds Sage Bionetworks’ recognition of the critical need for Alzheimer’s research and investigation of big data. We look forward to promoting the availability of this project to our broad and diverse international research community.”
Friend envisions a world where open science is flourishing and helping to afford individualized maps of disease and wellness to an engaged citizenry. In keeping with this vision, John Wilbanks, Chief Commons Officer at Sage Bionetworks and leading the organization’s groundbreaking work with online, patient-centered informed consent, was also chosen by the White House as one of only twelve open science leaders to present a scientific poster in affiliation with today’s Open Science Champions of Change event. Certainly Friend’s efforts at Sage Bionetworks, with DREAM and the early adopters of open science in arthritis, Alzheimer’s disease and other disease communities are leading us all in that direction and reflect what it means to be an Open Science Champion of Change.