We, along with the rest of the biotech world, were thrilled when the NIH announced recently the Accelerating Medicines Partnership (AMP).
AMP is a partnership between the NIH, 10 biopharmaceutical companies, and several non-profit organizations that builds on pioneering work done at Sage Bionetworks and the Structural Genomics Consortium on the Arch2POCM project (which is also driving novel cancer study models in Canada). AMP promises to “transform the model for developing new diagnostics and treatments by jointly identifying and validating promising biological targets of disease” – working collaboratively in the early phases, rather than individually.
AMP will begin with three to five year pilot projects in three disease areas:
- Alzheimer’s disease
- Type 2 diabetes
- Autoimmune disorders of rheumatoid arthritis and systemic lupus erythematosus (lupus)
And we couldn’t be happier to announce as part of the AMP-Alzheimers project, Sage Bionetworks will provide the data enablement for network analysis projects consisted of across-projects data integration and rapid sharing of data and analytical tools. We’re excited to see what our work in compute platforms, data governance, and patient engagement can do inside this promising and exciting new initiative. Stay tuned for more news!
Our president, Stephen Friend, joined a lively panel at the FasterCures 2013 conference earlier this month. The panel took on the question of failure in science, and its impacts on patients, during a session on “Learning to Love Failure,” moderated by Luke Timmerman, vice president of life sciences initiatives at Xconomy. Timmerman set the stage by saying that within “biomedical research, failure is the norm. But there is no culture talking about it.”
Dr Friend criticized the current scientific process as one that catalyzes failure because there is no way to learn from others. “Our understanding of disease is based on narrow or generalized knowledge. Just one finding is not enough.” He added that there needs to be a cultural change in science where scientific results are completely shared. “Good research shouldn’t have to always be a positive result. Negative results should also be reported.”
Watch the whole panel here:
We are pleased to announce the final results for the DREAM 8 Challenges. During the “Challenge season” that spanned June 10, 2013 to mid-September, 2013, Sage Bionetworks and DREAM ran three DREAM 8 Challenges linked below. More than 600 individuals signed up for the Challenges and in aggregate built and submitted >1000 predictive models across the three Challenges in a timespan of roughly three months. The top performing teams presented their winning models at the November 8, 2013 DREAM Conference.
Go check out the winners for each of the challenges:
HPN-DREAM Breast Cancer Network Inference Challenge, NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge, and the Whole-Cell Parameter Estimation DREAM Challenge.
We are also very very excited to announce three new DREAM 8.5 challenges. Best performers in all DREAM 8.5 Challenges will be invited to present at the 2014 DREAM conference (date and location to be determined) with travel expenses covered by the organizers. We are also working to establish publishing partners for each of these challenges. The DREAM 8.5 Challenges are now open for registration, and will begin active problem-solving in late 2013 or early 2014.
This round of challenges include the first Alzheimer’s Disease Big Data DREAM Challenge, the ICGC-TCGA-DREAM Somatic Mutation Calling Challenge, and the Rheumatoid Arthritis Responder Challenge.
Today’s an exciting day. On the heels of yesterday’s publication of the TCGA Pan-Cancer analysis – which proves how scientists can use collaborative tools in our Synapse platform to turn data into knowledge – we announce the launch of our BRIDGE project to connect communities of activated patients with the world’s scientists.
Three different communities of patients, in Fanconi Anemia, Type 2 Diabetes, and sleep disorder, have joined with us and the Robert Wood Johnson Foundation to build on open data, patient wisdom, and the Synapse platform to directly engage the public in biomedical research.
Until now, we have focused the majority of our resources on developing Synapse, a computational “geek’s sandbox” where open data can be aggregated and be used by researchers in real time (as in the TCGA papers and in our DREAM challenges). Now we begin building of the next piece of open infrastructure: a system that lets non-scientists add data, connect to each other, and interact directly with the results of the research in real time. Like all our tools, BRIDGE will be an open source project.
Four new reports issuing in Nature Genetics today highlight the benefits of making large biomedical research data sets open as a community resource – when those data sets are matched to open science software that facilitates rapid learning and future discovery.
The science in these papers emerged from the collaborative work of the Pan-Cancer project that Synapse enabled. It’s not easy to collaborate on this kind of complex data, across space and time. Synapse provided data versioning, provenance tracking, data annotation, query language, governance, group security, citation management, programmatic clients for R, Python, Java, and command line, rich descriptions, and evaluation queues (leaderboards) for the TCGA project. We’ve gone into detail on how Synapse drives open science and open collaboration forward in a Commentary in Nature Genetics published today as one of the four reports. 14 more papers from the collaboration are accepted and in press.
The papers report on the genetic profiles of 12 cancer types, describe the collaborative approach taken by The Cancer Genome Atlas (TCGA) Pan-Cancer Project researchers and highlight the new bioinformatics tools that Sage Bionetworks provided to the effort. TCGA includes 250 researchers spread across 30 institutions and running a total of 60 different research projects, all affiliated with the same set of nearly 2000 biomedical data files covering 12 different cancer types. For the duration of the Pan-Cancer project, TCGA members agreed to pilot Synapse, Sage Bionetworks’ software platform, for managing the myriad interdependencies of these projects and for facilitating the sharing and evolving of data and findings in real time.
Anyone can register to use Synapse on our servers, check out our developer documentation, and of course the code itself is available under an open source license at github for anyone who would like to run their own copy.
On Thursday, June 20th, the White House will honor Stephen Friend as one of thirteen Champions of Change who are promoting and using open scientific data and publications to accelerate progress and improve our world. At the event, these champs will highlight previous initiatives that help make “open” the default in scientific research.
Open sharing of research results is a proven strategy for driving positive change. For example, the rapid and open sharing of genomic data from the Human Genome Project revolutionized biomedical research, and spurred major growth in the biotechnology industry. Additionally, the Federal Government’s liberation of Global Positioning System (GPS) satellite data for use by the private sector led to an explosion of geospatial information systems and the creation of many companies, smartphone apps, and car navigation systems.
The White House Champions of Change program was created as part of President Obama’s Winning the Future initiative. Through this program, the White House highlights individuals, businesses, and organizations whose extraordinary stories and accomplishments positively impact our communities.
To watch this event live, visit www.whitehouse.gov/live at 1:00 pm ET on June 20th. To learn more about the White House Champions of Change program, visit www.whitehouse.gov/champions.
Sage Bionetworks and the DREAM Initiative are convinced that running open computational Challenges focused on important unsolved questions in systems biomedicine can help advance basic and translational science. By presenting the research community with well-formulated questions that usually involves complex data, we effectively enable the sharing and improvement of predictive models, accelerating many-fold the analysis of such data. The ultimate goal, beyond the competitive aspect of the Challenges, is to foster collaborations of like-minded researchers that together will find the solution of vexing problems that matter most to citizens and patients.
During the “Challenge season” spanning from May to September 2013 Sage Bionetworks and DREAM plan to run a series of Challenges – click here to find their high-level descriptions as well as information to start participating.
The Scientist chimes in with some fantastic coverage of the Sage-DREAM Breast Cancer Challenge.
Three of the better quotes follow, but it’s worth reading the whole thing!
Though teams from computational big hitters like IBM were early leaders, the winners were a small group from Columbia University’s School of Engineering led by electrical engineer turned computational biologist Dimitris Anastassio. Their model hinged on three gene signatures, previously identified by Anastassio’s research group to be associated with several cancers, that proved to be highly prognostic in breast cancer—so much so that their model predicts with 76 percent accuracy which of two breast cancer patients will live longer.
“Their solution was out-of-the-box,” said DREAM founder Gustavo Stolovitzky, who has overseen 24 open computational challenges over the last 6 years. “They were not prejudiced by the old way of doing things, by the same-old, same-old. This allowed them to take an approach that was completely novel and, as it turns out, the best solution.”
A testament to Friend’s belief that money is not driving participation, he and his colleagues did not offer a high-dollar bounty to the BCC winners. Rather, the prize was a publication in Science Translational Medicine—a reward that organizers refer to a “powerful intellectual currency,” Friend said. For the BCC, the journal’s editors scrapped the usual system of blind peer-review and instead selected reviewers to be embedded with the competition itself. The editors also helped develop criteria for determining the winning models; if these criteria were not met, there would have been no winner and no publication. Despite these stipulations, the publication-as-prize model was a ringing success, with the BCC attracting some 350 teams from 30 countries. And the winning team’s model met Science Translational Medicine’s criteria, earning itself a spot in the journal this past April.
The 4th, and last, Sage Commons Congress is in the books. We thank the more than 250 delegates who joined together in San Francisco for another remarkable set of meetings, conversations, workshops, and barn-raising.
Complete video archives of the Congress, including the Friday night sessions, are online at Fora.tv. Project descriptions, team members, and reports for the Over To You workshops are also online for review. Tweets from the Congress are viewable using the #sagecon hashtag and Andy Oram’s written up a lovely summary of the Congress on the Health Care Blog, where he asks why you should care about our work and the Congress:
Well, first, if you’re one of the 48% of Americans who took a prescription drug this month, you should be concerned about where new breakthrough drugs will emerge. If you visit this web site because you want a more responsive health care system that can match patients to treatments more quickly and cheaply, recognize that new methods are important nowhere as much as at the foundation of the system where new treatments are discovered. And if you are just curious about the potential for global cross-institutional teams and loose networks connecting experts with ordinary members of the public to find creative solutions to old problems, this article will provide insights.
Couldn’t have said it better ourselves.
We also ran a survey, in partnership with Traitwise, of attendees to see how the Congress stood up against its goals. It’s one of our 2013_Objectives to have the Congress exceed expectations. See the survey results for yourself and see how we did: SageCongress2013Results.
Thanks again, everyone. We’re looking forward to the next phase of the Congress – although it won’t be the Sage Commons Congress anymore, we’ll certainly stay deeply involved in making sure there is a Congress in 2014 and forward. See you next year in Boston.
Our work with the DREAM team on the Breast Cancer Challenge didn’t just make the cover of Science Translational Medicine last week, it generated a lot of mainstream press attention. While we’re working on a summary of the Sage Commons Congress that just wrapped up on Saturday, have a look at what the mainstream and scientific press is saying about our work.