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“The way biomedical research is carried out is changing fundamentally,” Sage Bionetworks President Stephen Friend declared at the beginning of a webinar about the crowdsourced computational challenges Sage is facilitating in partnership with the DREAM (Dialogue for Reverse Engineering Assessment and Methods) project that originated at IBM. Friend laid out five opportunities he believes are giving rise to new ways to generate, analyze, and support new research models:

- It’s now possible to generate massive amounts of human “omic’s” data.
- Network modeling approaches for diseases are emerging.
- Information technology infrastructure and cloud computing capacity allow an open approach to biomedical problem solving.
- There’s an emerging movement for patients to control their own sensitive information, allowing sharing.
- Open social media allows citizens and experts to use gaming to solve problems.

“The usual rule of anointed experts being the only ones who can solve problems has really been shattered,” said Friend.

For several years, Sage has been grappling with how to bring about a better understanding of the complexity of biology, given these trends. One initiative central to their efforts has been the creation of a technology platform for data sharing and analysis called Synapse, built on the model of “github” from the open-source software world, which allows distributed projects to get done and provides the foundation for running the DREAM Challenges.

Friend noted that computational biology has been driven by crowdsourcing for a long time, and challenges like those that DREAM has been running for many years have been integral to its successes. There are increasingly large and powerful sets of data in the public domain, and putting them out for many people to look at (some of them from outside the field of biology) and make predictions and unbiased evaluations based on the data is critical to solving complex problems in biology in this day and age. Data is getting so complex that it’s impossible for any single researcher or institution to analyze it effectively. As John Wilbanks, Sage’s Chief Commons Officer and a FasterCures Senior Fellow, noted, “One of the hardest things to do in the emerging Big Data world is to get your data analyzed.”

An important aim of these challenges is to foster a new culture in research. As Friend argues, “We have a serious need not just to solve specific problems, but … to build communities so that people begin to think of each other as colleagues and collaborators.” DREAM Challenges are carefully constructed to provide opportunities for publications in journals and for other forms of recognition that are important to researchers, often more important than the promise of a monetary prize.

First of the four past challenges run by Sage and DREAM (along with partners from academia, industry, government, and patient groups) was the Breast Cancer Prognosis Challenge, created to forge a computational model that accurately predicts breast cancer survival. The winning team was from the academic lab that invented the MP3 format for digital audio, bringing their expertise in data compression to the task. Hundreds of teams comprised of thousands of individuals have participated, and a number of publications have resulted, along with other opportunities for professional advancement for “solvers.”

Challenges currently open include:

- The Somatic Mutation Calling Challenge, to predict cancer-associated mutations from whole-genomic sequencing data;
- The Rheumatoid Arthritis Responder Challenge (in partnership with the Arthritis Foundation, among others), to predict which patients will not respond to anti-TNF therapy – a clinical trial could follow if a powerful classifier emerges from the Challenge for validation; and
- The Alzheimer’s Disease Big Data Challenge, which seeks to predict early AD-related cognitive decline and the mismatch between high amyloid levels and cognitive decline. Massive amounts of data in the public domain has been aggregated, collated, massaged and curated for the task.

Two more are set to open this summer, in partnership with the Broad Institute and MD Anderson Cancer Center, and several more are being considered for launch by the end of 2014. All stakeholders – including and perhaps especially patient groups – are invited to participate by proposing ideas for challenges, contributing data, recruiting teams to participate. The Sage-DREAM Challenges are looking for partners who want not only to find the answers to tough questions in their fields, but who want to help create the conditions for the real collaboration necessary to bring about “the next generation of biomedical research.”

For more information on how to get involved with an open DREAM Challenge, click here.

View webinar slides and recording

(Cross posted from http://fastercures.tumblr.com/post/81603549119/crowdsourcing-data-challenges-to-speed-the-search-for and written by Gillian Parrish)

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Sage Bionetworks CEO spoke from the main stage yesterday at TED 2014 in Vancouver. He announced the Resilience Project, a new collaboration between us and Mt Sinai that is looking for healthy individuals who carry genetic mutations that should have made them ill as children.

The project is searching for rare genetic mutations that should have cause catastrophic illness. Somehow certain individuals are “resilient” – they have been protected via genetic or environmental factors. Our calculations indicate that 1 in 15,000 people is resilient in some form. It’s simply been too expensive to find them until now.

Thanks to incredible support from 23andme, Children’s Hospital of Philadelphia, Lund University, and the Beijing Genomics Institute, we’ve already begun profiling hundreds of thousands of individual samples and re-analyzing data sets. Candidates for resilience are already emerging from that analysis.

In the coming weeks, we’ll open the project for large-scale public enrollment with electronic consent and more. Sign up to be notified when we launch at resilienceproject.me.

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John Wilbanks, our Chief Commons Officer, was recently part of the NPR TED Radio Hour talking about the biomedical research commons we are building here at Sage Bionetworks.

The show was based around the idea of the “End of Privacy” – featuring experts in security, open government, and more. Wilbanks’ piece features his TED Talk and explores whether the desire to protect privacy is slowing research, and if opening up medical data could create a wave of health care innovation.

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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!

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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:

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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.

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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.

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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.

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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.

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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.