Dialogue for Reverse Engineering Assessments and Methods
The DREAM8.5 Challenges are now open:
- The Alzheimer’s Disease (AD) Big Data DREAM Challenge #1: Predict the best biomarkers for early AD-related cognitive decline, and the mismatch between high amyloid levels and cognitive decline. Open for registration.
- The ICGC-TCGA DREAM Somatic Mutation Calling Challenge: Predict cancer-associated mutations from whole-genome sequencing data. Open for participation.
- The Rheumatoid Arthritis Responder Challenge: Predict which patients will not respond to anti-TNF therapy. Open for registration.
Our DREAM8.5 Challenges, opening here at the tail end of DREAM8, respond to the shared mission that both DREAM and Sage Bionetworks have of using Challenges to accelerate the solutions to problems that matter to patients. The DREAM8.5 Challenges tackle important questions related to cancer, rheumatoid arthritis and Alzheimer’s Disease. The traditional DREAM schedule of three-month long Challenges opening in the spring and completing in the fall seems insufficient to process the massive amount of data being generated in different disease areas that can be used in translational research. Help us journey forward as we strive to maintain DREAM’s high level of excellence in systems biology while also welcoming new DREAMers to help us innovate and extend the wisdom of the crowds into new arenas of human health.
The 8.5 "Challenge season" has started and will wrap up in early Summer, 2014. Best performers from the 8.5 Challenges will be invited to co-author a Challenge-specific paper for submission to a scientific journal and to present their winning Challenge model at the 2014 DREAM conference (date and location to be determined).
To register for a Challenge, read details and get started, please go to https://www.synapse.org/#!Challenges:DREAM8.5
Announcing the final results of the 2013 DREAM8 Challenges
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 the three DREAM8 Challenges described 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.
DREAM (Dialogue for Reverse Engineering Assessments and Methods) poses fundamental questions about systems biology, and invites participants to propose solutions. The main objective is to catalyze the interaction between theory and experiment, specifically in the area of cellular network inference and quantitative model building. DREAM challenges address how we can assess the quality of our descriptions of networks that underlie biological systems, and of our predictions of the outcomes of novel experiments. These are not simple questions. Researchers have used a variety of algorithms to deduce the structure of biological networks and/or to predict the outcome of perturbations to their systems. They have also evaluated the success of their methodologies using a diverse set of non-standardised metrics. What is still needed, and what DREAM aims to achieve, is a fair comparison of the strengths and weaknesses of these methods and a clear sense of the reliability of the models that researchers create.
The DREAM project is composed of three interrelated thrusts.
- The organization of periodic Conferences
- The organization of Systems Biology Challenges
- An online forum for the Discussion of systems biology topics around model building, and computational biology methods.
DREAM 2 through 8
To view challenges of years before 2013 please please click in the Challenges tab.
How to cite DREAM
If you use a DREAM data set in your publication, please cite both the main DREAM publication for the Conference and the publication of the data producer, which you can find in the Challenges section of this web site.
The main DREAM publications are:
- on a DREAM5 (2010) challenge:Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, The DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G., Wisdom of crowds for robust gene network inference, Nature Methods, 2012, in press.Advanced online publication, 15 July 2012.
- on a DREAM4 (2009) challenge:Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G., Crowdsourcing Network Inference: The DREAM4 Predictive Signaling Network Challenge,Science Signaling 2011 Sep 6;4(189):mr7.
on a DREAM3 (2008) challenge: Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G., Revealing strengths and weaknesses of methods for gene network inference, Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6286-91.
- DREAM3 (2008): Prill RJ, Marbach D, Saez-Rodriguez J, SorgerPK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, and Stolovitzky G. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One, 5(2):e9202, 2010. [ Read at PLoS ONE ]
- DREAM2 (2007): Stolovitzky G, Prill RJ, Califano A. "Lessons from the DREAM2 Challenges", in Stolovitzky G, Kahlem P, Califano A, Eds, Annals of the New York Academy of Sciences, 1158:159-95 (2009)
- DREAM1 (2006): Stolovitzky G, Monroe D, Califano A. "Dialogue on Reverse-Engineering Assessment and Methods: The DREAM of High-Throughput Pathway Inference", in Stolovitzky G and Califano A, Eds, Annals of the New York Academy of Sciences, 1115:11-22 (2007)
- Gustavo Stolovitzky, IBM Computational Biology Center
- Andrea Califano, Columbia University
If you would like to design a challenge, or donate unpublished data to be the basis of a challenge, please contact Gustavo Stolovitzky.
- Columbia University Center for Multiscale Analysis Genomic and Cellular Networks (MAGNet)
- NIH Roadmap Initiative
- IBM Computational Biology Center
- The New York Academy of Sciences