Dialogue for Reverse Engineering Assessments and Methods
DREAM8 Challenges Are Open
We are pleased to announce that the DREAM8 Challenges are now open for participation. During the “Challenge season” spanning from June 10 to September 15, 2013, Sage Bionetworks and DREAM will run the following three Challenges:
1. HPN-DREAM Breast Cancer Network Inference Challenge – Infer the signaling networks in breast cancer cell lines
2. NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge – Predict individual response to environmental and pharmaceutical chemicals
3. The Whole-Cell Parameter Estimation DREAM Challenge – Infer the kinetic parameters underlying biological processes in whole cell models
To sign up for a Challenge, and access the data sets and descriptions of the DREAM8 Challenges, please go to https://www.synapse.org/#!Challenges:DREAM8.
As we have done for the past 5 years, DREAM joined forces with the RECOMB satellite conferences on Regulatory Genomics and Systems Biology to put together a great conference. Our joint conference, the RECOMB Regulatory Systems Genomics with DREAM challenges, is now an official International Society for Computational Biology (ISCB) Conference. The conference this year will be from Nov 8 to Nov 12 in Toronto.
DREAM7 Challenge Results
We are pleased to announce that the DREAM7 challenges have successfully come to a conclusion, and the submission results have been posted. We had a total of 123 teams submitting their predictions to the four DREAM7 challenges.
We congratulate the Best Performing Teams and all participants for making DREAM happen.
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 6
To view challenges of years before 2012 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)
DREAM 7 Organizers
- Erhan Bilal, IBM Computational Biology Center
- Thomas Cokelaer, European Bioinformatics Institute (EMBL-EBI)
- James Costello, Boston University
- Pablo Meyer, IBM Computational Biology Center
- Raquel Norel, IBM Computational Biology Center
- Robert Küffner, Ludwig-Maximilians-Universität München
- Julio Saez-Rodriguez, European Bioinformatics Institute (EMBL-EBI)
- Gustavo Stolovitzky, (chair) IBM Computational Biology Center
- 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