Please visit the new site http://the-dream-project.org.
Dialogue for Reverse Engineering Assessments and Methods
DREAM is a Dialogue for Reverse Engineering Assessments and Methods. The main objective is to catalyze the interaction between experiment and theory in the area of cellular network inference and quantitative model building in systems biology. The fundamental questions for DREAM are simple: How can we assess how well we are describing the networks of interacting molecules that underlie biological systems? and How can we know how well we are predicting the outcome of previously unseen experiments from our models? The answer to these questions are not so simple. 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 eveluated the success success of their methodologies using diverse non-standardized metrics. However what is still needed, and what DREAM aims to achieve, is a fair comparison of the strengths and weaknesses of the 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 Reverse-Engineering Challenges
- An online venue to Discuss reverse-engineering topics and curate Data, Literature, and Reverse-Engineering Methods.
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:
- DREAM3 (2008): Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, 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
- Robert Prill, IBM Computational Biology Center
- Julio Saez Rodriguez, Harvard/MIT
If you would like to design a challenge, or donate unpublished data to be the basis of a challenge, please contact Gustavo Stolovitzky.
Alexander Hartemink, Andre Levchenko, Benno Schwikowski, Diego Di Bernardo, Eran Segal, Fritz Roth, Hamid Bulouri, Harmen Bussemaker, Jim Collins, Joel Bader, John Moult, Marc Vidal, Mark Gerstein, Mike Snyder, Mike Yaffee, Pedro Mendes, Ron Shamir, Tim Gardner, Trey Ideker
- Columbia University Center for Multiscale Analysis Genomic and Cellular Networks (MAGNet)
- NIH Roadmap Initiative
- IBM Computational Biology Center
- The New York Academy of Sciences