Dialogue for Reverse Engineering Assessments and Methods

 

DREAM6 (2011)

 

Gold Standard available for download

for all the 4 challenges.

Go to the end of the challenge

page (follow the link)

  



Important Note

You cannot publish the Gold Standard for Alternative Splicing Challenge without the explicit permission by Gustavo Stolovitzky (gustavo AT us.ibm.com) and Myke Snyder (michael.snyder AT yale.edu)

Overview

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.  

Thrusts

The DREAM project is composed of three interrelated thrusts.

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 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.
  • 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.
  • 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)

Organizers

  • Gustavo Stolovitzky, IBM Computational Biology Center
  • Robert Prill, IBM Computational Biology Center
  • Julio Saez-Rodriguez, European Bioinformatics Institute (EMBL-EBI)
  • Raquel Norel,  IBM Computational Biology Center
  • Pablo Meyer, IBM Computational Biology Center

DREAM Founders

If you would like to design a challenge, or donate unpublished data to be the basis of a challenge, please contact Gustavo Stolovitzky.

 

To view challenges of years before 2011, visit the older website here.

Steering Committee

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

Sponsors

  • Columbia University Center for Multiscale Analysis Genomic and Cellular Networks (MAGNet)
  • NIH Roadmap Initiative
  • IBM Computational Biology Center
  • The New York Academy of Sciences

 

The DREAM website has been set up and maintained with the support of  the External Services Team of the European Bioinformatics Institute