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.

Dialogue for Reverse Engineering Assessments and Methods

DREAM7 (2012)

We are currently preparing the challenges for DREAM 7. We plan to release the challenges in the spring 2012, with a deadline for submission end of the summer. We will hold our annual meeting where the challenges will be discussed in November 12-16 in San Francisco.

Planned challenges:

DREAM7 Estimation of Model Parameters Challenge - Inference of the kinetic parameters and structure of gene regulatory networks by iterative optimization and experimental design. This challenge will build upon the DREAM6 Estimation of Model Parameters challenge.
Expected date for challenge release: First sub challenge May 2012, and a second sub challenge end of June 2012.
Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge. We are preparing together with the non-profit organization SageBionetworks (http://sagebase.org/) a challenge about predicting time to recurrence in breast cancer patients.
Expected date for challenge release: May 2012.
The DREAM Phil Bowen ALS Prediction Prize4Life. In collaboration with Prize4Life (http://www.prize4life.org/), we will pose a challenge to predict the progression of ALS (amyotrophic lateral sclerosis, also known as Lou Gehrig's disease) in patients. Expected date for challenge release: Early July 2012.
A fourth challenge is likely to be posted soon - stay tuned!

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.

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:

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, 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

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.

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

Primary links