Click here to join the DREAM Challenges.

Challenges engage wider, diverse communities to competitively solve a specific problem in a given time period. The concept fosters collaboration between scientists through shared data and approaches.

The past two decades have seen an amazing growth in the ability to generate genomic data. However, with a few exceptions, acquisition of this type of data has so far failed to generate significant improvements in the treatment of human diseases. The Challenge concept engages the statistical, machine learning and computational biology communities to improve the analysis of clinical genomics data and fosters collaboration between scientists though shared data and approaches.

Started in 2006 by IBM Research’s Dr. Gustavo Stolovitzky, the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project consists of a distributed community of computational biologists who have been collaborating to run open DREAM Challenges every year: these Challenges engage diverse communities of scientists to competitively solve a specific problem in biomedicine in a given time period. In the past 7 years, DREAM has run 27 successful Challenges in systems biology, published over 60 DREAM Challenge-related papers, and aggregated a “crowd” of thousands of “DREAMERs.”

In 2013, Sage Bionetworks joined with the DREAM community to co-lead a new generation of Challenges that leverage collaborative data hosting and analysis tools available on Synapse (www.synapse.org), Sage Bionetworks’ open bioinformatics compute space. Running on Synapse, the last 6 DREAM Challenges made use of engaging features such as real-time Challenge leaderboards that score participants’ predictions and immediately report the result. In the first three month season of running Challenges together, DREAM and Sage Bionetworks were delighted to see the level of participation nearly double: Synapse’s Challenge leaderboards allowed participants to submit more than 2,000 predictions for scoring and to evolve their models throughout the competition period.

June 2,2014: Sage Bionetworks and DREAM Announce the opening of the 9th Season of DREAM Challenges

Working with partners at the Broad Institute, MD Anderson Cancer Center, Rice University and the Global CEO Initiative for Alzheimer’s Disease, DREAM and Sage Bionetworks today opened three computational Challenges, leveraging big data in cancer and Alzheimer’s Disease. These Challenges will run until mid-September and are expected to attract the participation of hundreds of scientific teams.

The Alzheimer’s Disease Big Data DREAM Challenge #1
• Originally announced at the White House on June 20, 2013 (http://www.whitehouse.gov/blog/2013/06/20/big-data-and-personalized-medicine). Running as a delayed DREAM8.5 Challenge.
• Data provided by Alzheimer’s Disease Neuroimaging Initiative (ADNI), Rush University Medical Center, and The AddNeuroMed Study.
• Funders: Alzheimer’s Research UK, Bright Focus Foundation, Pfizer Inc, the Ray and Dagmar Dolby Family Fund, the Rosenberg Alzheimer’s Project, Sanofi, Takeda.
• Sponsor: European Medicines Agency.
• Computational resources donated by IBM.
• Publishing partners: Nature Neuroscience.
• Challenge Focus: Predict the best biomarkers for early AD-related cognitive decline and for the mismatch between high amyloid levels and cognitive decline.
• Best performers will be invited to present their results at the International Biomedical Commons Congress, to be held in Paris in April 2015.

The Broad-DREAM Gene Essentiality Prediction Challenge
• Data provided by the Broad Institute.
• Data Funding: NCI Cancer Target Discovery and Development (CTD2), Instituto Carlos Slim de la Salud (ICSS), EMD Serono, NCI Integrative Cancer Biology Program (ICBP), Eli Lilly and Company, Novartis and Pfizer.
• Challenge Funding: NCI CTD2 and ICBP.
• Computational resources donated by IBM.
• Challenge Focus: Develop predictive models that can infer levels of gene dependencies (i.e. how essential each gene is to a cancer cell’s survival when suppressed), using features of the cell lines. (see Broad Institute blog about the Challenge)
• Best performers will be invited to present their results at the DREAM track of the RECOMB/ISCB Systems and Regulatory Genomics/DREAM Conference, to be held in San Diego, California November 10-14, 2014.

• The DREAM9 Acute Myeloid Leukemia (AML) Outcome Prediction Challenge (https://www.synapse.org/#!Synapse:syn2455683):
• Data provided by the MD Anderson Cancer Center.
• Funders: Integrated Cancer Biology Program (ICBP) and Rice University.
• Challenge Focus: Predict the outcome of treatment of AML patients (resistant or remission), their remission duration and overall survival based on clinical cytogentics, known genetics markers and phosphoproteomic data.
• Publishing partner: PLoS Computational Biology.
• Best performers will be invited to present their results at the DREAM track of the RECOMB/ISCB Systems and Regulatory Genomics/DREAM Conference, to be held in San Diego, California November 10-14, 2014.

The AD#1 Challenge is the first in what DREAM and Sage Bionetworks envision as a series of Grand Challenges that disrupt the “business as usual” approach to research with innovative Big Data techniques. Remarks George Vradenburg, Convener of The Global CEO Initiative on Alzheimer’s Disease, “There is high expectation internationally for the prospects of using Big Data to accelerate discovery and drug development in the Alzheimer’s space. This is an exciting, first-of-its-kind global Challenge using open science techniques and big data processes to advance Alzheimer’s discovery. The CEOi is pressing the edge of innovative science to accelerate Alzheimer’s discovery and to achieve our national goal of preventing this disease by 2025.”

The Broad-DREAM Gene Essentiality Prediction Challenge seeks to broaden the impact of targeted cancer therapy by identifying drug targets as well as new biomarkers that can be used to identify patient populations likely to respond to a particular therapy. William Hahn, a senior associate member at the Broad Institute and an associate professor of medicine at the Dana-Farber Cancer Institute and Harvard Medical School, says “We are excited to be a part of the DREAM competition. The next frontier of understanding cancer vulnerabilities will be shaped by predictive modeling and we look forward to the potential impact winning models will have”.

With only 25% of people diagnosed with AML surviving beyond 5 years, there is a high level of urgency to find better treatments. The DREAM9 Acute Myeloid Leukemia (AML) Outcome Prediction Challenge is designed to identify potential new drug targets as well as predictive clinical models that surpass current standards. Remarked Professor Steven Kornblau, from the Department of Leukemia at the MD Anderson Cancer Center, “It’s very exciting to have my dataset selected for use in the DREAM competition. My goal has been to use proteomic information to improve patient outcomes by enabling us to match the right therapy to the right patient. I hope that the collective minds that work on this project help us to achieve this goal.”

Ongoing DREAM8.5 Challenges

ICGC-TCGA-DREAM Somatic Mutation Calling Challenge
• Opened November 8, 2013, final submissions deadline August 16, 2014.
• Challenge Focus: Predict cancer-associated mutations from whole-genome sequencing data.

The Rheumatoid Arthritis Responder Challenge:
• Opened February 10, 2014, final submissions deadline June 4, 2014.
• Challenge Focus: Predict which Rheumatoid Arthritis patients will not respond to anti-TNF therapy.
To sign up for a Challenge and access the data sets and descriptions of the DREAM8.5 and DREAM9 Challenges, please go to: https://www.synapse.org/#!Challenges:DREAM


Find out more about DREAM.