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SYS-CON MEDIA Authors: Esmeralda Swartz, Andy Jonak, Carmen Gonzalez, John Wetherill, Lori MacVittie

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DREAM and Sage Bionetworks Open Three Big Data Challenges to Impact Biomedical and Clinical Research

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 (https://www.synapse.org/#!Challenges:DREAM), 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.

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.

States DREAM Founder Dr. Gustavo Stolovitzky, “It is really gratifying to be opening the 9th season of DREAM Challenges where we will focus on important questions in cancer and Alzheimer’s Disease. Each year I grow more convinced that with DREAM Challenges, we’ve really hit upon a powerful approach for accelerating research. The combination of hosting exciting data sets and posing impactful Challenge questions that can be objectively evaluated makes DREAM Challenges a powerful catalyst for building new communities of experts that keep working together even after a Challenge closes.”

Anyone can sign up for the three DREAM Challenges that opened today (signup is open at https://www.synapse.org/#!Challenges:DREAM) and will close in the fall. Challenge winners will be announced in early October. Key information about each of the Challenges is provided below:

  • The Alzheimer’s Disease Big Data DREAM Challenge #1 (https://www.synapse.org/#!Synapse:syn2290704):
    • 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 partner: 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 (https://www.synapse.org/Portal.html#!Synapse:syn2384331/wiki/):
    • 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, ICBP and Washington State Life Sciences Discovery Fund (LSDF).
    • 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: www.broadinstitute.org/node/5775)
    • 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: NCI Integrated Cancer Biology Program (ICBP), Washington State Life Sciences Discovery Fund (LSDF) 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 cytogenetics, 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. Remarks 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.”

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

ABOUT THE DREAM PROJECT

The Dialogue on Reverse Engineering Assessment and Methods Project (DREAM Project), founded in 2006 by Andrea Califano (Columbia University) and Gustavo Stolovitzky (IBM), was originally conceived as an initiative to advance the nascent field of network biology through the organization of Challenges on network reconstruction and pathway inference. Since the first set of network inference challenges of 2007 (DREAM2) the concept of using collaborative-competitions as a vehicle to carry on a meaningful dialogue in the computational biology community has evolved significantly. The DREAM Challenges have brought rigor in the process of verification of computational methods, have enabled the democratization of different kinds of biological data, and have facilitated the collaboration of dozens of research teams. This success has triggered considerable interest by different government institutions and private organizations in working with DREAM to engage distributed teams to solve tough computational problems in biomedical research.

ABOUT SAGE BIONETWORKS

Sage Bionetworks is a nonprofit biomedical research organization, founded in 2009, with a vision to promote innovations in personalized medicine by enabling a community-based approach to scientific inquiries and discoveries. Sage Bionetworks strives to activate patients and to incentivize scientists, funders and researchers to work in fundamentally new ways in order to shape research, accelerate access to knowledge and transform human health. It is located on the campus of the Fred Hutchinson Cancer Research Center in Seattle, Washington and is supported through a portfolio of philanthropic donations, competitive research grants, and commercial partnerships. More information is available at www.sagebase.org.

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