April 19, 2013

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

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

Press Release | Fri Apr 19, 2013 5:15pm EDT

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

DREAM8 Challenges Tackle Tough Problems from Toxicology to Cancer

DREAM and Sage Bionetworks today announced that they will run four Big Data open science Challenges between now and the fall. These open computational Challenges are a new method in biomedicine to rapidly share and evolve predictive models for important questions and were featured at today’s session of the Sage Bionetworks Commons Congress taking place in San Francisco.

Challenges have been used successfully in other research fields, and in the past 6 years the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project has run 24 successful Challenges in Systems Biology. Due to efforts like DREAM, the “Challenge” concept has reached a status of legitimacy and maturity: the NIH and private companies are investing in the Challenge model to solve complex problems. In February 2013, and based on the success of collaborating to run the 2012 Sage Bionetworks/DREAM Breast Cancer Prognosis Challenge, Sage Bionetworks merged its open science efforts with those of DREAM.

This year’s so-called DREAM8 Challenges mark the eighth year that DREAM founder Dr. Gustavo Stolovitzky has been working with his distributed group of systems biology scientists to engage wider and more diverse communities of scientists to competitively solve important problems in biomedicine. Says Stolovitzky about this year’s Challenges, “The Challenge infrastructure, computational model archive and data governance systems that Sage Bionetworks has established allows the DREAM Challenges to shift in exciting new ways. In DREAM8 and future Challenges, we will use the solutions from some Challenges to serve as seeds for subsequent Challenges and for basic and clinical validation of the models that show outstanding performance. And we are already planting the seeds for Challenges that start with citizens and patients donating their data so that we can run Challenges that answer questions that are directly relevant to their disease progression and treatment options.”

The first four DREAM8 Challenges announced today will launch later this spring and be open for participation by anyone interested (signup is open at DREAM8@sagebase.org). The model submission phase will close in the fall and the Challenge winners will be announced at the DREAM8 Conference taking place in early November. Sage Bionetworks and DREAM expect to launch another round of DREAM8 Challenges in the fall. Brief information about each of the announced DREAM8 Challenges is provided below:

1. Heritage-DREAM Breast Cancer Challenge (read HPN press release:http://www.prnewswire.com/news-releases/heritage-dream-national-cancer-institute-breast-cancer-network-inference-prize-announced-203812141.html)

a. Data provided by Oregon Health Sciences University (OHSU) and the MD Anderson Cancer Center
b. Sponsored by the Heritage Provider Network (HPN) and the National Cancer Institute (NCI), Division of Cancer Biology
c. Challenge Focus: To use proteomics data to build network models that represent the active pathways in breast cancer cells and to predict their responses to different drug treatments.

2. NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge

a. Data provided by National Institute for Environmental Health Sciences (NIEHS), the National Center for Advancing Translational Sciences (NCATS), and the University of North Carolina at Chapel Hill (UNC).
b. Challenge Focus:
i. To use genetics, genomic and toxicity data to predict individual response to exposure to common environmental and pharmaceutical chemicals.
ii. To predict variation in toxicities across populations exposed to compounds based on the chemical information of the toxic agent and population genetics information.

3. National Brain Tumor Society-DREAM Breast Cancer Prediction Challenge (read NBTS press release: http://www.braintumor.org/news/latest-nbts-news/announcing-the-national-brain.html)

a. Sponsored by the National Brain Tumor Society.
b. Jointly led by experts from the National Brain Tumor Society (NTBS), Columbia University and DREAM/Sage Bionetworks.
c. Challenge Focus: to predict the specific drugs that will elicit the strongest therapeutic response in mice transplanted with human brain tumors, based on their genomic characterization.

4. DREAM Whole Cell Parameter Estimation Challenge

a. Data and models provided by Stanford University
b. Sponsored by IBM
c. Challenge Focus: to predict kinetic parameters of a whole-cell computational model of the human pathogen Mycoplasma genitalium, using algorithms that use experiments as part of the parameter inference process.

Click here to be contacted when the DREAM8 Challenges open for competition.

Read more about the DREAM8 Challenges here.

Press Release