Welcome!

News Feed Item

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.

More Stories By Business Wire

Copyright © 2009 Business Wire. All rights reserved. Republication or redistribution of Business Wire content is expressly prohibited without the prior written consent of Business Wire. Business Wire shall not be liable for any errors or delays in the content, or for any actions taken in reliance thereon.

Latest Stories
With over 720 million Internet users and 40–50% CAGR, the Chinese Cloud Computing market has been booming. When talking about cloud computing, what are the Chinese users of cloud thinking about? What is the most powerful force that can push them to make the buying decision? How to tap into them? In his session at 18th Cloud Expo, Yu Hao, CEO and co-founder of SpeedyCloud, answered these questions and discussed the results of SpeedyCloud’s survey.
The Internet of Things will challenge the status quo of how IT and development organizations operate. Or will it? Certainly the fog layer of IoT requires special insights about data ontology, security and transactional integrity. But the developmental challenges are the same: People, Process and Platform. In his session at @ThingsExpo, Craig Sproule, CEO of Metavine, demonstrated how to move beyond today's coding paradigm and shared the must-have mindsets for removing complexity from the develo...
SYS-CON Events announced today that MangoApps will exhibit at the 19th International Cloud Expo, which will take place on November 1–3, 2016, at the Santa Clara Convention Center in Santa Clara, CA. MangoApps provides modern company intranets and team collaboration software, allowing workers to stay connected and productive from anywhere in the world and from any device.
Large scale deployments present unique planning challenges, system commissioning hurdles between IT and OT and demand careful system hand-off orchestration. In his session at @ThingsExpo, Jeff Smith, Senior Director and a founding member of Incenergy, will discuss some of the key tactics to ensure delivery success based on his experience of the last two years deploying Industrial IoT systems across four continents.
Redis is not only the fastest database, but it is the most popular among the new wave of databases running in containers. Redis speeds up just about every data interaction between your users or operational systems. In his session at 19th Cloud Expo, Dave Nielsen, Developer Advocate, Redis Labs, will share the functions and data structures used to solve everyday use cases that are driving Redis' popularity.
Basho Technologies has announced the latest release of Basho Riak TS, version 1.3. Riak TS is an enterprise-grade NoSQL database optimized for Internet of Things (IoT). The open source version enables developers to download the software for free and use it in production as well as make contributions to the code and develop applications around Riak TS. Enhancements to Riak TS make it quick, easy and cost-effective to spin up an instance to test new ideas and build IoT applications. In addition to...
Predictive analytics tools monitor, report, and troubleshoot in order to make proactive decisions about the health, performance, and utilization of storage. Most enterprises combine cloud and on-premise storage, resulting in blended environments of physical, virtual, cloud, and other platforms, which justifies more sophisticated storage analytics. In his session at 18th Cloud Expo, Peter McCallum, Vice President of Datacenter Solutions at FalconStor, discussed using predictive analytics to mon...
Identity is in everything and customers are looking to their providers to ensure the security of their identities, transactions and data. With the increased reliance on cloud-based services, service providers must build security and trust into their offerings, adding value to customers and improving the user experience. Making identity, security and privacy easy for customers provides a unique advantage over the competition.
SYS-CON Events announced today that Isomorphic Software will exhibit at DevOps Summit at 19th International Cloud Expo, which will take place on November 1–3, 2016, at the Santa Clara Convention Center in Santa Clara, CA. Isomorphic Software provides the SmartClient HTML5/AJAX platform, the most advanced technology for building rich, cutting-edge enterprise web applications for desktop and mobile. SmartClient combines the productivity and performance of traditional desktop software with the simp...
In his session at @DevOpsSummit at 19th Cloud Expo, Yoseph Reuveni, Director of Software Engineering at Jet.com, will discuss Jet.com's journey into containerizing Microsoft-based technologies like C# and F# into Docker. He will talk about lessons learned and challenges faced, the Mono framework tryout and how they deployed everything into Azure cloud. Yoseph Reuveni is a technology leader with unique experience developing and running high throughput (over 1M tps) distributed systems with extre...
"We've discovered that after shows 80% if leads that people get, 80% of the conversations end up on the show floor, meaning people forget about it, people forget who they talk to, people forget that there are actual business opportunities to be had here so we try to help out and keep the conversations going," explained Jeff Mesnik, Founder and President of ContentMX, in this SYS-CON.tv interview at 18th Cloud Expo, held June 7-9, 2016, at the Javits Center in New York City, NY.
"There's a growing demand from users for things to be faster. When you think about all the transactions or interactions users will have with your product and everything that is between those transactions and interactions - what drives us at Catchpoint Systems is the idea to measure that and to analyze it," explained Leo Vasiliou, Director of Web Performance Engineering at Catchpoint Systems, in this SYS-CON.tv interview at 18th Cloud Expo, held June 7-9, 2016, at the Javits Center in New York Ci...
As companies gain momentum, the need to maintain high quality products can outstrip their development team’s bandwidth for QA. Building out a large QA team (whether in-house or outsourced) can slow down development and significantly increases costs. This eBook takes QA profiles from 5 companies who successfully scaled up production without building a large QA team and includes: What to consider when choosing CI/CD tools How culture and communication can make or break implementation
"When you think about the data center today, there's constant evolution, The evolution of the data center and the needs of the consumer of technology change, and they change constantly," stated Matt Kalmenson, VP of Sales, Service and Cloud Providers at Veeam Software, in this SYS-CON.tv interview at 18th Cloud Expo, held June 7-9, 2016, at the Javits Center in New York City, NY.
Internet of @ThingsExpo, taking place November 1-3, 2016, at the Santa Clara Convention Center in Santa Clara, CA, is co-located with the 19th International Cloud Expo and will feature technical sessions from a rock star conference faculty and the leading industry players in the world and ThingsExpo Silicon Valley Call for Papers is now open.