Welcome!

Open Source Cloud Authors: Jnan Dash, Scott Allen, SmartBear Blog, David Bermingham, Blue Box Blog

News Feed Item

Two Science Translational Medicine Reports: DREAM and Sage Bionetworks Tap into the Wisdom of the Crowd to Fight the Challenge of Breast Cancer Prognosis and Treatment

Two new reports issuing in Science Translational Medicine (STM) today showcase the potential of teams of scientists working together to solve increasingly complex medical problems.

The results demonstrate that better predictors of breast cancer progression than those currently available can be rapidly evolved by running open Big Data Challenges such as The Sage Bionetworks/DREAM Breast Cancer Prognosis Challenge (BCC).

In breast cancer, a key undertaking is determining those patients whose disease is most likely to progress rapidly and therefore tailor the best course of treatment for them. Currently oncologists are using gene-expression based assays such as MammaPrint and Oncotype Dx, that are based on 10 year old science, and both do better with breast cancer risk prediction than models based only on clinical data.

Dr. Stephen Friend, the Founder of Sage Bionetworks and one of the organizers of the BCC reflects, “Ten years ago, members of our research group used gene expression profiling to build one of the first breast cancer predictors. Mammaprint and Oncotype Dx were developed off of that but further improvement seems to have stalled. We wondered if running a Challenge like BCC would motivate lots of different groups to tackle this problem, some working collaboratively, and if that might be more fruitful than the current 'go it alone' single researcher approach.”

To push the envelope on all the innovations that could be incorporated into the BCC, Sage partnered with the DREAM Project, a visionary distributed systems biology group that has run 24 successful open computational challenges over the last five years.

DREAM’s founder and leader, Dr. Gustavo Stolovitzky saw the BCC as an opportunity to, “… refocus our efforts to create a collaborative research environment that fosters a complementary way of doing science, which accelerates the pace of discovery with the goal of contributing to a faster reduction of suffering due to disease. This seems to me like an ethical imperative.”

The goal of the BCC was to build a computational model that accurately predicts breast cancer survival. To do this, participants of the Challenge used genomic and clinical information from 2000 women diagnosed with breast cancer (the METABRIC data set). They accessed this data on Synapse, Sage Bionetworks’ open compute platform for data sharing and analysis: Google donated cloud-based standardized virtual machines that each participant used to train their models against the data. Individual participants and/or teams submitted their computational models to Synapse as open source code made viewable to all: their models were assessed against a hidden dataset and their scores were reported on a real-time leaderboard. The combination of immediate feedback and code-sharing allowed participants to improve their leaderboard ranking by adjusting their own models or by borrowing the code of others to forge new models.

Throughout the July-October 2012 model-training phase, a crowd of 350 players from 35 countries across the globe joined the Challenge and submitted a total of 1700 computational models for scoring. The winning model was determined by scoring the predictive accuracy of players’ models against a newly generated data set: for this, the Avon Foundation For Women funded the generation of gene expression and copy number data as well as collection of corresponding clinical information from 180 breast cancer patients. Finally, the BCC organizers recognized that the basic science community might be most energized to participate if the Challenge prize were not money but the invitation to publish an article about the winning model in a top tier journal. The editors of STM saw the unique opportunity to run their own experiment on how to structure the peer-review process for competition-based crowdsourcing studies such as the BCC. Today’s issue of STM features not only the winner’s article (the BCC Challenge prize) and a report from the BCC organizers on the Challenge’s conception, execution and insights -- STM also chose to highlight the BCC with an Editorial Summary and an iconic cover of “Rosie the Riveter,” intended to symbolize the power of women and their data to transform health.

Quipped Challenge participant Richard Savage (MRC Fellow in Biostatistics at the University of Warwick) on the prospect of winning the opportunity to publish in STM, “This is huge and a genuinely new way to do some great science. I really think the organizers are onto something with this.”

The winner turned out not to be a breast cancer doctor, or even a breast cancer researcher: the winning team (“Attractor Metagenes”) hails from Professor Dimitris Anastassiou’s laboratory at Columbia University's School of Engineering and Applied Science. Anastassiou, now a member of the Columbia Initiative in Systems Biology, funded this research from his own inventor’s research allocation of patent royalties related to his previous work on digital television, which is now used in all DVDs and TV broadcasting systems worldwide. Working with two of his Ph.D. students, they developed the winning model underpinned by so-called “attractor metagenes,” gene signatures that they had identified as behaving similarly in multiple cancer types. They refer to attractor metagenes as “bioinformatic hallmarks of cancer.” Remarks Professor Anastassiou, “We had discovered these ‘pan-cancer’ gene signatures previously, and so we hypothesized that they play important roles in cancer in general. The BCC allowed us to prove that they are indeed highly prognostic at least in breast cancer.” Indeed, the winning model’s predictive accuracy for breast cancer survival outperformed the best 60 models of a pre-competition group of expert programmers and bested current clinical standards. He is now excited with the prospect of collaborating with medical researchers to make good use of these signatures of cancer for potential use in diagnostic, prognostic and eventually therapeutic products applicable in multiple cancer types.

Based on the success of the BCC, Sage Bionetworks and DREAM announced earlier this year that they would merge to run open science computational Challenges which foster the broader collaboration of the research community and provide a meaningful impact to both discovery and clinical research. Their merger provides a collaborative framework that will bring the ideals of open science one step closer to reality.

The BCC demonstrated the wisdom of the crowd to develop predictive models but also highlighted that the value of those models is limited by the questions being posed and by the data being utilized. Even as the BCC reports in this week’s issue of STM, Sage Bionetworks and DREAM are announcing five DREAM8 Challenges at Sage’s 4th Commons Congress taking place in San Francisco and working with the Avon Foundation For Women, Susan G. Komen, the Breast Cancer Research Foundation to develop the next BCC which will start by mobilizing breast cancer patients to donate their data to drive the solving of a clinically relevant question in breast cancer with the potential to transform patient treatment.

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. In 2012, the last DREAM7 project featured four powerful challenges of which one was on network biology and the other three dealt with three important problems in translational medicine. With the experience gathered by the launching of 24 successful challenges over the past five years, the “Challenge” concept has reached a status of legitimacy and maturity. 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.

@ThingsExpo Stories
With an estimated 50 billion devices connected to the Internet by 2020, several industries will begin to expand their capabilities for retaining end point data at the edge to better utilize the range of data types and sheer volume of M2M data generated by the Internet of Things. In his session at @ThingsExpo, Don DeLoach, CEO and President of Infobright, will discuss the infrastructures businesses will need to implement to handle this explosion of data by providing specific use cases for filte...
SYS-CON Events announced today that VAI, a leading ERP software provider, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. VAI (Vormittag Associates, Inc.) is a leading independent mid-market ERP software developer renowned for its flexible solutions and ability to automate critical business functions for the distribution, manufacturing, specialty retail and service sectors. An IBM Premier Business Part...
Cognitive Computing is becoming the foundation for a new generation of solutions that have the potential to transform business. Unlike traditional approaches to building solutions, a cognitive computing approach allows the data to help determine the way applications are designed. This contrasts with conventional software development that begins with defining logic based on the current way a business operates. In her session at 18th Cloud Expo, Judith S. Hurwitz, President and CEO of Hurwitz & ...
Fortunately, meaningful and tangible business cases for IoT are plentiful in a broad array of industries and vertical markets. These range from simple warranty cost reduction for capital intensive assets, to minimizing downtime for vital business tools, to creating feedback loops improving product design, to improving and enhancing enterprise customer experiences. All of these business cases, which will be briefly explored in this session, hinge on cost effectively extracting relevant data from ...
SYS-CON Events announced today that Men & Mice, the leading global provider of DNS, DHCP and IP address management overlay solutions, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. The Men & Mice Suite overlay solution is already known for its powerful application in heterogeneous operating environments, enabling enterprises to scale without fuss. Building on a solid range of diverse platform support,...
As enterprises work to take advantage of Big Data technologies, they frequently become distracted by product-level decisions. In most new Big Data builds this approach is completely counter-productive: it presupposes tools that may not be a fit for development teams, forces IT to take on the burden of evaluating and maintaining unfamiliar technology, and represents a major up-front expense. In his session at @BigDataExpo at @ThingsExpo, Andrew Warfield, CTO and Co-Founder of Coho Data, will dis...
SYS-CON Events announced today that Pythian, a global IT services company specializing in helping companies adopt disruptive technologies to optimize revenue-generating systems, has been named “Bronze Sponsor” of SYS-CON's 18th Cloud Expo, which will take place on June 7-9, 2015 at the Javits Center in New York, New York. Founded in 1997, Pythian is a global IT services company that helps companies compete by adopting disruptive technologies such as cloud, Big Data, advanced analytics, and DevO...
SYS-CON Events announced today that iDevices®, the preeminent brand in the connected home industry, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. iDevices, the preeminent brand in the connected home industry, has a growing line of HomeKit-enabled products available at the largest retailers worldwide. Through the “Designed with iDevices” co-development program and its custom-built IoT Cloud Infrastruc...
SYS-CON Events announced today that Alert Logic, Inc., the leading provider of Security-as-a-Service solutions for the cloud, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. Alert Logic, Inc., provides Security-as-a-Service for on-premises, cloud, and hybrid infrastructures, delivering deep security insight and continuous protection for customers at a lower cost than traditional security solutions. Ful...
SYS-CON Events announced today that Interoute, owner-operator of one of Europe's largest networks and a global cloud services platform, has been named “Bronze Sponsor” of SYS-CON's 18th Cloud Expo, which will take place on June 7-9, 2015 at the Javits Center in New York, New York. Interoute is the owner-operator of one of Europe's largest networks and a global cloud services platform which encompasses 12 data centers, 14 virtual data centers and 31 colocation centers, with connections to 195 ad...
SYS-CON Events announced today that Commvault, a global leader in enterprise data protection and information management, has been named “Bronze Sponsor” of SYS-CON's 18th International Cloud Expo, which will take place on June 7–9, 2016, at the Javits Center in New York City, NY, and the 19th International Cloud Expo, which will take place on November 1–3, 2016, at the Santa Clara Convention Center in Santa Clara, CA. Commvault is a leading provider of data protection and information management...
Eighty percent of a data scientist’s time is spent gathering and cleaning up data, and 80% of all data is unstructured and almost never analyzed. Cognitive computing, in combination with Big Data, is changing the equation by creating data reservoirs and using natural language processing to enable analysis of unstructured data sources. This is impacting every aspect of the analytics profession from how data is mined (and by whom) to how it is delivered. This is not some futuristic vision: it's ha...
With the Apple Watch making its way onto wrists all over the world, it’s only a matter of time before it becomes a staple in the workplace. In fact, Forrester reported that 68 percent of technology and business decision-makers characterize wearables as a top priority for 2015. Recognizing their business value early on, FinancialForce.com was the first to bring ERP to wearables, helping streamline communication across front and back office functions. In his session at @ThingsExpo, Kevin Roberts...
One of the bewildering things about DevOps is integrating the massive toolchain including the dozens of new tools that seem to crop up every year. Part of DevOps is Continuous Delivery and having a complex toolchain can add additional integration and setup to your developer environment. In his session at @DevOpsSummit at 18th Cloud Expo, Miko Matsumura, Chief Marketing Officer of Gradle Inc., will discuss which tools to use in a developer stack, how to provision the toolchain to minimize onboa...
The cloud promises new levels of agility and cost-savings for Big Data, data warehousing and analytics. But it’s challenging to understand all the options – from IaaS and PaaS to newer services like HaaS (Hadoop as a Service) and BDaaS (Big Data as a Service). In her session at @BigDataExpo at @ThingsExpo, Hannah Smalltree, a director at Cazena, will provide an educational overview of emerging “as-a-service” options for Big Data in the cloud. This is critical background for IT and data profes...
Silver Spring Networks, Inc. (NYSE: SSNI) extended its Internet of Things technology platform with performance enhancements to Gen5 – its fifth generation critical infrastructure networking platform. Already delivering nearly 23 million devices on five continents as one of the leading networking providers in the market, Silver Spring announced it is doubling the maximum speed of its Gen5 network to up to 2.4 Mbps, increasing computational performance by 10x, supporting simultaneous mesh communic...
SYS-CON Events announced today that Fusion, a leading provider of cloud services, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. Fusion, a leading provider of integrated cloud solutions to small, medium and large businesses, is the industry's single source for the cloud. Fusion's advanced, proprietary cloud service platform enables the integration of leading edge solutions in the cloud, including clou...
Most people haven’t heard the word, “gamification,” even though they probably, and perhaps unwittingly, participate in it every day. Gamification is “the process of adding games or game-like elements to something (as a task) so as to encourage participation.” Further, gamification is about bringing game mechanics – rules, constructs, processes, and methods – into the real world in an effort to engage people. In his session at @ThingsExpo, Robert Endo, owner and engagement manager of Intrepid D...
WebRTC has had a real tough three or four years, and so have those working with it. Only a few short years ago, the development world were excited about WebRTC and proclaiming how awesome it was. You might have played with the technology a couple of years ago, only to find the extra infrastructure requirements were painful to implement and poorly documented. This probably left a bitter taste in your mouth, especially when things went wrong.
Learn how IoT, cloud, social networks and last but not least, humans, can be integrated into a seamless integration of cooperative organisms both cybernetic and biological. This has been enabled by recent advances in IoT device capabilities, messaging frameworks, presence and collaboration services, where devices can share information and make independent and human assisted decisions based upon social status from other entities. In his session at @ThingsExpo, Michael Heydt, founder of Seamless...