Click here to close now.


Open Source Cloud Authors: Liz McMillan, Elizabeth White, Victoria Livschitz, Mike Kavis, Lori MacVittie

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.


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.


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

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
SYS-CON Events announced today that Dyn, the worldwide leader in Internet Performance, will exhibit at SYS-CON's 17th International Cloud Expo®, which will take place on November 3-5, 2015, at the Santa Clara Convention Center in Santa Clara, CA. Dyn is a cloud-based Internet Performance company. Dyn helps companies monitor, control, and optimize online infrastructure for an exceptional end-user experience. Through a world-class network and unrivaled, objective intelligence into Internet conditions, Dyn ensures traffic gets delivered faster, safer, and more reliably than ever.
Today air travel is a minefield of delays, hassles and customer disappointment. Airlines struggle to revitalize the experience. GE and M2Mi will demonstrate practical examples of how IoT solutions are helping airlines bring back personalization, reduce trip time and improve reliability. In their session at @ThingsExpo, Shyam Varan Nath, Principal Architect with GE, and Dr. Sarah Cooper, M2Mi's VP Business Development and Engineering, will explore the IoT cloud-based platform technologies driving this change including privacy controls, data transparency and integration of real time context w...
Who are you? How do you introduce yourself? Do you use a name, or do you greet a friend by the last four digits of his social security number? Assuming you don’t, why are we content to associate our identity with 10 random digits assigned by our phone company? Identity is an issue that affects everyone, but as individuals we don’t spend a lot of time thinking about it. In his session at @ThingsExpo, Ben Klang, Founder & President of Mojo Lingo, will discuss the impact of technology on identity. Should we federate, or not? How should identity be secured? Who owns the identity? How is identity ...
The IoT market is on track to hit $7.1 trillion in 2020. The reality is that only a handful of companies are ready for this massive demand. There are a lot of barriers, paint points, traps, and hidden roadblocks. How can we deal with these issues and challenges? The paradigm has changed. Old-style ad-hoc trial-and-error ways will certainly lead you to the dead end. What is mandatory is an overarching and adaptive approach to effectively handle the rapid changes and exponential growth.
The buzz continues for cloud, data analytics and the Internet of Things (IoT) and their collective impact across all industries. But a new conversation is emerging - how do companies use industry disruption and technology enablers to lead in markets undergoing change, uncertainty and ambiguity? Organizations of all sizes need to evolve and transform, often under massive pressure, as industry lines blur and merge and traditional business models are assaulted and turned upside down. In this new data-driven world, marketplaces reign supreme while interoperability, APIs and applications deliver un...
Too often with compelling new technologies market participants become overly enamored with that attractiveness of the technology and neglect underlying business drivers. This tendency, what some call the “newest shiny object syndrome,” is understandable given that virtually all of us are heavily engaged in technology. But it is also mistaken. Without concrete business cases driving its deployment, IoT, like many other technologies before it, will fade into obscurity.
Electric power utilities face relentless pressure on their financial performance, and reducing distribution grid losses is one of the last untapped opportunities to meet their business goals. Combining IoT-enabled sensors and cloud-based data analytics, utilities now are able to find, quantify and reduce losses faster – and with a smaller IT footprint. Solutions exist using Internet-enabled sensors deployed temporarily at strategic locations within the distribution grid to measure actual line loads.
The Internet of Everything is re-shaping technology trends–moving away from “request/response” architecture to an “always-on” Streaming Web where data is in constant motion and secure, reliable communication is an absolute necessity. As more and more THINGS go online, the challenges that developers will need to address will only increase exponentially. In his session at @ThingsExpo, Todd Greene, Founder & CEO of PubNub, will explore the current state of IoT connectivity and review key trends and technology requirements that will drive the Internet of Things from hype to reality.
The Internet of Things (IoT) is growing rapidly by extending current technologies, products and networks. By 2020, Cisco estimates there will be 50 billion connected devices. Gartner has forecast revenues of over $300 billion, just to IoT suppliers. Now is the time to figure out how you’ll make money – not just create innovative products. With hundreds of new products and companies jumping into the IoT fray every month, there’s no shortage of innovation. Despite this, McKinsey/VisionMobile data shows "less than 10 percent of IoT developers are making enough to support a reasonably sized team....
You have your devices and your data, but what about the rest of your Internet of Things story? Two popular classes of technologies that nicely handle the Big Data analytics for Internet of Things are Apache Hadoop and NoSQL. Hadoop is designed for parallelizing analytical work across many servers and is ideal for the massive data volumes you create with IoT devices. NoSQL databases such as Apache HBase are ideal for storing and retrieving IoT data as “time series data.”
Today’s connected world is moving from devices towards things, what this means is that by using increasingly low cost sensors embedded in devices we can create many new use cases. These span across use cases in cities, vehicles, home, offices, factories, retail environments, worksites, health, logistics, and health. These use cases rely on ubiquitous connectivity and generate massive amounts of data at scale. These technologies enable new business opportunities, ways to optimize and automate, along with new ways to engage with users.
The IoT is upon us, but today’s databases, built on 30-year-old math, require multiple platforms to create a single solution. Data demands of the IoT require Big Data systems that can handle ingest, transactions and analytics concurrently adapting to varied situations as they occur, with speed at scale. In his session at @ThingsExpo, Chad Jones, chief strategy officer at Deep Information Sciences, will look differently at IoT data so enterprises can fully leverage their IoT potential. He’ll share tips on how to speed up business initiatives, harness Big Data and remain one step ahead by apply...
There will be 20 billion IoT devices connected to the Internet soon. What if we could control these devices with our voice, mind, or gestures? What if we could teach these devices how to talk to each other? What if these devices could learn how to interact with us (and each other) to make our lives better? What if Jarvis was real? How can I gain these super powers? In his session at 17th Cloud Expo, Chris Matthieu, co-founder and CTO of Octoblu, will show you!
As a company adopts a DevOps approach to software development, what are key things that both the Dev and Ops side of the business must keep in mind to ensure effective continuous delivery? In his session at DevOps Summit, Mark Hydar, Head of DevOps, Ericsson TV Platforms, will share best practices and provide helpful tips for Ops teams to adopt an open line of communication with the development side of the house to ensure success between the two sides.
SYS-CON Events announced today that ProfitBricks, the provider of painless cloud infrastructure, will exhibit at SYS-CON's 17th International Cloud Expo®, which will take place on November 3–5, 2015, at the Santa Clara Convention Center in Santa Clara, CA. ProfitBricks is the IaaS provider that offers a painless cloud experience for all IT users, with no learning curve. ProfitBricks boasts flexible cloud servers and networking, an integrated Data Center Designer tool for visual control over the cloud and the best price/performance value available. ProfitBricks was named one of the coolest Clo...
SYS-CON Events announced today that IBM Cloud Data Services has been named “Bronze Sponsor” of SYS-CON's 17th Cloud Expo, which will take place on November 3–5, 2015, at the Santa Clara Convention Center in Santa Clara, CA. IBM Cloud Data Services offers a portfolio of integrated, best-of-breed cloud data services for developers focused on mobile computing and analytics use cases.
SYS-CON Events announced today that Sandy Carter, IBM General Manager Cloud Ecosystem and Developers, and a Social Business Evangelist, will keynote at the 17th International Cloud Expo®, which will take place on November 3–5, 2015, at the Santa Clara Convention Center in Santa Clara, CA.
Developing software for the Internet of Things (IoT) comes with its own set of challenges. Security, privacy, and unified standards are a few key issues. In addition, each IoT product is comprised of at least three separate application components: the software embedded in the device, the backend big-data service, and the mobile application for the end user's controls. Each component is developed by a different team, using different technologies and practices, and deployed to a different stack/target - this makes the integration of these separate pipelines and the coordination of software upd...
Mobile messaging has been a popular communication channel for more than 20 years. Finnish engineer Matti Makkonen invented the idea for SMS (Short Message Service) in 1984, making his vision a reality on December 3, 1992 by sending the first message ("Happy Christmas") from a PC to a cell phone. Since then, the technology has evolved immensely, from both a technology standpoint, and in our everyday uses for it. Originally used for person-to-person (P2P) communication, i.e., Sally sends a text message to Betty – mobile messaging now offers tremendous value to businesses for customer and empl...
"Matrix is an ambitious open standard and implementation that's set up to break down the fragmentation problems that exist in IP messaging and VoIP communication," explained John Woolf, Technical Evangelist at Matrix, in this interview at @ThingsExpo, held Nov 4–6, 2014, at the Santa Clara Convention Center in Santa Clara, CA.