Welcome!

Open Source Cloud Authors: Carmen Gonzalez, Yeshim Deniz, Elizabeth White, XebiaLabs Blog, Derek Weeks

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
SYS-CON Events announced today that Juniper Networks (NYSE: JNPR), an industry leader in automated, scalable and secure networks, will exhibit at SYS-CON's 20th International Cloud Expo®, which will take place on June 6-8, 2017, at the Javits Center in New York City, NY. Juniper Networks challenges the status quo with products, solutions and services that transform the economics of networking. The company co-innovates with customers and partners to deliver automated, scalable and secure network...
Grape Up is a software company, specialized in cloud native application development and professional services related to Cloud Foundry PaaS. With five expert teams that operate in various sectors of the market across the USA and Europe, we work with a variety of customers from emerging startups to Fortune 1000 companies.
Financial Technology has become a topic of intense interest throughout the cloud developer and enterprise IT communities. Accordingly, attendees at the upcoming 20th Cloud Expo at the Javits Center in New York, June 6-8, 2017, will find fresh new content in a new track called FinTech.
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 20th Cloud Expo, which will take place on June 6-8, 2017 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 add...
In his keynote at @ThingsExpo, Chris Matthieu, Director of IoT Engineering at Citrix and co-founder and CTO of Octoblu, focused on building an IoT platform and company. He provided a behind-the-scenes look at Octoblu’s platform, business, and pivots along the way (including the Citrix acquisition of Octoblu).
SYS-CON Events announced today that CollabNet, a global leader in enterprise software development, release automation and DevOps solutions, will be a Bronze Sponsor of SYS-CON's 20th International Cloud Expo®, taking place from June 6-8, 2017, at the Javits Center in New York City, NY. CollabNet offers a broad range of solutions with the mission of helping modern organizations deliver quality software at speed. The company’s latest innovation, the DevOps Lifecycle Manager (DLM), supports Value S...
NHK, Japan Broadcasting, will feature the upcoming @ThingsExpo Silicon Valley in a special 'Internet of Things' and smart technology documentary that will be filmed on the expo floor between November 3 to 5, 2015, in Santa Clara. NHK is the sole public TV network in Japan equivalent to the BBC in the UK and the largest in Asia with many award-winning science and technology programs. Japanese TV is producing a documentary about IoT and Smart technology and will be covering @ThingsExpo Silicon Val...
@GonzalezCarmen has been ranked the Number One Influencer and @ThingsExpo has been named the Number One Brand in the “M2M 2016: Top 100 Influencers and Brands” by Analytic. Onalytica analyzed tweets over the last 6 months mentioning the keywords M2M OR “Machine to Machine.” They then identified the top 100 most influential brands and individuals leading the discussion on Twitter.
The 20th International Cloud Expo has announced that its Call for Papers is open. Cloud Expo, to be held June 6-8, 2017, at the Javits Center in New York City, brings together Cloud Computing, Big Data, Internet of Things, DevOps, Containers, Microservices and WebRTC to one location. With cloud computing driving a higher percentage of enterprise IT budgets every year, it becomes increasingly important to plant your flag in this fast-expanding business opportunity. Submit your speaking proposal ...
The age of Digital Disruption is evolving into the next era – Digital Cohesion, an age in which applications securely self-assemble and deliver predictive services that continuously adapt to user behavior. Information from devices, sensors and applications around us will drive services seamlessly across mobile and fixed devices/infrastructure. This evolution is happening now in software defined services and secure networking. Four key drivers – Performance, Economics, Interoperability and Trust ...
NHK, Japan Broadcasting, will feature the upcoming @ThingsExpo Silicon Valley in a special 'Internet of Things' and smart technology documentary that will be filmed on the expo floor between November 3 to 5, 2015, in Santa Clara. NHK is the sole public TV network in Japan equivalent to the BBC in the UK and the largest in Asia with many award-winning science and technology programs. Japanese TV is producing a documentary about IoT and Smart technology and will be covering @ThingsExpo Silicon Val...
The Internet of Things is clearly many things: data collection and analytics, wearables, Smart Grids and Smart Cities, the Industrial Internet, and more. Cool platforms like Arduino, Raspberry Pi, Intel's Galileo and Edison, and a diverse world of sensors are making the IoT a great toy box for developers in all these areas. In this Power Panel at @ThingsExpo, moderated by Conference Chair Roger Strukhoff, panelists discussed what things are the most important, which will have the most profound e...
Multiple data types are pouring into IoT deployments. Data is coming in small packages as well as enormous files and data streams of many sizes. Widespread use of mobile devices adds to the total. In this power panel at @ThingsExpo, moderated by Conference Chair Roger Strukhoff, panelists will look at the tools and environments that are being put to use in IoT deployments, as well as the team skills a modern enterprise IT shop needs to keep things running, get a handle on all this data, and deli...
With billions of sensors deployed worldwide, the amount of machine-generated data will soon exceed what our networks can handle. But consumers and businesses will expect seamless experiences and real-time responsiveness. What does this mean for IoT devices and the infrastructure that supports them? More of the data will need to be handled at - or closer to - the devices themselves.
SYS-CON Events announced today that Grape Up will exhibit at SYS-CON's 21st International Cloud Expo®, which will take place on Oct. 31 – Nov 2, 2017, at the Santa Clara Convention Center in Santa Clara, CA. Grape Up is a software company specializing in cloud native application development and professional services related to Cloud Foundry PaaS. With five expert teams that operate in various sectors of the market across the U.S. and Europe, Grape Up works with a variety of customers from emergi...
@ThingsExpo has been named the Most Influential ‘Smart Cities - IIoT' Account and @BigDataExpo has been named fourteenth by Right Relevance (RR), which provides curated information and intelligence on approximately 50,000 topics. In addition, Right Relevance provides an Insights offering that combines the above Topics and Influencers information with real time conversations to provide actionable intelligence with visualizations to enable decision making. The Insights service is applicable to eve...
DevOps is often described as a combination of technology and culture. Without both, DevOps isn't complete. However, applying the culture to outdated technology is a recipe for disaster; as response times grow and connections between teams are delayed by technology, the culture will die. A Nutanix Enterprise Cloud has many benefits that provide the needed base for a true DevOps paradigm.
Bert Loomis was a visionary. This general session will highlight how Bert Loomis and people like him inspire us to build great things with small inventions. In their general session at 19th Cloud Expo, Harold Hannon, Architect at IBM Bluemix, and Michael O'Neill, Strategic Business Development at Nvidia, discussed the accelerating pace of AI development and how IBM Cloud and NVIDIA are partnering to bring AI capabilities to "every day," on-demand. They also reviewed two "free infrastructure" pr...
New competitors, disruptive technologies, and growing expectations are pushing every business to both adopt and deliver new digital services. This ‘Digital Transformation’ demands rapid delivery and continuous iteration of new competitive services via multiple channels, which in turn demands new service delivery techniques – including DevOps. In this power panel at @DevOpsSummit 20th Cloud Expo, moderated by DevOps Conference Co-Chair Andi Mann, panelists will examine how DevOps helps to meet th...
Five years ago development was seen as a dead-end career, now it’s anything but – with an explosion in mobile and IoT initiatives increasing the demand for skilled engineers. But apart from having a ready supply of great coders, what constitutes true ‘DevOps Royalty’? It’ll be the ability to craft resilient architectures, supportability, security everywhere across the software lifecycle. In his keynote at @DevOpsSummit at 20th Cloud Expo, Jeffrey Scheaffer, GM and SVP, Continuous Delivery Busine...