Welcome!

Open Source Cloud Authors: Pat Romanski, Elizabeth White, Automic Blog, Christopher Keene, AppNeta 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
Pulzze Systems was happy to participate in such a premier event and thankful to be receiving the winning investment and global network support from G-Startup Worldwide. It is an exciting time for Pulzze to showcase the effectiveness of innovative technologies and enable them to make the world smarter and better. The reputable contest is held to identify promising startups around the globe that are assured to change the world through their innovative products and disruptive technologies. There w...
SYS-CON Events announced today Telecom Reseller has been named “Media Sponsor” of SYS-CON's 19th International Cloud Expo, which will take place on November 1–3, 2016, at the Santa Clara Convention Center in Santa Clara, CA. Telecom Reseller reports on Unified Communications, UCaaS, BPaaS for enterprise and SMBs. They report extensively on both customer premises based solutions such as IP-PBX as well as cloud based and hosted platforms.
SYS-CON Events announced today that Venafi, the Immune System for the Internet™ and the leading provider of Next Generation Trust Protection, will exhibit at @DevOpsSummit at 19th International Cloud Expo, which will take place on November 1–3, 2016, at the Santa Clara Convention Center in Santa Clara, CA. Venafi is the Immune System for the Internet™ that protects the foundation of all cybersecurity – cryptographic keys and digital certificates – so they can’t be misused by bad guys in attacks...
Smart Cities are here to stay, but for their promise to be delivered, the data they produce must not be put in new siloes. In his session at @ThingsExpo, Mathias Herberts, Co-founder and CTO of Cityzen Data, will deep dive into best practices that will ensure a successful smart city journey.
The 19th International Cloud Expo has announced that its Call for Papers is open. Cloud Expo, to be held November 1-3, 2016, at the Santa Clara Convention Center in Santa Clara, CA, brings together Cloud Computing, Big Data, Internet of Things, DevOps, Digital Transformation, 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 opportuni...
DevOps at Cloud Expo, taking place Nov 1-3, 2016, at the Santa Clara Convention Center in Santa Clara, CA, is co-located with 19th Cloud Expo and will feature technical sessions from a rock star conference faculty and the leading industry players in the world. The widespread success of cloud computing is driving the DevOps revolution in enterprise IT. Now as never before, development teams must communicate and collaborate in a dynamic, 24/7/365 environment. There is no time to wait for long dev...
In today's uber-connected, consumer-centric, cloud-enabled, insights-driven, multi-device, global world, the focus of solutions has shifted from the product that is sold to the person who is buying the product or service. Enterprises have rebranded their business around the consumers of their products. The buyer is the person and the focus is not on the offering. The person is connected through multiple devices, wearables, at home, on the road, and in multiple locations, sometimes simultaneously...
Internet of @ThingsExpo, taking place November 1-3, 2016, at the Santa Clara Convention Center in Santa Clara, CA, is co-located with 19th Cloud Expo and will feature technical sessions from a rock star conference faculty and the leading industry players in the world. The Internet of Things (IoT) is the most profound change in personal and enterprise IT since the creation of the Worldwide Web more than 20 years ago. All major researchers estimate there will be tens of billions devices - comp...
For basic one-to-one voice or video calling solutions, WebRTC has proven to be a very powerful technology. Although WebRTC’s core functionality is to provide secure, real-time p2p media streaming, leveraging native platform features and server-side components brings up new communication capabilities for web and native mobile applications, allowing for advanced multi-user use cases such as video broadcasting, conferencing, and media recording.
Data is the fuel that drives the machine learning algorithmic engines and ultimately provides the business value. In his session at Cloud Expo, Ed Featherston, a director and senior enterprise architect at Collaborative Consulting, will discuss the key considerations around quality, volume, timeliness, and pedigree that must be dealt with in order to properly fuel that engine.
SYS-CON Events announced today that 910Telecom 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. Housed in the classic Denver Gas & Electric Building, 910 15th St., 910Telecom is a carrier-neutral telecom hotel located in the heart of Denver. Adjacent to CenturyLink, AT&T, and Denver Main, 910Telecom offers connectivity to all major carriers, Internet service providers, Internet backbones and ...
Amazon has gradually rolled out parts of its IoT offerings in the last year, but these are just the tip of the iceberg. In addition to optimizing their back-end AWS offerings, Amazon is laying the ground work to be a major force in IoT – especially in the connected home and office. Amazon is extending its reach by building on its dominant Cloud IoT platform, its Dash Button strategy, recently announced Replenishment Services, the Echo/Alexa voice recognition control platform, the 6-7 strategic...
19th Cloud Expo, taking place November 1-3, 2016, at the Santa Clara Convention Center in Santa Clara, CA, will feature technical sessions from a rock star conference faculty and the leading industry players in the world. Cloud computing is now being embraced by a majority of enterprises of all sizes. Yesterday's debate about public vs. private has transformed into the reality of hybrid cloud: a recent survey shows that 74% of enterprises have a hybrid cloud strategy. Meanwhile, 94% of enterpri...
Akana has announced the availability of version 8 of its API Management solution. The Akana Platform provides an end-to-end API Management solution for designing, implementing, securing, managing, monitoring, and publishing APIs. It is available as a SaaS platform, on-premises, and as a hybrid deployment. Version 8 introduces a lot of new functionality, all aimed at offering customers the richest API Management capabilities in a way that is easier than ever for API and app developers to use.
Personalization has long been the holy grail of marketing. Simply stated, communicate the most relevant offer to the right person and you will increase sales. To achieve this, you must understand the individual. Consequently, digital marketers developed many ways to gather and leverage customer information to deliver targeted experiences. In his session at @ThingsExpo, Lou Casal, Founder and Principal Consultant at Practicala, discussed how the Internet of Things (IoT) has accelerated our abil...
With so much going on in this space you could be forgiven for thinking you were always working with yesterday’s technologies. So much change, so quickly. What do you do if you have to build a solution from the ground up that is expected to live in the field for at least 5-10 years? This is the challenge we faced when we looked to refresh our existing 10-year-old custom hardware stack to measure the fullness of trash cans and compactors.
The emerging Internet of Everything creates tremendous new opportunities for customer engagement and business model innovation. However, enterprises must overcome a number of critical challenges to bring these new solutions to market. In his session at @ThingsExpo, Michael Martin, CTO/CIO at nfrastructure, outlined these key challenges and recommended approaches for overcoming them to achieve speed and agility in the design, development and implementation of Internet of Everything solutions wi...
Cloud computing is being adopted in one form or another by 94% of enterprises today. Tens of billions of new devices are being connected to The Internet of Things. And Big Data is driving this bus. An exponential increase is expected in the amount of information being processed, managed, analyzed, and acted upon by enterprise IT. This amazing is not part of some distant future - it is happening today. One report shows a 650% increase in enterprise data by 2020. Other estimates are even higher....
I wanted to gather all of my Internet of Things (IOT) blogs into a single blog (that I could later use with my University of San Francisco (USF) Big Data “MBA” course). However as I started to pull these blogs together, I realized that my IOT discussion lacked a vision; it lacked an end point towards which an organization could drive their IOT envisioning, proof of value, app dev, data engineering and data science efforts. And I think that the IOT end point is really quite simple…
"My role is working with customers, helping them go through this digital transformation. I spend a lot of time talking to banks, big industries, manufacturers working through how they are integrating and transforming their IT platforms and moving them forward," explained William Morrish, General Manager Product Sales at Interoute, in this SYS-CON.tv interview at 18th Cloud Expo, held June 7-9, 2016, at the Javits Center in New York City, NY.