|By Business Wire||
|November 7, 2013 08:00 PM EST||
Cancer research leaders from the Ontario Institute for Cancer Research (OICR) and the University of California, Santa Cruz (UCSC), in collaboration with Sage Bionetworks and IBM’s DREAM, will announce tomorrow the opening of the ICGC-TCGA-DREAM Somatic Mutation Calling (SMC) Challenge (https://www.synapse.org/#!Challenges:DREAM) at the Sixth Annual RECOMB/ISCB conference (http://www.iscb.org/recomb-regsysgen2013).
Like previous DREAM Challenges in the series, this new Challenge will engage a diverse community of scientists to solve a specific problem in a given time period by placing scientific data, tools, scoreboards and the resulting predictive models into an open Commons.
The specific problem the SMC Challenge will address is the need for accurate methods to identify cancer-associated mutations from whole-genome sequencing data. Cancer is a disease of the genome, caused by disruptions in DNA that alter specific gene functions. Although today’s DNA sequencing instruments can amass great quantities of sequence data from a patient’s normal and tumor tissues, the ability to identify DNA mutations and rearrangements accurately on the basis of those data remains elusive; current studies agree in only about 20% of their predictions.
To address this need, the Challenge will post the raw DNA sequencing data of 10 human tumor-normal pairs (5 prostate, 5 pancreatic), comprising approximately 9 terabytes of data to a high-speed distribution server. Contestants will have 6 months to optimize their predictive models. After the Challenge closes in July, 2014, at least 5,000 DNA candidate mutations predicted by different participating teams will be prospectively validated on an independent sequencing platform by the Challenge organizers. The accuracy of participants’ predictions will be ranked using the newly generated validation data based on sensitivity, specificity and balanced accuracy amongst other metrics.
To participate in the Challenge that opens tomorrow, individuals will need to register at https://www.synapse.org/ #!Challenges:DREAM. In addition, they must be approved by OICR’s ICGC Data Access Compliance Office to access the data.
As Canadian OICR researcher and Challenge organizer Professor Paul Boutros puts it, “Governments around the world have committed hundreds of millions of dollars to sequence cancer genomes to find new drug targets and to develop treatments that are personalized to each person’s cancer genome. But realizing these goals is currently blocked by scientists’ inability to identify mutations in cancer genomes. It is really tremendous that ICGC and TCGA are coming together with Sage Bionetworks and DREAM to address this problem using a DREAM Challenge that will set a gold standard that groups around the world can use to understand the cancer genome!”
To help realize this Challenge, industrial partners have stepped up. Google is making their Google Cloud Platform available to OICR-approved participants, including free access to the contest data in Google Cloud Storage and discounted Google Compute Engine cycles. Cloud processing will open the door for a whole new set of participants who do not have access to large compute clusters at their own institutions. Hitachi has provided free storage to host the data on a 1PB disk donated for cancer genomics. Annai Systems (http://www.annaisystems.com/) is providing their Annai-GNOS™ data management platform to facilitate upload, hosting and access to the data in the Hitachi store. Annai’s GeneTorrent software will provide high-speed data transfer to the Challenge participants.
Challenge participants will use the Synapse infrastructure (http://www.synapse.org), built by Sage Bionetworks, that allows collaboration by Challenge teams on an open platform. Synapse’s tools and forum will allow Challenge participants to: (1) record what processing and analysis they’ve done on the data; (2) submit their predictive models to a real-time leaderboard for scoring; and (3) share their ideas, model code and analysis results with others in the Challenge.
Publications based on the highest-ranking predictive methods from the Challenge will be considered with Nature Publishing Group. Nature Genetics editor Myles Axton will advise the Challenge on publication strategy and work with Synapse to understand the scientific quality control that can be obtained via competitive collaboration. “The exciting thing about this exercise from an editorial standpoint is that we can analyze just how much the strategies are improved during the contest and how much peer review is then needed to obtain a useful research publication at the end. The beauty of doing this on an open platform is to see the rigor, transparency and detail of each group’s approach and to be able to replay each strategy in a robust way,” Myles says. “This is a good use of editorial time since peer review improves the strategies, it improves the resulting publications and it improves the databases and journals by preparing us for the future of knowledge production. I really hope the winners combine elements of the best strategies into fuller publishable units, in that way they will get the best out of the challenge as well as our involvement with it.”
Explains UC Santa Cruz Professor Josh Stuart, “The timing of this Challenge couldn’t be better. ICGC and TCGA recently announced that they plan to jointly analyze a dataset of approximately 2,000 pairs of tumor-normal whole genomes as part of a 2014-2015 Pan-Cancer effort to elucidate comprehensively the genomic changes present in many forms of cancers. Thus, the winning algorithms selected by this DREAM Challenge will help ICGC/TCGA researchers provide the largest unified view of cancer genome variation to date.”
Cancer researcher Dr. Stephen Friend founded Sage Bionetworks out of a conviction that “…the best approach towards developing robust and accurate predictions such as those needed for mutation calling is to enable an open diverse community where data access is simple and people are incentivized to share. Sage and DREAM have already shown that in the span of several months, DREAM Challenges can attract hundreds of teams who end up submitting thousands of predictive models to a Challenge. Sage and DREAM couldn’t be more delighted to be partnered with the ICGC and TCGA research communities to provide the largest public methodology assessment for the field of somatic mutation identification.”
ABOUT ONTARIO INSTITUTE FOR CANCER RESEARCH: www.oicr.on.ca
OICR is an innovative cancer research and development institute dedicated to prevention, early detection, diagnosis and treatment of cancer. The Institute is an independent, not-for-profit corporation, supported by the Government of Ontario. OICR research supports more than 1,600 investigators, clinician scientists, research staff and trainees located at its headquarters and in research institutes and academia across the Province of Ontario. OICR has key research efforts underway in small molecules, biologics, stem cells, imaging, genomics, informatics and bio-computing. For more information, please visit the website at www.oicr.on.ca
ABOUT SAGE BIONETWORKS: http://sagebase.org/
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. Sage Bionetworks 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.
ABOUT THE DREAM PROJECT: http://www.the-dream-project.org
The Dialogue on Reverse Engineering Assessment and Methods (DREAM) project is an initiative to advance the field of systems biology through the organization of Challenges to foster the development of predictive models of relevance in biomedicine. With the experience gathered by the launching of 27 successful DREAM challenges over the past seven years, the “Challenge” concept has reached a status of legitimacy and maturity. 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 ANNAI SYSTEMS INC.: (http://www.annaisystems.com)
Annai Systems Inc., located in California’s Silicon Valley, is a technology company with a core competency in big data management solutions. We are focused on applying our technology to the field of genomics to enable easier, more efficient access to genomic data. Our technology enables the producers and consumers of genomic data to achieve better results faster and at lower operating costs by providing products that overcome key data-related bottlenecks and roadblocks that are impeding progress in the growing fields of genomic research and medicine. Annai Systems offers a variety of products and services to address the “big data” challenges associated with using genomic data in personalized medicine and healthcare improvement.
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...
Aug. 25, 2016 02:00 PM EDT Reads: 3,540
Kubernetes, Docker and containers are changing the world, and how companies are deploying their software and running their infrastructure. With the shift in how applications are built and deployed, new challenges must be solved. In his session at @DevOpsSummit at19th Cloud Expo, Sebastian Scheele, co-founder of Loodse, will discuss the implications of containerized applications/infrastructures and their impact on the enterprise. In a real world example based on Kubernetes, he will show how to ...
Aug. 25, 2016 01:45 PM EDT Reads: 1,351
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...
Aug. 25, 2016 01:00 PM EDT Reads: 3,878
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...
Aug. 25, 2016 01:00 PM EDT Reads: 2,584
SYS-CON Events announced today that Hitrons Solutions 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. Hitrons Solutions Inc. is distributor in the North American market for unique products and services of small and medium-size businesses, including cloud services and solutions, SEO marketing platforms, and mobile applications.
Aug. 25, 2016 12:51 PM EDT Reads: 257
Is the ongoing quest for agility in the data center forcing you to evaluate how to be a part of infrastructure automation efforts? As organizations evolve toward bimodal IT operations, they are embracing new service delivery models and leveraging virtualization to increase infrastructure agility. Therefore, the network must evolve in parallel to become equally agile. Read this essential piece of Gartner research for recommendations on achieving greater agility.
Aug. 25, 2016 12:45 PM EDT Reads: 570
As the world moves toward more DevOps and Microservices, application deployment to the cloud ought to become a lot simpler. The Microservices architecture, which is the basis of many new age distributed systems such as OpenStack, NetFlix and so on, is at the heart of Cloud Foundry - a complete developer-oriented Platform as a Service (PaaS) that is IaaS agnostic and supports vCloud, OpenStack and AWS. Serverless computing is revolutionizing computing. In his session at 19th Cloud Expo, Raghav...
Aug. 25, 2016 12:45 PM EDT Reads: 550
DevOps at Cloud Expo – being held November 1-3, 2016, at the Santa Clara Convention Center in Santa Clara, CA – announces that its Call for Papers is open. Born out of proven success in agile development, cloud computing, and process automation, DevOps is a macro trend you cannot afford to miss. From showcase success stories from early adopters and web-scale businesses, DevOps is expanding to organizations of all sizes, including the world's largest enterprises – and delivering real results. Am...
Aug. 25, 2016 12:15 PM EDT Reads: 3,377
Fact: storage performance problems have only gotten more complicated, as applications not only have become largely virtualized, but also have moved to cloud-based infrastructures. Storage performance in virtualized environments isn’t just about IOPS anymore. Instead, you need to guarantee performance for individual VMs, helping applications maintain performance as the number of VMs continues to go up in real time. In his session at Cloud Expo, Dhiraj Sehgal, Product and Marketing at Tintri, wil...
Aug. 25, 2016 11:00 AM EDT Reads: 523
Ixia (Nasdaq: XXIA) has announced that NoviFlow Inc.has deployed IxNetwork® to validate the company’s designs and accelerate the delivery of its proven, reliable products. Based in Montréal, NoviFlow Inc. supports network carriers, hyperscale data center operators, and enterprises seeking greater network control and flexibility, network scalability, and the capacity to handle extremely large numbers of flows, while maintaining maximum network performance. To meet these requirements, NoviFlow in...
Aug. 25, 2016 11:00 AM EDT Reads: 1,824
StarNet Communications Corp has announced the addition of three Secure Remote Desktop modules to its flagship X-Win32 PC X server. The new modules enable X-Win32 to safely tunnel the remote desktops from Linux and Unix servers to the user’s PC over encrypted SSH. Traditionally, users of PC X servers deploy the XDMCP protocol to display remote desktop environments such as the Gnome and KDE desktops on Linux servers and the CDE environment on Solaris Unix machines. XDMCP is used primarily on comp...
Aug. 25, 2016 10:30 AM EDT Reads: 479
SYS-CON Events announced today that StarNet Communications 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. StarNet Communications’ FastX is the industry first cloud-based remote X Windows emulator. Using standard Web browsers (FireFox, Chrome, Safari, etc.) users from around the world gain highly secure access to applications and data hosted on Linux-based servers in a central data center. ...
Aug. 25, 2016 09:15 AM EDT Reads: 591
SYS-CON Events announced today that eCube Systems, a leading provider of middleware modernization, integration, and management solutions, 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. eCube Systems offers a family of middleware evolution products and services that maximize return on technology investment by leveraging existing technical equity to meet evolving business needs. ...
Aug. 25, 2016 09:00 AM EDT Reads: 492
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.
Aug. 25, 2016 09:00 AM EDT Reads: 566
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.
Aug. 25, 2016 08:45 AM EDT Reads: 2,108