Sophisticated software cuts through the complexity of genomic data and makes it accessible to researchers and practitioners
CANARIE and Compute Canada, two critical components of Canada’s national digital infrastructure supporting research, education and innovation, today announced the launch of GenAP, a tool that enables Canadian researchers to easily access and use genomic data to advance our knowledge of human health and disease.
While data from human genomes is an extraordinarily rich resource for researchers and physicians, the size of the datasets is daunting. Recent predictions estimate that fast machines for DNA sequencing will be capable of producing 85 petabytes of data this year worldwide. For comparison, all the master copies of movies held by Netflix take up 2.6 petabytes of storage.1 Further, the complexity of the datasets, combined with stringent privacy and confidentiality requirements, creates an environment in which the power of genomic data demands an equally powerful access and processing environment.
GenAP (https://www.genap.ca) is a revolutionary software platform that delivers that power. Through a simple point-and-click web interface, GenAP enables researchers to access genome datasets and send them for processing at Compute Canada’s high performance computing facilities across the country. Given the vast amounts of data available and the myriad ways that the data may be analyzed, GenAP’s sophisticated software paves the way for more researchers to conduct more analyses. This in turn accelerates the creation of new knowledge, with immediate applications for human health and ground breaking approaches to the treatment of disease.
GenAP was funded by CANARIE through its Research Software program, and by Genome Quebec, and created by a team of Compute Canada and Calcul Quebec experts at McGill University and Universitéde Sherbrooke. CANARIE funds the development of Research Platforms, like GenAP, along with Research Services, reusable software components that may be used in any research software application. Through its Research Software program CANARIE aims to give Canadians a first-mover advantage in leveraging digital infrastructure resources (like the CANARIE network and Compute Canada’s high performance computing facilities) to speed up discovery and spark innovation.
GenAP’s leading-edge functionality has been recognized internationally, as it powers key capabilities of the International Human Epigenome Consorium (IHEC) Data Portal.
The epigenome consists of chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it and when to do it. The marks, which are not part of the DNA itself, can be passed on from cell to cell as cells divide, and from one generation to the next.2 The GenAP tool within the IHEC Data Portal allows users to search, view and download epigenomic data. The Canadian Institutes of Health Research (CIHR) recognized the potential of this research area and have made significant investment in epigenomic research and the inclusion of Canadian software to enable access and use of over 5,500 epigenomic datasets further leverages CIHR’s investment in this area. The release announcing the IHEC Data Portal may be found here: http://ihec-epigenomes.org/news-events/details/article/large-ihec-data-release-over-5500-datasets-now-accessible-via-the-ihec-data-portal/.
“Providing a wide range of researchers and clinicians with access to this data both creates a new playing field and strengthens the team that is investigating the genomic factors impacting disease,” says Dr. Guillaume Bourque, Principal Investigator at GenAP. “GenAP has the potential to accelerate the interpretation of genetic information into knowledge that can then be applied in diagnosing, treating and preventing disease.”
“Software is the gateway for a large number of users to access genomic data and explore new avenues of research and discovery,” says Mark Wolff, Chief Technology Officer at CANARIE. “The software builds on the power of Canada’s National Research and Education Network – made up of CANARIE and its Regional Advanced Network partners – to seamlessly move data to where it’s needed.“
“The promise of personalized medicine is on our doorstep, accelerating our ability to improve the health and wellbeing of Canadians,” says Mark Dietrich, President and CEO of Compute Canada. “The availability of advanced scientific and computational technologies is the backbone required for the development of new medicines. GenAP is one of a suite of genomics and other discipline-specific services provided by Compute Canada that store, manage and exploit big data for the benefit of Canadians.”
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CANARIE designs and delivers digital infrastructure and drives its adoption for Canada’s research, education and innovation communities. CANARIE keeps Canada at the forefront of digital research and innovation, fundamental to a vibrant digital economy.
CANARIE’s roots are in advanced networking, and CANARIE continues to evolve the national ultra-high-speed backbone network that enables data-intensive, leading-edge research and big science across Canada and around the world. One million researchers, scientists and students at over 2,000 Canadian institutions, including universities, colleges, research institutes, hospitals, and government laboratories have access to the CANARIE Network.
CANARIE also leads the development of research software tools that enable researchers to more quickly and easily access research data, tools, and peers. In support of Canada’s high-tech entrepreneurs, CANARIE offers cloud-computing services to help them accelerate product development and gain a competitive edge in the marketplace.
Twelve provincial and territorial network partners, together with CANARIE, collectively form Canada’s National Research and Education Network (NREN). This powerful digital infrastructure connects Canadians to national and global data, tools, colleagues, and classrooms that fuel the engine of innovation in today’s digital economy.
Established in 1993, CANARIE is a non-profit corporation, with the major investment in its programs and activities provided by the Government of Canada.
About Compute Canada
Compute Canada, in partnership with regional organizations ACENET, Calcul Québec, Compute Ontario and WestGrid, leads the acceleration of research innovation by deploying state-of-the-art advanced research computing (ARC) systems, storage and software solutions. Together we provide essential ARC services and infrastructure for Canadian researchers and their collaborators in all academic and industrial sectors. Our world-class team of more than 200 experts employed by 35 partner universities and research institutions across the country provide direct support to research teams. Compute Canada is a proud ambassador for Canadian excellence in advanced research computing nationally and internationally.
2National Human Genome Research Institute. http://www.genome.gov/27532724