May 7, 2021
The Canadian VirusSeq Data Portal is critical to sharing information to better understand the virus
Adaptation has been key to living and working during the COVID-19 pandemic. The agility of OICR’s software engineering team was recently on full display when they built a COVID-19 data portal in just four weeks – a record time for the group. The freshly launched Canadian VirusSeq Data Portal, part of Genome Canada’s CanCOGeN COVID-19 research initiative, provides a vital link between Canada’s public health units and researchers tracking the evolution of the virus and variants of concern.
“When you are building something this complex in such little time there really is no roadmap. Luckily our team was able to draw on our deep experience in building similar platforms, which helped us get this urgent project done on time,” says Dr. Christina Yung, Director, Genome Informatics, OICR. “This experience, incredible teamwork and a deep desire to assist in Canada’s response to the pandemic fueled our sprint to complete this project.”
Having created data portals for many major research projects, including the International Cancer Genome Consortium, Yung’s team was well prepared to meet the challenge and create this vital resource for Canada’s fight against COVID-19. Over the past several years the team has worked to package their software tools into a modular system called Overture.
“Overture provided us with a robust framework from which to start building the VirusSeq portal. From there we were able to customize the portal to meet the specific needs of users,” explains Yung. “By making it as easy to use as possible we hope to attract the participation of many public health units and researchers.”
The Canadian VirusSeq Data Portal allows public health units to easily submit genomic sequencing data of SARS-CoV-2 infections. The deidentified data is then validated and quickly released into the data portal where it can be used by experts such as virologists and epidemiologists. The data available through the portal will aid in better understanding the virus and provide increased surveillance for variants of concern.
“Our next steps will be to make updates and improvements to the portal as more users come onboard and provide feedback,” says Yung. “I encourage public health units and researchers to take advantage of this tool to deepen collaboration in our efforts against COVID-19.”
The following individuals at OICR contributed to the development of the Canadian VirusSeq Data Portal: Yelizar Alturmessov, Dusan Andric, Rosita Bajari, Jared Baker, Kim Cullion, Henrich Feher, Atul Kachru, Alexandru Lepsa, Justin Richardsson, Jaser Uddin, Linda Xiang.
April 8, 2021
Genome Canada has announced the launch of a new, Canadian SARS-CoV-2 Data Portal that will manage and facilitate data sharing of viral genome sequences among Canadian public health labs, researchers and other groups interested in accessing the data for research purposes.
McGill University’s, Dr. Guillaume Bourque and his team will lead the project in collaboration with the Canadian COVID Genomics Network (CanCOGeN) and a number of world-leading genomics scientists specializing in data science, including Dr. Christina Yung, Director of Genome Informatics, OICR, and Dr. Lincoln Stein, Head, Adaptive Oncology, OICR.
The team will also collaborate with DNA Stack, a CanCOGeN industry partner led by OICR Associate Dr. Marc Fiume. The Data Portal will make use of DNA Stack’s COVID Cloud platform to develop and provide real-time analytical dashboards, data exploration and standards-compliant data interfaces.
October 15, 2020
OICR team awarded $300,000 to expand cancer research software tools for more researchers, new disease applications and greater impact
OICR’s Genome Informatics team receives federal funding from Canada’s National Research and Education Network to expand Overture, an open-source software suite for big data genomic research
Software tools are key to turning big data into discoveries in science and medicine. Reusing existing software accelerates the pace of discovery and can maximize the impact of public funding for research but only if the software is accessible and useable.
Today, Canada’s National Research and Education Network, CANARIE, announced their support of 12 teams across Canada as they adapt their existing research platforms for re-use by other research teams. With this funding, the OICR Genome Informatics team will evolve the accessibility and functionality of Overture, their software suite for big data genomic research.
“Our team has a longstanding commitment to the community,” says Dr. Christina Yung, Director of Genome Informatics. “We want to maximize the impact with the resources we have, which means focusing on key challenges and making our tools the most useful for the research community. This funding will allow us to do just that.”
Overture is a software suite of customizable and extendable tools for big data genomic research. One of Overture’s key products allows research teams to store and distribute genomic datasets while providing an authentication and authorization system for secure and safe data sharing. Overture also provides user-friendly portals for browsing and querying data, which was developed as part of the International Cancer Genome Consortium (ICGC) and the European-Canadian Cancer Network (EUCANCan).
CANARIE’s support will allow OICR’s team to simplify Overture installation and configuration, provide additional authentication functionality and improve the customizability of the data portal.
“With this support, we will add new features to increase adoption by new research teams,” says Yung. “The hope is to enable research teams from across Canada and around the world to re-use the software that we developed and accelerate their own discoveries. We’re grateful for how the community has contributed to our research through sharing open-source software and we’re proud to give back.”
“The ability to connect, share data and work collaboratively with researchers from across Canada and the world is a priority for our government,” said the Honourable Navdeep Bains, Minister of Innovation, Science and Industry [link to release]. “Today’s funding will help accelerate Canadian discoveries by making it easier for our researchers to find, access, and reuse data with collaborators across the country and around the world.”
June 26, 2020
OICR’s Genome Informatics team announces international release of the ICGC-ARGO Data Platform, the all-in-one data hub for the largest clinical-genomic data sharing initiative in the world
We’re in the midst of an era of big data that is changing the way we understand the world – including how we study, diagnose and treat cancers.
Improvements in sequencing technology and computational power have allowed us to collect massive amounts of information about cancer patients and their tumours. This information, however, is only powerful if it can be accessed by those who can transform big data into new discoveries.
Over the last decade, OICR’s Genome Informatics has built a reputation for developing robust big data portals that provide cancer data access to thousands of researchers around the world. Now, the Genome Informatics team has set out to do it again – this time with bigger data.Continue reading – Opening the virtual floodgates for cancer research and discovery
September 11, 2018
OICR’s Genome Informatics team plays key role in development of the Gabriella Miller Kids First Data Resource Portal
Toronto (September 11, 2018) – Today, the Gabriella Miller Kids First Data Resource Center (DRC) at the Children’s Hospital of Philadelphia launched the Kids First Data Resource Portal, which will advance personalized medicine for the detection, therapy, and management of childhood cancer and structural birth defects. As the Kids First DRC’s chief outward-facing tool, the Kids First Data Resource Portal serves the needs of a diverse group of patients, researchers, and clinicians partnering to create the world’s largest database of pediatric genomic data, and provides the necessary tools and computational resources for their analysis and interpretation.
September 6, 2018
OICR welcomes Dr. Christina Yung as Director of Genome Informatics. Yung is returning to OICR from the University of Chicago where she led and managed the National Cancer Institute’s Genomic Data Commons (GDC) – a unified data system that promotes the sharing of genomic and clinical data between researchers.