Neuroinformatics

Dr. Stephen Strother sets up neuroinformatics frameworks to speed up the translation of imaging neuroscience for clinical studies of brain disorders

Neuroinformatics Research Compute Canada Dr Stephen Stother

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Dr. Stephen Strother

Dr. Stephen Strother

Research area
Dr. Stephen Strother spent a year in medical school before realizing his real passion was in math and physics. So he fashioned a career that would allow him to combine those passions with his interest in medical research, specifically how the brain works. He completed a PhD at McGill University’s Montreal Neurological Institute and today, he works as a medical biophysicist who specializes in neuroinformatics, neuroimaging and machine learning approaches to neuroscience research using high performance computing (HPC). He works at the Rotman Research Institute at Baycrest Health Sciences in Toronto, conducting multi-disciplinary research. In short, he finds himself where medical imaging, computer science, statistics and computational neuroscience meet neurology and psychiatry.

Relevance to other sectors
Dr. Strother’s primary role is to facilitate studies and techniques across a range of disease systems in the brain — everything from autism, depression, epilepsy and traumatic brain injury. “What I do doesn’t directly help Canadians, but it helps others help Canadians,” he explained. More formally, he sets up neuroinformatics frameworks to speed up the translation of imaging neuroscience for clinical studies of brain disorders. Through the Brain-CODE data repository, he ensures that his team standardizes high-quality neuroimaging data collection. Working with biostatisticians, he ensures that once data is in the repository, they have the techniques to easily detect biomarkers and statistical trends. For example, they’ll be able to see how quickly an ALS patient declines. “I think of myself as part of the glue in the background that keeps high-quality studies running to ensure their impact on the health of Canadians is maximized,” he said.

A consortium, which brings together several institutions and is led by Ken Evans of InDOC, under contract from the Ontario Brain Institute (OBI), is building Brain-CODE to support collaborative, integrated neuroscience work across Ontario. For his part, Dr. Strother leads Brain-CODE’s neuroimaging program, which provides the first standardized and validated quality-control and assurance program for integrating data across 12 centres in Ontario.

So what are “neuroinformatics” and “workflows” and what does he mean by neuroinformatics frameworks and neuroscience workflows?
Dr. Strother believes the future of understanding, diagnosing and monitoring treatment for brain disease requires researchers to collect much larger data samples. To that end, neuroinformatics combines the rapidly advancing fields of neuroscience and information science. Both fields have undergone exponential development in the last 30 years, and the idea that their intersection was an important area of research focus emerged in the 1990s in the middle of Dr. Strother’s career. The goal of neuroinformatics is to develop digital frameworks to make it easier to read data, use tools and share neuroscience results among many partners. Researchers use the frameworks to speed up scientific discovery and apply those findings to clinical studies to ultimately find effective disease treatments. Neuroscience workflows, meanwhile, refer to the set of often complex steps involved in experimental data acquisition, processing and analysis. Improving the utility and accessibility of specialized neuroscience workflows is a key focus of this research.

What is the current focus of Dr. Strother’s research?
His work moves in multiple complementary directions. In addition to helping build Brain-CODE for OBI, he is heavily involved in the neuroimaging component of two depression and neurodegeneration disease programs also funded by OBI. This gives his students and collaborators — who are funded through regular CIHR and NSERC grants — the opportunity to translate research on optimized neuroimaging workflows into large-scale clinical studies. The HPC Virtual Laboratory (HPCVL) at Queen’s supports this work through regular Compute Canada-managed accounts and with the specialized HPCVL environment developed for Brain-CODE. His projects are also funded by Brain Canada, in collaboration with McGill University’s Alan Evans, to link Brain-CODE with the LORIS database being used to support the national Canadian Consortium on Neurodegeneration in Aging, funded by the CIHR and partners. As part of this project, Dr. Strother will be linking Brain-CODE to the CBrain portal developed by Dr. Evans’ group, which facilitates access to multiple Compute Canada centres for neuroimage data processing and analysis.

There are more than 30 institutions and 100s of researchers represented in the OBI-funded disease programs. How did Dr. Strother make this massive amount of data easy for researchers to navigate?
Dr. Strother notes that investigators are starting to collaborate instead of working in silos, so rather than being judged on the number of papers they publish individually, they are being encouraged to work with others, to the collective benefit of mankind. “It’s a different way of working and a big change, but overall it’s the way all industries are moving because it’s effective,” he said. “Just think of the ideas that will be discovered when there are 100 people trying to answer one question instead of just one person.”

Dr. Strother’s own team is working in close collaboration with Ken Edgecombe, Chris Macphee and Costa Dafnas at HPCVL, and Moyez Dharsee and Rachad Badrawi at InDOC. They  have just rolled out prototype dashboards using Spotfire that allow clinical co-ordinators to track overall data acquisition of clinical, neuropsychological, neuroimaging and genomic data. He and colleagues are also developing specialized dashboards to allow neuroimaging centres to track their quality control and assurance results and compare their performance to other centres.

How does Compute Canada play a role in making this data more widely available?
Much of his neuroinformatics research would be very difficult to impossible to perform without Compute Canada’s support. Having HPCVL integrated as a member of the development consortium for Brain-CODE has been critical to making progress. Furthermore, optimizing complex workflows can take days to run and quickly saturates local computing resources at Baycrest. Having access to regular Compute Canada research accounts has been critical to accelerating research on neuroimaging workflows.

Only a small number of researchers who used Compute Canada in the past year were from the neurosciences. Will that number grow?
Absolutely. Dr. Strother only started using Compute Canada resources five to six years ago and a growing number of his colleagues have become users since then. In addition, he advocates for the neuroscience community and its vitally important contributions as a member of the Advisory Council on Research for the Board of Directors of Compute Canada. While there is still a fairly steep learning curve for a cognitive psychologist to use some of the more traditional Compute Canada infrastructure, many developments are improving this situation. Of key importance is a growing realization among more traditional disciplines, such as psychology and even biophysics, of the importance of obtaining strong multi-disciplinary skills in computer science and data analysis.

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