September 2, 2020
By Rob Mitchum
In supporting the University of Chicago community in its research and scholarship through computational expertise and resources, the Research Computing Center is used to adapting to different needs and situations. But there’s never been a challenge like this year, when coronavirus forced campus closures and remote learning and research.
As the threat of coronavirus mounted in early 2020, the RCC quickly mobilized its staff and resources to address this new challenge in two ways: making sure that ongoing UChicago research was not disrupted, while also spinning up new efforts to support new studies of the virus and the dangerous illness it causes.
RCC COVID-19 resources include a repository for COVID-19 datasets from the Illinois Department of Public Health and other public sources, special online workshops for analyzing COVID-19 data, and staff assistance in executing new projects using GIS, statistics, data visualization, machine learning, bioinformatics, and other tools.
But most notably, a special allocation on Midway2, the University of Chicago’s high-performance computing cluster, has provided over 4 million compute hours for UChicago scientists using computational tools to study the biological, medical, economic, and social implications of COVID-19. After just two months, these rapid research efforts have already produced several important results, predictions, and models to aid vaccine producers, public health officials, policymakers, and other groups fighting the pandemic and its consequences.
“There are so many COVID-related projects on campus these days, and in some of them, we are really playing an active role,” said Hakizumwami Birali Runesha, Director of the Research Computing Center and Assistant Vice President for Research Computing at UChicago. “We are enabling many of these projects in their pilot phase, and for us, that's the exciting part, because some of these faculty are not traditionally familiar with tools such as machine learning or AI.”
A Rapid, Multi-Dimensional Response to a Global Crisis
The scope of the COVID-19 pandemic is so large that it already touches upon virtually every field of research. Biologists study the molecular structure of the virus, clinical researchers test treatments and vaccine targets, public health experts measure its spread and the effectiveness of preventative measures, and economists and public policy researchers model the societal effects of illness and mitigation efforts.
Through its resources and staff, the RCC supports new projects in all of these areas. Thus far, the special Midway2 allocation — which grants priority access to the cluster for COVID-19 research — has served nine research groups from the Biological Sciences Division, the Social Sciences Division, the Pritzker School of Molecular Engineering, University of Chicago Medicine, and the Harris School of Public Policy, dedicating over 4 million hours of compute time to these studies.
Ishanu Chattopadhyay, assistant professor in the Committee on Genetics, Genomics and Systems Biology, has used nearly 2 million of those hours for his research into the origins and genetic evolution of the SARS-CoV-2 virus responsible for the current pandemic. With the PREEMPT (PREventing EMerging Pathogenic Threats) project from the Biological technologies Office (BTO) of the Defense Advanced Research Projects Agency (DARPA), Chattopadhyay previously built tools to study genetic differences in diseases such as influenza. But when COVID-19 appeared, he quickly adapted those models to study tens of thousands of samples of the new coronavirus.
By finding the hidden rules that govern the genetic “drift” of viruses, his research has the potential to improve the effectiveness of future vaccines as well as help scientists monitor other dangerous viruses before they make the jump from animals to humans. Chattopadhyay has already published research that would have taken two-to-three times longer without the priority access to Midway2.
“This would not be possible without RCC computing facilities and if they had not prioritized COVID work. I don't think we would have been able to do it before at least the end of summer,” Chattopadhyay said. “Most of the work that I do, I wouldn’t be able to do without RCC. It’s amazing.”
Another recipient of COVID-19 priority hours, Greg Kaplan, approaches the disease from a completely different angle. Kaplan, professor in Economics and The College, studies income inequality through the lens of macroeconomics, running complex models to test and predict the effects of economic shocks and policies on individuals across different levels of wealth.
The pandemic, and the lockdown policies deployed around the world to slow the spread of disease, presents a particularly extreme shock. Kaplan is combining macroeconomic models with epidemiological models to study how these policies affect people across different income levels and occupation types, and to test out different economic stimulus approaches under consideration by the world’s governments. Kaplan and his colleagues have already presented preliminary findings from those simulations to policymakers in the US and UK, and will soon present a working paper.
Like Chattopadhyay, Kaplan said that RCC support was essential for this quick turnaround, particularly as his group repeatedly redesigns and fine-tunes the new models.
“We're not running just one run of the model, we're running thousands and thousands, especially when we're trying to calibrate the data,” Kaplan said. “So when I submit 1000 runs in a night, I need to be confident that when I wake up in the morning they're going to be run, so that I can analyze the output and know where to go from there.”
“The RCC is a fantastic resource,” he added. “They make my job easier.”
Remote Scholarship Without Disruption
For many UChicago researchers, the remote spring and summer presented new challenges in keeping projects running while campus was largely closed. Research Computing Center staff and resources helped make this abrupt transition as smooth as possible, assisting faculty and students as they continue work away from their laboratories and offices.
The RCC systems and operations team responsible for the administration of Midway2 and other computational resources were deemed essential UChicago workers, and kept the systems up and running, maintaining normal service. That’s been critical, Runesha said, as Midway2 usage actually increased in spring quarter — an indication that many UChicago researchers working from home are launching or revisiting research ideas that utilize high-performance computing.
Other RCC services launched before the pandemic have proven critical for avoiding interruptions to important projects. The Secure Data Enclave — launched in 2019 in collaboration with IT Services, University Research Administration, and the Office of Legal Counsel — allows UChicago researchers to store and work with sensitive data remotely. Skyway is a new platform that helps RCC users easily seamlessly deploy resources and run computing tasks in the cloud the same way they would at the RCC without needing to learn how to provision cloud resources. Skyway is currently in its final pilot phase.
RCC staff has also continued to offer training and workshops in spring and summer quarters, shifting in-person events to online meeting software. An April workshop, “COVID-19 Epidemic Data Visualization,” was so popular it was held twice, attracting over 200 attendees. And the RCC team of computational experts remains available for remote support and consultations on various methods and approaches.
“It's not just access to our hardware, but it's also the access to all the support that we can provide in these difficult times,” Runesha said. “As always, the RCC is here to help you. Even if HPC and AI might not be your area of expertise, some of these resources can really transform your research by just trying them out.”