A special podcast series from researchers at the Biocomplexity Institute (NSSAC Division), University of Virginia on supporting COVID-19 response in the US over the past year.
Hosts: Srini Venkatramanan and Erin Raymond.
Twitter: @UVA_NSSAC #COVIDChasers
Deadlines and Lifelines
Join us for a look behind the curtain - researchers can only do their best work when they can focus on research. We'll introduce you to Edwina Lamm and Kristy Hall, two of the phenomenal administrators who make sure that all of the T's are crossed and I's are dotted.
Edwina Lamm is the Manager of Research Administration at the University of Virginia's Biocomplexity Institute. Edwina joined the Biocomplexity team while they were at Virginia Tech back in 2011 and has over 13 years in research administration. She has managed both preaward and postaward areas as well as being involved in contract negotiations. She is a graduate of Point University and a Certified Research Administrator.
Kristy Hall is the Sr. Advisor for Strategic Projects at the University of Virginia’s Biocomplexity Institute. Previously at UVA, Kristy was the Director of Contracts at the Office of Sponsored Programs and served as a Sr. Contract Negotiator at the UVA School of Medicine. She started her legal career as an associate at a law firm in Washington, D.C., focusing on communications law and corporate contracts. Prior to coming to UVA, Kristy was the Regional Counsel and Director of Government Affairs for a major cable company and also spent time working with non-profits and start-up companies. She earned her B.A., Magna Cum Laude, in 1996 from Olivet Nazarene University and her J.D. in 1999 from George Mason University.
Synth-pop is cool again!
Right around the time (late 80s and early 90s), synth-pop as a musical genre was fading from popularity, a group of scientists from Los Alamos National Laboratory were wondering how to revive at least the moniker. This work led to the development of synthetic representation of cities and countries populated by statistically similar individuals with households, activities, the whole shebang. In this episode, we talk to Dr. Samarth Swarup, who will walk us through some of the history and also how they are being used in current form to support epidemic models.
Samarth Swarup is a Research Associate Professor in the Network Systems Science and Advanced Computing division, Biocomplexity Institute, UVA. His research interests include resilience and sustainability, computational social science, and simulation analytics. You can see his full bio here.
Building as the earth quakes
A building, even a skyscraper, is only as strong as its foundation. Models and data-driven portals function robustly in the presence of a strong software infrastructure. In this episode, we talk to Drs. Henning Mortveit and Stefan Hoops about some of the infrastructure that supports the complex computer simulations used for pandemic response. They also reminisce about their shared alma mater and what has kept them going during the year of remote work.
Stefan Hoops is a Research Associate Professor in the Network Systems Science and Advanced Computing division, Biocomplexity Institute, UVA. His research interests include modeling and simulation of biochemical systems, management and analysis of systems biology data sets, and reverse-engineering of biochemical networks. You can read his full bio here.
Henning Mortveit is an associate professor in the Network Systems Science and Advanced Computing division, Biocomplexity Institute, and in the Department of Engineering Systems and Environment, UVA. His research work revolves around massively interacting systems whose network components co-evolve with time and is rooted in the framework of Graph Dynamical Systems (GDS). Part of his work covers software and system design for scalable, scientific computing. You can read his full bio here.
When the pipeline is clogged
Software packages rarely work in isolation. Accomplishing any useful task requires piecing together multiple software modules to work seamlessly and in a time critical manner. In this episode, we discuss with Przemek Porebski and Parantapa Bhattacharya about the software pipelines that support the weekly model updates and more complex counterfactual studies.
Przemek Porebski is a research scientist in the Network Systems Science and Advanced Computing division, Biocomplexity Institute, University of Virginia. As a software developer, structural biologist and bioinformatician he contributed to diverse biomedical research fields such as antibiotic resistance, enzymology, cancer development, allergy and blood physiology. His research interests include software development, interactive data visualization, data mining, data management. https://biocomplexity.virginia.edu/person/przemyslaw-przemek-porebski
Parantapa Bhattacharya is a postdoctoral research associate in the Network Systems Science and Advanced Computing division, Biocomplexity Institute, University of Virginia. Bhattacharya is interested in building tools and systems that allow humans to extract information out of large amounts of data, and analyzing and modeling behavior of large groups of humans on online social media. Full bio at https://biocomplexity.virginia.edu/person/parantapa-bhattacharya
Burning the midnight CPUs
High performance computing has become ubiquitous in modern-day science. COVID-19 response has been supported by computational modeling that requires such cutting edge platforms. In this episode, we talk to Dustin Machi who has helped coordinate the various COVID-19 response projects that require HPC backend, and recollects the experiences in working with the Pittsburgh Supercomputing Center. https://www.psc.edu/
Dustin Machi is a senior software architect in the Network Systems Science and Advanced Computing division, Biocomplexity Institute, University of Virginia. His research interests include Cyberinfrastructure, High-performance Computing (HPC), software engineering. Full bio at https://biocomplexity.virginia.edu/person/dustin-machi
Special Episode: COVID-19 and the Multiverse of Badness
Researchers in the University of Virginia’s Biocomplexity Institute’s Network Systems Science and Advanced Computing Division have been building scenario-based models for the last two decades, providing critical information to decision makers at the state and federal levels.
Since January 2020, they have focused their efforts on modeling COVID-19 and participated in a variety of independent and collaborative efforts to provide policymakers with up-to-date counterfactual analysis of COVID-19 spread. Their work with the COVID19 Scenario Modeling Hub (https://covid19scenariomodelinghub.org/) was highlighted in the May 5th edition of the CDC’s Morbidity and Mortality Weekly Report (MMWR). https://www.cdc.gov/mmwr/volumes/70/wr/mm7019e3.htm
On this special edition of COVID Chasers, we want to offer you some insight into this team and provide additional depth to our decades-long work in scenario-based modeling. You’ve met all of these researchers on past episodes, and we hope you enjoy this opportunity to dig a little deeper into this critical work.
Bonus link: Do check out the Twitter thread by co-host Srini Venkatramanan explaining how such scenario based approaches aid in epidemic response. https://twitter.com/sriniv_venkat/status/1390431794722394119