COVID Chasers

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.

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.

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.

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

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

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.

In this episode, we chat with Dr. Andrew Warren and Dr. Rebecca Wattam about how the constantly shape-shifting SARS-CoV-2 is keeping humanity on its toes. In addition to discussing the variants of concern, we discuss how scientists and policymakers have responded in this fluid landscape. 

Dr. Andrew Warren is a Research Assistant Professor at the Biocomplexity Institute and Initiative at the University of Virginia, a Senior Scientist and Senior Software Engineer for BVBRC under NIAID. His research interests include developing and applying algorithms for processing biological data for insight and hypothesis testing using comparative genomics, experimental analysis, machine learning, data mining, and graph modeling. Full bio at https://biocomplexity.virginia.edu/person/andrew-warren

Dr. Rebecca Wattam is a Research Associate Professor in the Network Simulation Science and Advanced Computing (NSSAC) Division within the Biocomplexity Institute, University of Virginia. Rebecca received her B.S. and M.S. degrees from the University of New Mexico in Biology, and a joint Ph.D. in Entomology and Veterinary Science at the University of Wisconsin-Madison. Rebecca received a MacArthur Fellowship to conduct postdoctoral research at the University of Arizona in Tucson, and she completed a second postdoctoral fellowship there as well before accepting a position on the faculty at Virginia Tech. She joined NSSAC in 2018. Full bio at https://biocomplexity.virginia.edu/person/rebecca-wattam

In this episode we invite Dr. Achla Marathe and Dr. Mark Orr to discuss how human behavior and economics interact during pandemics. In addition to describing how their research has contributed to understanding this aspect of COVID-19, they talk about the personal and professional challenges they have navigated during the pandemic.  

Dr. Achla Marathe is a professor at the Biocomplexity Institute and at the Department of Public Health Sciences, School of Medicine, at the University of Virginia. Marathe is also a member of the Network Systems Science and Advanced Computing division at the Biocomplexity Institute. Her research interests include health economics, data driven modeling of socially coupled systems, disaster economics, and energy markets. Full bio at https://biocomplexity.virginia.edu/person/achla-marathe

Dr. Mark Orr is a research associate professor in the Network Systems Science and Advanced Computing division. Orr was originally trained as a cognitive psychologist at the University of Illinois at Chicago. Orr received augmentation to this training with postdoctoral fellowships in computational modeling (Carnegie Mellon), neuroscience (Albert Einstein College of Medicine), and epidemiology/complex systems (Columbia University). Over the past decade, he has become heavily involved in understanding dynamic processes and drivers of risky behavior and decision making, primarily in a public health context, at the scale of the individual and populations. Full bio at https://biocomplexity.virginia.edu/person/mark-orr

In this episode, we talk to Drs. Abhijin Adiga, Sekharipuram Ravi, and Anil Vullikanti about developing models that can be trusted for large scale policymaking. Using examples from recent efforts beyond epidemiology, they discuss how with complex models come greater responsibility. 

Abhijin Adiga is a research assistant professor in the Network Systems Science and Advanced Computing division, Biocomplexity Institute, University of Virginia. His research interests include algorithms and graph theory, diffusion in complex networks, network science, game theory and geometric representation of graphs. Full bio at https://biocomplexity.virginia.edu/person/abhijin-adiga

Sekharipuram Ravi is a research professor in the Network Systems and Advanced Computing division, Biocomplexity Institute, University of Virginia and a distinguished teaching professor in the Department of Computer Science at the University at Albany-SUNY. His research interests include Design and Analysis of Algorithms, Data Mining, Wireless Networks, Operations Research, and Discrete Dynamical Systems. Full bio at https://biocomplexity.virginia.edu/person/ss-ravi

Anil Kumar S. Vullikanti is a professor in the Department of Computer Science and at the Biocomplexity Institute, University of Virginia. His research interests include modeling and simulation of social and infrastructure systems, epidemiology, distributed and mobile computing, combinatorial optimization, and combinatorial algorithms. Full bio at https://biocomplexity.virginia.edu/person/anil-vullikanti

In this episode, we talk to Drs. Mugdha Thakur and Baltazar Espinoza about the origins of mathematical models in epidemiology and how simple models can still reveal useful insights. As newly minted postdocs, they also talk about their transition into a large team working remotely during a pandemic.

Mugdha Thakur is a Postdoctoral Research Associate in the Network Systems Science and Advanced Computing division at the University of Virginia. Being skilled at mechanistic modeling, parameter translation and transdisciplinary communication, her research revolves around computational and mathematical epidemiology with a focus on the methods for incorporating results from public health and social studies research. 

Baltazar Espinoza is a Postdoctoral Research Associate in the Network Systems Science and Advanced Computing division at the University of Virginia. His research interests lie at the intersection of mathematical and computational models to study infectious diseases and population dynamics. Full bio at https://biocomplexity.virginia.edu/person/baltazar-espinoza