COVID Chasers
By COVID Chasers
Hosts: Srini Venkatramanan and Erin Raymond.
For more information:
Email: covidchasers@virginia.edu
Twitter: @UVA_NSSAC #COVIDChasers
Website: biocomplexity.virginia.edu/nssac
COVID ChasersApr 01, 2021
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
Virus makes a few typos
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
When the mind and money meet
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 models we trust?
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
An ode to ODEs
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
Plotting for a cause
In this episode, we will be talking to Dr. Alex Telionis, Dr. James Schlitt and Joseph Outten about the various analytics that help understand and respond to outbreaks and epidemics. Especially, they will discuss a few examples of visualizations that were generated to help policymakers during the COVID-19 response.
Alex Telionis is a postdoctoral researcher with the NSSAC Division, Biocomplexity Institute, University of Virginia. https://biocomplexity.virginia.edu/person/alex-telionis
James Schlitt is a postdoctoral researcher with the NSSAC Division, Biocomplexity Institute, University of Virginia. https://biocomplexity.virginia.edu/person/james-schlitt
Joseph Outten is a final year undergraduate student at University of Virginia, majoring in Computer Science and Biology. His research interests lie in the intersection of these two fields and include topics from biotechnology, synthetic biology, and bioinformatics. Full bio at https://biocomplexity.virginia.edu/person/joseph-outten
Crowd-y with a chance of masks
In this episode, we will be talking to Dr. Aniruddha Adiga, Lijing Wang, and Ben Hurt about the challenges of forecasting an ongoing epidemic such as COVID-19. In addition to the various statistical and machine learning techniques being used, they discuss the pros and cons of multiple external indicators such as mobility and behavior.
Aniruddha Adiga is a postdoctoral researcher with the NSSAC Division, Biocomplexity Institute, University of Virginia. His research interests include signal processing, machine learning, data mining, and big data analysis. https://biocomplexity.virginia.edu/person/aniruddha-adiga
Lijing Wang is a graduate student with the Department of Computer Science and student researcher with NSSAC Division, Biocomplexity Institute, University of Virginia. While her current research focuses on combining causal mechanistic models and deep neural network models for epidemic forecasting, she is also interested in machine learning, deep learning, artificial intelligence, time series analysis, and network science. https://biocomplexity.virginia.edu/person/lijing-wang
Benjamin Hurt is a data scientist with NSSAC Division, Biocomplexity Institute, University of Virginia. His research interests include machine learning, artificial intelligence, forecasting, and financial system analysis. https://biocomplexity.virginia.edu/person/ben-hurt
Dashing through the boards
In this episode, we will be talking with Mandy Wilson and Dawen Xie about designing and maintaining multiple dashboards that serve epidemiological information to multiple stakeholders. Ranging from disease surveillance to hospital capacity and intervention management, they discuss the trials and tribulations of building these platforms and constantly improving them based on user feedback.
Mandy Wilson is a research scientist at the NSSAC division, Biocomplexity Institute at the University of Virginia; prior to that, she was an employee of the Biocomplexity Institute of Virginia Tech from 2008 - 2018. Wilson has had a broad range of work experiences, including custom software development for the federal government and the private sector. Her research interests include synthetic biology, modeling behavior on social media, epidemiology, database architecture, and data mining. Full bio at https://biocomplexity.virginia.edu/person/mandy-wilson
Dawen Xie is a research scientist at the NSSAC division, Biocomplexity Institute at the University of Virginia. Xie is interested in the Geographic Information System (GIS), visual analytics, information management system, and database with a current focus on building different dynamic web systems. Full bio at https://biocomplexity.virginia.edu/person/dawen-xie
Data, data, everywhere!
In this episode, we will be talking to Brian Klahn and Akhil Sai Peddireddy about the challenges of dealing with the constantly shifting data landscape. In addition to describing the how they curated the varied datasets being used by modelers, they talk about the lessons that can be carried forward.
Brian Klahn is a research scientist in the NSSAC division of Biocomplexity Institute, University of Virginia. Klahn served in the U.S. Navy’s Nuclear Power Program, which included active duty in the first Persian Gulf War. Upon honorable discharge, Klahn went on to earn a B.S. in Molecular Biology, followed by an M.S. in Neuro-Physiology from the University of Wisconsin. His research interests include open, robust and maintainable software systems, biological modeling of many kinds and scales, genomic classification and characterization system. Full bio at https://biocomplexity.virginia.edu/person/brian-klahn
Akhil Sai Peddireddy is a Graduate Research Assistant in the NSSAC division of Biocomplexity Institute, University of Virginia. He is pursuing an MS in Computer Science at the University of Virginia. His research interests include global surveillance of epidemics and time-series forecasting of infectious diseases using statistical and machine learning models. Full bio at https://biocomplexity.virginia.edu/person/akhil-peddireddy
Keep Calm and Compute on
In this episode, we talk to Dr. Jiangzhuo Chen about various computational models that have been used by the team to support COVID-19 response. Our co-host, Srini Venkatramanan will also join in describing how these different approaches complement each other.
Jiangzhuo Chen is a research associate professor with the NSSAC division, Biocomplexity Institute, University of Virginia. His research interests include big data analytics, model-based forecasting, modeling, simulation, and analysis of large-scale social networks, computational epidemiology, and computational economics. Full bio at https://biocomplexity.virginia.edu/person/jiangzhuo-chen
Srini Venkatramanan is a research scientist with the NSSAC division, Biocomplexity Institute, University of Virginia. His research interests include infectious disease modeling, model calibration and forecasting, resource allocation optimization, simulation analytics, and network science. Full bio at https://biocomplexity.virginia.edu/person/srinivasan-venkatramanan
Every Model needs a Messenger
In this episode we talk to Dr. Bryan Lewis about the challenges associated with communicating about epidemic models and analytics with policymakers and public health departments. We also discuss how the team has coordinated over the past year for keeping the weekly delivery pipeline up to date and running, while maintaining work-life balance (case in point, Bryan's German Shepard puppy who makes a special appearance!).
Bryan Lewis is a research associate professor in the NSSAC division, Biocomplexity Institute, University of Virginia. His research interests include public health and epidemiology, epidemic modeling, social network construction, and graph measures and dynamic networks. As a computational epidemiologist, Lewis acts as a liaison between the computer scientists and mathematicians designing and building simulation software and decision makers who want answers to pressing public policy questions. Full bio at https://biocomplexity.virginia.edu/person/bryan-lewis
Smells like Team Spirit
In this episode, we talk to Dr. Stephen Eubank and Dr. Madhav Marathe of the Biocomplexity Institute, University of Virginia about aspects of team science and cultivating a trans-disciplinary research environment. We also discuss the team's origins and how it has evolved over the years, rising up to the challenges of supporting pandemic response in real-time.
Dr. Stephen Eubank is deputy director in the Network Systems Science and Advanced Computing division and a tenured professor, Department of Public Health Sciences, University of Virginia. His research interests include simulating large socio-technical systems, computational epidemiology, scaling in complex systems, and network structure and graph theory. Full bio at https://biocomplexity.virginia.edu/person/stephen-eubank
Dr. Madhav Marathe is an endowed Distinguished Professor in Biocomplexity, Director of the Network Systems Science and Advanced Computing (NSSAC) Division, and a tenured Professor of Computer Science at the University of Virginia. His research interests include science of massively interacting networked systems, machine learning and artificial intelligence, computational modeling and simulation, and theoretical computer science. Full bio at https://biocomplexity.virginia.edu/person/madhav-marathe
Science goes Marching in
Introducing COVID Chasers.
A special podcast series from researchers at the Biocomplexity Institute (NSSAC Division), University of Virginia on supporting COVID-19 response in the United States over the past year. In this episode, the hosts discuss the motivation behind the podcast series, and why it is important to do it in the current, hopefully final, phase of the pandemic.
Hosts: Srini Venkatramanan and Erin Raymond.
Email us at covidchasers@virginia.edu or tweet us at @UVA_NSSAC with the hashtag #COVIDChasers.
Additional Notes:
Biocomplexity Institute COVID-19 response: https://biocomplexity.virginia.edu/project/covid-19-pandemic-response
Network Systems Science and Advanced Computing Division: http://biocomplexity.virginia.edu/nssac