Network Modeling for Epidemics (NME) is a 5-day short course at the University of Washington that provides an introduction to stochastic network models for infectious disease transmission dynamics, with a focus on empirically based modeling of HIV transmission. It is a ‘’hands-on’’ course, using the EpiModel software package in R (www.epimodel.org).

EpiModel provides a unified framework for statistically based modeling of dynamic networks from empirical data, and simulation of epidemic dynamics on these networks. It has a flexible open-source platform for learning and building several types of epidemic models: deterministic compartmental, stochastic individual-based, and stochastic network models. Resources include simple models that run in a browser window, built-in generic models that provide basic control over population contact patterns, pathogen properties and demographics, and templates for user-programmed modules that allow EpiModel to be extended to the full range of pathogens, hosts, and disease dynamics for advanced research.

This course will touch on the deterministic and individual-based models, but its primary focus is on the theory, methods and application of network models. The course uses a mix of lectures, tutorials, and labs with students working in small groups. On the final day, students work to develop an EpiModel prototype model (either individually or in groups based on shared research interests), with input from the instructors. Students are required to bring their own laptop computer to the course.

Prior to the course, students are recommended to review the materials on the PREP page. Each day’s materials will be posted on the respective page linked above.

2020 Course Information

The 2020 Network Modeling for Epidemics course will be offered from Monday, August 17 to Friday, August 21 at the University of Washington in Seattle. The course scheduled will run from approximately 9 am to 5 pm each day, with breaks for coffee and lunch. (Coffee, refreshments and meals are not provided, but a variety of options for each are available near the course location.)

April 2020 COVID-19 Update

Due to the travel restrictions associated with the COVID-19 global pandemic, we have updated our plans for NME 2020 as follows:

  • In addition to the standard in-person workshop format, we will be offering a concurrent virtual, web-based option for participation in NME 2020. This web-based option will be hosted live via Zoom (or related technology), concurrent with the in-person workshop. Virtual students will access our lectures live (during our regular class hours) and/or in recorded form, complete and submit the interactive lab activities online for instructor comment and evaluation, and discuss the material with the instructors via video-based and text-based chats. Although the class interactions will be more limited with the virtual option, the instructors will make every effort to deliver and discuss the material collectively to engage both in-person and virtual students. If you are interested in the virtual option, please indicate this on your application.
  • We will continue to monitor whether we can hold the in-person NME 2020 due to ongoing travel restrictions over the next 2 months. By June 1, we will make the final determination about whether the in-person NME 2020 will be held. If an in-person NME is not possible, we will conduct NME 2020 fully in a virtual format. We will contact everyone registered for NME 2020 by email on June 1 with our decision.

Course Syllabus

The course uses mornings for lectures, and afternoons for labs with students working in small groups. On the final day, students have the option of developing an EpiModel prototype for their own research projects, with input from the instructors, which includes the EpiModel software developers.

Day Topics
1 Introduction to epidemic modeling; Stochastic models for epidemics; Classical descriptive network analysis
2 Cross-sectional statistical network analysis (ERGMs); Dynamic statistical network analysis (STERGMs)
3 Simple epidemic models on networks; Epidemics in fixed populations with network dynamics independent of disease state
4 General epidemic models on networks; Epidemics in open populations, with interactions between networks, demographics and infection
5 Extending EpiModel for original research projects; Individual consultations on participant projects

Application Information

Dates
  • Apr 19: Fee-waiver application deadline. Decisions will be made by Apr 30, and response required by May 15.
  • May 17: General application deadline. Decisions will be made by May 30 and a response required by June 15.
  • A waitlist will be established along with rolling admission through June 30 if space allows.
Costs

Course fee is $800 for the in-person option and $500 for the virtual option. Travel and accommodation costs are the responsibility of the participant, although discounted hotel rates are available. We offer a limited number of fee waivers for pre-doctoral students or for attendees from low income countries. These cover waiver of the registration fee only; travel and accommodation are still the responsibility of the fee waiver recipient.

Returning Students

We encourage previous attendees with active modeling projects to apply to return for a refresher course. The EpiModel package has been significantly enhanced over the last few years. Returning students with active projects will have the opportunity to work with course instructors to address key challenges in the design of their network model code.

Previous Course Offerings

This course, either in its entirety or parts of it, has been offered at the following locations:

Other

Email Lists

We encourage you to join the email lists for Statnet and EpiModel as a place to ask questions, report bugs, and tell us about your research using these tools.

Funding

This course is supported by grant number R01 AI138783 from the National Institutes of Health.