This website provides materials covering introductions to both immunology and simulation modeling of pathogens and the immune response on the within-host level. The focus is on the modeling aspect.

You will learn what simulation models are and how they can be used to study pathogen and immune response dynamics within an infected host.


We assume some general familiarity with basic biology, maybe some immunology, and some statistical, modeling or coding experience. We understand every student will come with different skill sets. Since this is an introductory course, we try to make things as understandable as possible for anyone, no matter their previous knowledge. That means that some of the material might be too basic for you, will others will be new to you (and likely challenging).

Additional resources

We wrote an R package that provides a hands-on approach to learning the topics covered here. The R package is called Dynamical Systems Approach to Immune Response Modeling (DSAIRM). We will often refer to it and assume that you will be using it together with the materials on this website. The first module provides instructions on how to get DSAIRM up and running.