Last update/recompile: 2022-09-23 13:17:59

This site will not be further updated. It will remain here for reference. We are only keeping the logistic parts here. The content has been moved (and continues to be updated) at our permanent, stand-alone site/course Simulation Modeling in Immunology.

Welcome to the website for the course/module called Infectious Diseases, Immunology and Within-Host Models, which is part of the 2021 Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID).

The course is taught by Andreas Handel and Paul Thomas. Our teaching assistant (TA) for the course is Cody Dailey. You can reach us all on Slack (see the Communication page).


We are making some last-minute updates to the DSAIRM package. To make sure you have the latest, install it from GitHub the day before the workshop starts. (You can install it any time prior, or install from CRAN, just make sure if you do that to re-install the day before the workshop by typing these commands into the R console):

install.packages('remotes') #if you don't have the remotes package installed yet

Then load the package and open the menu with these commands:


For more details, see the Software Setup module of the SMI site.

Website content

The Syllabus provides a brief overview with a few logistic details.

The Schedule lists the topics, with links to materials. Most of the materials are on a separate site called Simulation Modeling in Immunology which we use as the main, permanent repository for teaching materials related to this course (and other workshops).

The Communication section provides information on how course communications are planned to happen.

The Resources section contains a listing of the main sources and materials we’ll be using in this course, as well as links to further resources.

The Project section has information and instructions for a - completely optional - course project you can do if you want.

Getting started

Start by briefly going through all the sections on this website. The go through and do everything listed in the Before course start section of the Schedule.


We are a Module of SISMID. However, for our purposes, we refer to our module as a course or class, and use module for individual segments, which are further divided into units. We hope this is not too confusing.

By default, all links open in the current tab. You’ll likely want external ones to open in a separate tab or window. To do so, you can (with most browsers) hold the Ctrl button when clicking, or do a right-click and select open in new tab/window.


This course was developed and is maintained by Andreas Handel and Paul Thomas.


The materials are licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Linked and embedded materials are governed by their own licenses. We assume that all external materials used or embedded here are covered under the educational fair use policy. If this is not the case and any material displayed here violates copyright, please let me know and we will remove it.