SISMID 2023 Course Schedule

This is the schedule for the course. From here, you can access all instructions and materials to help you prepare.

This schedule is subject to change, so check for updates.

Notes

• Abbreviations used:

  • DSAIRM = Dynamical Systems Approach to Immune Response Modeling - R package.
  • SMI = Simulation Modeling in Immunology - website.

• SISMID was online in 2020-2022 and we recorded our lectures. These recorded lectures and a lot of other materials are available on our Simulation Modeling for Immunology (SMI) website. This website is continuously online and will receive future updates as we produce more content.

• This course website will likely remain online, but will not be further updated after the course.

• The DSAIRM package and other mentioned R packages will continue to be available and might receive occasional updates.

• Some of the slides below are in html. If you prefer pdf, it is easiest to open the html file in your browser, click the menu bar on the bottom left, under “Tools”, choose “PDF export mode” and then go to the print menu of the browser and print/save as pdf. The Chrome browser generally works best for this.

Before course start

• Familiarize yourself with this website. Read through all of it.
• Browse through our paper Simulation Modelling for Immunologists.
• Set up the tools needed for this course, namely R, Rstudio and the DSAIRM package.
  • Here are instructions for setting up R and RStudio.
  • This explains how to install and use the DSAIRM package.
  • This is the DSAIRM website with more details.
• If you can, take a look at these apps in DSAIRM: Basic Bacteria Model and Basic Virus Model. Play around with them and go through (some of) the tasks to get familiar with DSAIRM.

Course schedule

Monday 7/17

Unit 1, 8.30AM - 10AM: Introduction to Immunology (Paul) - Slides

Unit 2, 10.30AM - noon: Introduction to Modeling (Andreas) - Slides

Unit 3, 1:30PM – 3PM: Immunology of viral infections (Paul) - Slides

Unit 4, 3.30PM – 5PM: Modeling of viral infections (Andreas) - Slides

Homework for tomorrow:

• If you haven’t already, take a look at the “Basic Bacteria Model” app and go through - in as much detail as you have time - the “What to do” tasks. You can try yourself first, or walk through it with the help of the solution.
• Take an especially close look at the solution for task 6 and the R code for it, we will use a similar approach tomorrow.

Tuesday 7/18

Unit 5, 8.30AM - 10AM: Immunology of bacterial infections (Paul) - Slides

Unit 6 10.30AM - noon: Modeling of bacterial infections (Andreas) - Slides, Code

Unit 7, 1:30PM – 3PM: Immunology of drug and vaccine treatments (Paul) - Slides

Unit 8, 3.30PM – 5PM: Modeling drug and vaccine treatments (Andreas) - Slides, Code 1, Code 2

Wednesday 7/19

Unit 9, 8.30AM - 10AM: A worked modeling example (Andreas)

Unit 10, 10.30AM - noon: Topics as requested (Paul/Andreas)

Any time during and after the course

Go through any additional content on the SMI website that you are interested in. Explore the DSAIRM models. Ask us questions about any of those topics.