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 regularly for updates. We will also adjust as needed, e.g. if we run over or end early, we just move breaks around. It’s the same Zoom link for all meetings (see Slack for link).
SISMID was online last year and we recorded our lectures. Instead of repeating the same lectures from last year, we figured you will get more out of the course if you watch (some of) our lectures from last year on your own time in advance, and then in our Zoom meetings we will just be emphasizing some of the highlights of our lectures, followed by discussion and Q&A time. This only works if you actually watch the lectures. If not, you’ll likely feel lost. You have been warned 😄.
Time zones: Seattle is in the PT zone. Your instructors are in ET (Andreas) and CT (Paul) zones. Some of you are likely in yet other locations and time zones. We hope we can keep things straight. For any times in this course we will use PT/Seattle time as reference. We also plan to be clear when posting any time by stating the time zone explicitly. If ever in doubt, i.e. if you see us posting a time without specifying the zone, please tell us to clarify.
For details on Slack and Zoom use, see the Communication section.
Abbreviations used: DSAIRM = Dynamical Systems Approach to Immune Response Modeling - R package. SMI = Simulation Modeling in Immunology - website.
As preparation before we meet, do the following:
Watch the Introduction to Innate Immunity and Introduction to Adaptive Immunity lecture recordings, which you can find here.
Watch the Introduction to Modeling and Introduction to Simple Models lecture recordings, which you can find here. You are welcome to read through the additional content provided in that module, but you don’t have to.
11.30PT (1.30CT/2.30ET) - 12.15PT - Zoom: Welcome and Introduction
break
12.30PT (2.30CT/3.30ET) - 1.30PT - Zoom: Introduction to Immunology - Highlights and Discussion (Paul)
break
1.45PT (3.45CT/4.45ET) - 2.30PT - Zoom: Introduction to Modeling - Highlights and Discussion (Andreas)
Rest of day - On your own: Explore DSAIRM. Go through SMI materials. Prepare for tomorrow. Communication through Slack.
As preparation before we meet, do the following:
Watch the Introduction to Influenza lecture recording, which you can find here.
Go through the Using Models for Exploration unit on SMI, which you can find here.
Take a look at these apps in DSAIRM: Basic Bacteria Model and Bacteria Model Exploration. You don’t need to fully work through them, but read the Model sections and play with them briefly so you are a bit familiar with them. We’ll investigate them today during our live DSAIRM exercise sessions.
The SMI site also contains a lecture on HCV in the Viral Infections module, lectures on TB and Malaria in the Complex Pathogens module, and several additional units in the Using Simulation Models module. Feel free to go through any of them and ask any questions about those topics during our discussions (or on Slack).
8PT (10CT/11ET) - 8.45PT - Zoom: SARS-Cov-2 Virology and Immunology (Paul)
break
9.00PT (11CT/12ET) - 9.30PT - Zoom: Discussing SARS-Cov-2, Influenza and other virus infections and immunology (Paul)
break
9.45PT (11.45CT/12.45ET) - 11.00PT - Zoom: DSAIRM level I exercise (Andreas)
11PT (1CT/2ET) - 12PT Lunch Break - Go through SMI materials or explore DSAIRM on your own. Communication through Slack.
12PT (2CT/3ET) - 12.45PT – Zoom: Infection and Immunology of Helminths (Paul)
break
1.00PT (3CT/4ET) - 1.20PT – Zoom: Discussing Helminths and other complex pathogens (Paul)
break
1.30PT (3.30CT/4.30ET) - 2.30PT - Zoom: DSAIRM level II exercise, part 1 (Andreas)
Rest of day - On your own: Explore DSAIRM. Go through SMI materials. Prepare for tomorrow. Communication through Slack.
As preparation before we meet, do the following:
Go through the Parameter Uncertainty unit on SMI, which you can find here.
Take a look at these apps in DSAIRM: Uncertainty and Sensitivity Analysis. You don’t need to fully work through them, but read the Model section and play with them briefly so you are a bit familiar with them. We’ll investigate them today during our live DSAIRM exercise sessions.
8PT (10CT/11ET) - 9PT - Zoom: DSAIRM level II exercise, part 2 (Andreas)
break
9.15PT (11.15CT/12.15ET) - 10PT - Zoom: Further immunology or modeling topics based on requests (Paul/Andreas)
break
10.15PT (12.15CT/1.15ET) - 11PT - Zoom: DSAIRM level III exercise, part 1 (Andreas)
11PT (1CT/2ET) - 12PT Lunch Break - Go through SMI materials or explore DSAIRM on your own. Communication through Slack.
12PT (2CT/3ET) - 1.30PT – Zoom: DSAIRM level III exercise, part 2 (Andreas)
break
1.45PT (3.45CT/4.45ET) - 2.30PT - Zoom: Final Q&A, course wrap-up (Paul/Andreas)
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 on Slack.