Day 1 (Monday, 10 June)

• 09h00-09h20 Organizing Session: Introductions, Overview (everyone, Main Hall)
• 09h20-10h30 Discussion: Public health, epidemiology, and infectious disease modelling (Carl, Main Hall)
• 10h30-11h00 Coffee
• 11h00-12h00 Lecture: Introduction to infectious disease dynamics, Part I (Zinhle, Main Hall)
• 12h00-12h10 A brief stretch
• 12h10-13h00 Discussion: How to read a scientific paper (Carl, Main Hall)
  • Reference Paper
• 13h00-14h00 Lunch
• 14h00-15h30 Comp. Session: Tutorial 1: Introduction to R and Epidemic curves (Bria, Comp. Lab)
• 15h30-16h00 Free - take a walk!
• 16h00-17h00 Comp. Session: Tutorial 1 cont. (Bria, Comp. Lab)
• 17h00-17h45 Organizing Session: Introduction to projects (Carl, Main Hall)
  • Pilot Project Prompt
  • Project Groups

Day 2

• 08h30-09h00 Reading time for a scientific paper (own choice)
• 09h00-10h30 Lecture: Introduction to infectious disease dynamics, Part II (Zinhle, Main Hall)
  • “The” R0 paper (might need unpaywall or similar tools to access)
• 10h30-11h00 Coffee
• 11h00-12h00 Lecture: Dynamics of directly transmitted pathogens (Carl, Main Hall)
• 12h00-13h00 Comp. Session: Tutorial 2: More on Vectors, Data Frames, and Functions, and SEIR (Emmanuel, Comp. Lab)
• 13h00-14h00 Lunch
  • 13h30 Check in with mentors re reading papers plans
• 14h00-15h30 Comp. Session: Tutorial 2 & benchmark questions, and SEIR & Benchmark questions, project development as available (Emmanuel, Comp. Lab)
• 15h30-16h00 Free - take a walk!
• 16h00-18h00 Group Work: Project development (Group Breakouts)
  • from 17h00, each group will check in with Carl (odd, in 105) or Zinhle (even, lobby): 17h00 1 and 2, 17h12 3 and 4, 17h24 5 and 6, 17h36 7 and 8, 17h48 9

Day 3

• 08h30-09h00 Discussion: Tutorial 2 & SEIR Review (Emmanuel, Comp. Lab)
• 09h00-10h30 Discussion: How to read a scientific paper (mentors, Comp. Lab)
  • Reference Paper
• 10h30-11h00 Coffee
• 11h00-11h45 Lecture: Study Design and Analysis in Epidemiology: Where does modeling fit? (Cari, Main Hall)
• 11h45-13h00 Comp. Session: Lab 3: Study Design in Epidemiology (Tumelo, Comp. Lab)
• 13h00-14h00 Lunch
• 14h00-15h30 Comp. Session: Binomial Distribution Tutorial (Tumelo, Comp. Lab)
• 15h30-16h00 Free - take a walk!
• 16h00-18h00 Group Work: Project development (Group Breakouts)

Day 4

• 08h30-09h15 Lecture: Study Design and Analysis, part II: RCT’s (Carl, Main Hall)
  • Side reading: CDC on the Tuskegee Experiment, Declaration of Helsinki, Belmont Report
• 09h15-10h30 Comp. Session: Lab 4: Study Design for Clinical Trials (Maryse, Comp. Lab)
• 10h30-11h00 Coffee
• 11h00-12h00 Lecture: Transmission in Finite Populations (Zinhle, Main Hall)
• 12h00-13h00 Group Work: Project work, with progress checkin (Comp. Lab or Group Breakouts)
  • All checkins in the lab. Odd groups check in with Carl, even with Zinhle. Be prepared to show your draft report, slides, poster, and code.
  • 12h00 1 and 2, 12h30 3 and 4
• 13h00-14h00 Lunch
• 14h00-15h30 Group Work: Project development (present on progress) (Comp. Lab or Group Breakouts)
  • 14h00 5 and 6, 14h30 7 and 8, 15h00 9
• 15h30-16h00 Free - take a walk!
• 16h00-18h00 Comp. Session: Review Questions from Lab 4: Study Design for Clinical Trials (Maryse), Tutorial 3: Probability Distributions and Control Structures, and review questions (Gillian, Comp. Lab)

Day 5

• 08h30-09h30 Lecture: Dynamics of vector-borne pathogens (Zinhle, Main Hall)
• 09h30-10h30 Group Work: Final Group Work (Group Breakouts)
• 10h30-11h00 Coffee
• 11h00-13h00 Group Work: Practice presentations and feedback (all, Main Hall)
  • 5 minutes + 2 minutes for questions + 3 minutes for feedback
  • 11h00-11h10 4, 11h10-11h20 1, 11h20-11h30 2, 11h30-11h40 3, 11h40-11h50 5, 11h50-12h00 6, 12h00-12h10 7, 12h10-12h20 8, 12h20-12h30 9 (with 30 minute buffer for overruns)
• 13h00-14h00 Lunch
• 14h00-15h00 Group Work: Revisions (Group Breakouts)
• 15h00-15h30 Discussion: Preview for next week, Pop Quiz (Main Hall)
• 15h30-16h00 Free - take a walk!
• 16h00-18h00 Group Work: Optional: re-present + re-feedback. Optional: poster feedback. (Main Hall)

Day 0 (Sunday, 16 June)

• 16h00–18h00 Organizing Session: Registration (Faikah, Lobby)
• Faculty meeting and dinner in E313 at 18h30; be sure to save food for late arrivals once known

Day 1

• 0730? whatsapp checkin
• 08h00-08h25 Organizing Session: Registration (Faikah, Lobby)
• 08h30-09h00 Welcome and Motivation for Workshop (Reshma, Mutono, and Tumelo, Main Hall)
• 09h00-10h00 Discussion: Public health, epidemiology, and models (Carl, Main Hall)
• 10h00-10h30 Coffee
• 10h30-10h45 MMED roadmap and program overview (Bobby, Main Hall)
• 10h45-11h30 Lecture: Simple Models (Carl, Main Hall)
• 11h30-12h30 Lecture: Foundations of dynamic modeling (Jonathan, Main Hall)
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch (technical assistance for participants, Comp. Lab)
• 14h00-15h00 Lecture: Introduction to infectious disease data (Bobby, Main Hall)
• 15h00-15h30 Comp. Session: Dynamical fever exercise (Bobby, Zinhle, Mutono, and Mentors, Comp. Lab)
  • Launch from R prompt with ICI3D::dynamicalFever()
• 15h30-16h00 Tea (poster setup, group 1) (Mutono, and Mentors, Main Hall)
• 16h00-17h00 Dynamical fever exercise, cont. (Comp. Lab)
  • Dynamical fever summary (Bobby, Comp. Lab)
• 17h00-18h00 Poster session 1 (Main Hall)
• graders: Bobby, Elisha, Jonathan, and Mutono; grades provided to participants by W1D3
• 18h00-18h30 Dinner
• 19h00-20h30 Ice-breaker/Card games (Faikah, Main Hall)

Day 2

• 0730? whatsapp checkin
• 08h30-09h15 (Hidden) assumptions of simple ODE models (Elisha, Main Hall)
  • note takers Rebecca, and Mutono
• 09h15-10h00 Live Coding: Introduction to model implementation in R (Reshma, Main Hall)
  • Resulting Code
  • note takers Elisha, and Mutono
• 10h00-10h30 Coffee
• 10h30-11h30 Thinking about Data (Mutono, Main Hall)
  • note takers Elisha, and Reshma
• 11h30-12h30 MMED projects (introduction + Q&A) (Rebecca, and Jonathan, Main Hall)
  • Signup Survey
  • note takers Reshma, and Mutono
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-15h30 R Tutorials: Lab 1 - ODE Models and Tutorial 4 - Visualizing Infectious Disease Data (Mutono, Rebecca, and Mentors, Comp. Lab)
• 15h30-16h00 Tea (poster setup, group 2) (Elisha, and Mentors, Main Hall)
• 16h00-17h00 Lab 1 and Tutorial 4, cont.
  • Summaries: Lab 1 and Tutorial 4 (Mutono, and Tumelo, Comp. Lab)
  • note takers Elisha, and Rebecca
• 17h00-18h00 Poster session 2 (Main Hall)
• graders: Bobby, Elisha, Jonathan, and Mutono; grades provided to participants by W1D3
• 18h00-18h30 Dinner
• 19h30 Project sign-up deadline
• 19h00-20h00 Tutorials catch-up (Elisha, Mutono, and Mentors, Comp. Lab)

Day 3

• 0730? whatsapp checkin
• 08h30-09h15 Lecture: Introduction stochastic simulation models (Rebecca, Main Hall)
  • note takers: Mutono, and Carl
• 09h15-10h00 Exercise 1 (Rebecca, Zinhle, Mutono, and Mentors, Comp. Lab)
  • note takers: Jonathan, and Elisha
  • Summary (Rebecca)
• 10h00-10h30 Coffee
• 10h30-10h45 Introduction to models and data: HIV in Harare (Reshma, Comp. Lab)
  • note takers: Jonathan, and Elisha (also for tutorial, summary etc)
• 10h45-12h30 Comp. Session: HIV in Harare tutorial (Reshma, Zinhle, Carl, and Mentors, Comp. Lab)
  • Launch from R prompt with ICI3D::hivTutorial()
  • If you finish all five versions of the model for the Harare data before lunch, move on to working on data from other countries.
  • Additional info: Distributed Delay Models of Survival (Boxcar Models) and example script
  • Summary of Harare tutorial (Carl)
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-14h30 Project group assignments (Rebecca, and Jonathan, Main Hall)
  • note takers: Reshma, and Carl
• 14h30-15h30 Discussion: Formulating research questions (Jonathan, and Elisha, Section 1, Section 2)
  • section 1: Reshma, section 2: Rebecca
• 15h30-16h00 Tea
• 16h00-17h00 Initial group work (Group Breakouts)
• 17h00-18h00 Lecture: Study design and analysis in epidemiology Review (Reshma, Main Hall)
  • note takers: Zinhle
• 18h00-18h30 Dinner
• 19h00-20h00 Optional: Lab 3 - study design I & Lab 4 - study design II (mentors, Comp. Lab)

Day 4

• 0730? whatsapp checkin
• 08h30-10h00 Discussion: Creating a model world to address a research question (Mutono, Zinhle, and Mentor, Section 1, Section 2)
  • note takers: section 1 Carl, section 2 Bobby
• 10h00-10h30 Coffee
• 10h30-12h00 Lecture: Introduction to statistical philosophy (Jonathan, Main Hall)
  • Quiz
  • note takers: Mutono, and Bobby
• 12h00-12h30 Group Work: MMED projects (Group Breakouts)
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-15h30 Live Coding: Participatory coding of a dynamical model (Carl, Main Hall)
  • This years results (past years generally available here)
  • note takers: Zinhle, and Reshma
• 15h30-16h00 Tea
• 16h00-16h45 Lecture: Introduction to likelihood (Bobby, Main Hall)
  • note takers: Carl, and Mutono
• 16h45-18h00 Comp. Session: Lab 5 - Introduction to likelihood (Reshma, Mutono, and Mentors, Comp. Lab)
  • note takers: Zinhle, and Mutono
  • Summary (Jeanette)
• 18h00-18h30 Dinner
• 19h00-21h00 Social Event: Drumming (Main Hall)

Day 5

• 0730? whatsapp checkin
• 08h30-10h00 Discussion: Description of proposed model and assumptions (Zinhle, Elisha, and Mentors, Section 1, Section 2)
  • note takers: section 1 Reshma, section 2 Mutono
• 10h00-10h30 Coffee
• 10h30-11h15 Lecture: Likelihood fitting & dynamic models I: Dynamic Model Fitting and Inference Robustness (Bobby, Main Hall)
  • note takers: Mutono, and Zinhle
• 11h15-12h30 Comp. Session: Lab 6 - MLE fitting of an SIR model to prevalence data (Reshma, Mutono, and Mentors, Comp. Lab)
  • note takers:
  • Summary (Reshma)
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch
• 14h00-15h30 Group Work: MMED project work (Group Breakouts)
  • 15h30 Initial project work update due
• 15h30-16h00 Tea
• 16h00-17h00 Mentor presentations (Mutono, Jeanette, Tumelo, and Mphatso, Main Hall)
  • note takers: Elisha, and Bobby
  • Tumelo: TALK
  • Jeanette: TALK
  • Mphatso: TALK
• 17h00-18h00 Mid-Clinic Feeback session (Faikah, Main Hall)
• 18h00-18h30 Dinner
• 19h30-21h30 Social Event: Movie Night (Main Hall)

Day 6

• 0730? whatsapp checkin
• 08h30-09h30 Lecture: Consequences of heterogeneity and modelling options (Jonathan, Main Hall)
  • note takers: Carl, and Bobby
• 09h30-10h30 Comp. Session: Lab 2 - Consequences of heterogeneity (Carl, Jonathan, Bobby, and Mentors, Comp. Lab)
  • note takers: Jonathan, and Bobby
  • run ICI3D::heterogeneityTutorial() at the R prompt
  • If you would like to look under the hood, the relevant code is available here
  • Summary (Carl)
• 10h30-11h00 Coffee
• 11h00-12h30 Tutorial catch-up (optional) (Mentors, Comp. Lab)
• Social Event: Optional: Group Lunch at Kalky’s (costs covered)
• 18h30 post-Kalky’s all hands faculty meeting in E313; beverages provided

Day 7

• Social Event: 09h55 to ~17h00 Optional: Meet in AIMS lobby for Cape Point trip (firm departure at 10h00). Wear comfortable clothes. We will be going on a boat! Box lunch provided.

Day 8 (Monday, 24 June)

• 08h30-08h45 Discussion: Feedback responses; Review Schedule & goals (Reshma, Main Hall)
• 08h45-09h30 Lecture: Life cycle of a modeling project (Bobby, Main Hall)
  • note takers: Carl, and Reshma
• 09h30-10h00 Group Work: MMED project work (Group Breakouts)
• 10h00-10h30 Coffee
• 10h30-11h30 Introduction to github (Carl, Zinhle, Elisha, and Mentors, Comp. Lab)
  • note takers: Elisha, and Zinhle
• 11h30-12h30 Group Work: MMED project work (Group Breakouts)
• 12h30-14h00 Lunch
• 14h00-15h30 Lecture: Likelihood fitting and dynamical models II (Bobby, Main Hall)
  • note takers: Carl, and Reshma
• 15h30-16h00 Tea
• 16h00-17h30 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• 18h00-18h30 Dinner
• 19h00-20h00 Optional: Github practice and and trouble-shooting / tutorial catch-up (Carl, and Mentors, Comp. Lab)

Day 9

• 08h30-10h00 Lecture: Introduction to Markov Chain Monte Carlo (MCMC) (Rebecca, Main Hall)
  • note takers: Carl, and Reshma
• 10h00-10h30 Coffee
• 10h30-11h30 Comp. Session: Lab 7 & Lab 8 MCMC model fitting (Reshma, Carl, and Mentors, Comp. Lab)
  • note takers: Rebecca, and Reshma
• 11h30-12h30 Group Work: MMED project work (Group Breakouts)
• 12h30-14h00 Lunch
  • 1300 ICI3D meeting with remoting adds
• 14h00-14h45 Lecture: Data management and cleaning (Carl, Main Hall)
  • note takers: Jonathan, and Rebecca
• 14h45-15h30 Comp. Session: Tutorial 5: Data cleaning, data (Carl, and Mentors, Comp. Lab)
  • Summary (Mphatso)
  • note takers: Elisha, and Jonathan
• 15h30-16h00 Tea
• 16h00-17h30 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• 18h00-18h30 Dinner
• 19h00-20h00 Lecture: Guest Lecture Slimane ben Miled: Coupling scale in epidemiology
  • Moderator: (Jonathan, Main Hall)
  • note takers Carl, and Jonathan

Day 10

• 08h30-09h30 Lecture: Model assessment (Jonathan, Main Hall)
  • note takers: Zinhle, and Reshma
  • Slides
• 09h30-10h00 Group Work: MMED project work (Group Breakouts)
• 10h00-10h30 Coffee
• 10h30-11h00 Group Work: MMED project work (Group Breakouts)
• 11h00-12h30 Live Coding: Participatory coding for study design and simulation based validation (Jonathan, and Reshma, Main Hall)
  • note takers: Zinhle, and Reshma
  • One-study code; Many-study code
  • Get a more direct summary title for this
• 12h30-14h00 Lunch NOTE: Bobby + mentors: technical check with virtual panelists
• 14h00-15h30 Group Work: MMED project work (Group Breakouts)
  • 15h30 Week 2 update due
• 15h30-16h00 Tea
• 16h00-17h30 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• 18h00-18h30 Dinner

Day 11

• 08h30-10h00 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• 10h00-10h30 Coffee
• 10h30-12h30 Group Work: MMED project work (Group Breakouts)
• 12h30-14h00 Lunch
• 14h00-15h30 either Group Work: MMED project work or Live Coding: Analysis pipelines (video + transcript) (resulting code) (Carl, Group Breakouts or Main Hall)
  • note takers: Zinhle, and Reshma
• 15h30-16h00 Tea
• 16h00-17h30 Discussion: Modelling for policy (Bobby, Main Hall)
  • note takers: Elisha, and Jonathan
• 18h00-18h30 Dinner

Day 12

• 08h30-10h00 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• 10h00-10h30 Coffee
• 10h30-12h30 Group Work: MMED project work + mentoring sessions (Group Breakouts)
  • 12h30 Report due
  • 13h00 Presentations due
• 12h30-13h30 Lunch
  • MMED group photo at 13h20. Please be prompt.
• 13h30-15h30 Group Work: Project presentations (Elisha, Main Hall)
  • note takers: Jonathan, and Bobby
• 15h30-16h00 Tea
• 16h00-17h00 Discussion: Feedback session II (Faikah, Main Hall)
• 17h15-17h45 Closing Remarks (Carl, Main Hall)
  • note takers: Elisha, and Bobby
• 18h00-18h30 Dinner

Day 13

• Clinic officially ends on Friday, but there will be an optional group trip on Saturday.