Day 1 (Monday, 9 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)
• 12h00-13h00 Lecture: Simple Models (Carl, Main Hall)
• 13h00-14h00 Lunch
• 14h00-15h30 Comp. Session: Tutorial 1: Introduction to R and Epidemic curves (Tutors, Comp. Lab)
• 15h30-16h00 Free - take a walk!
• 16h00-17h00 Comp. Session: Tutorial 1 cont. (Tutors, Comp. Lab)
• 17h00-17h45 Discussion: How to read a scientific paper (Carl, Main Hall)
  • Reference Paper
• 17h45-18h00 Organizing Session: Introduction to projects (Carl, Main Hall)
  • Project Groups
• End of Day Questions

Day 2

• 08h30-09h00 Reading time for a scientific paper
• 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 (Tutors, Comp. Lab)
• 13h00-14h00 Lunch
• 14h00-15h30 Comp. Session: Tutorial 2 & benchmark questions, and SEIR & Benchmark questions (Tutors, Comp. Lab)
• 15h30-16h00 Free - take a walk!
• 16h00-18h00 Group Work: Project development (Group Breakouts)
• End of Day Questions

Day 3

• 08h30-09h30 Group Work: Project development (Group Breakouts)
  • from 08h30, each group will check in with Carl (odd, in 105) or Zinhle (even, lobby): 08h30 1 and 2, 08h50 3 and 4, 09h10 5 and 6
  • Project Groups
• 09h30-10h30 Discussion: How did you read a scientific paper? (Carl, Comp. Lab)
  • Reference Paper
• 10h30-11h00 Coffee
• 11h00-11h45 Lecture: Study Design and Analysis in Epidemiology: Where does modeling fit? (Carl, Main Hall)
• 11h45-13h00 Comp. Session: Lab 3: Study Design in Epidemiology (Tutors, Comp. Lab)
• 13h00-14h00 Lunch
• 14h00-15h30 Comp. Session: Binomial Distribution Tutorial (Tutors, Comp. Lab)
• 15h30-16h00 Free - take a walk!
• 16h00-18h00 Group Work: Project development (Group Breakouts)
• End of Day Questions

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 (Tutors, Comp. Lab)
• 10h30-11h00 Coffee
• 11h00-12h00 Lecture: Transmission in Finite Populations (Zinhle, Main Hall)
• 12h00-13h00 Group Work: Project development, with progress checkin (Comp. Lab)
  • All checkins in the lab. Odd groups check in with Carl, even with Zinhle. Be prepared to show your draft report, slides, and poster.
  • Project Groups
• 13h00-14h00 Lunch
• 14h00-15h30 Group Work: Project development
• 15h30-16h00 Free - take a walk!
• 16h00-18h00 Comp. Session: If incomplete: review questions from Lab 4: Study Design for Clinical Trials (Tutors), Tutorial 3: Probability Distributions and Control Structures, and review questions (Tutors, Comp. Lab). Otherwise Project development
• Final Fundamentals Week Quiz (includes Qs from Friday)

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: Review / Preview (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, 15 June)

• On arrival Organizing Session: mentors and tutors will assist with direction to accommodations
• Faculty meeting and dinner in E313 from 16h30; be sure to save food for late arrivals once known

Day 1

• 0730? whatsapp checkin
• 07h30-08h20 Organizing Session: Registration (Faikah, Lobby)
• 08h30-09h00 Welcome and Motivation for Workshop (Reshma, Main Hall)
• 09h00-09h45 Discussion: Public health, epidemiology, and models (Carl, Main Hall)
• 09h45-10h00 MMED roadmap and program overview (Reshma, Main Hall)
• 10h00-10h30 Coffee
• 10h30-11h30 Lecture: Introduction to dynamic modeling (Reshma, Main Hall)
• 11h30-12h30 Lecture: Introduction to infectious disease data (Seth, Main Hall)
• 12h30-13h00 faculty meeting
• 12h30-14h00 Lunch (technical assistance for participants, Comp. Lab)
• 14h00-15h00 Lecture: Foundations of dynamical modelling (Jonathan, Main Hall)
• 15h00-15h30 Comp. Session: Dynamical fever exercise (Mutono, 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 (Mutono, Comp. Lab)
• 17h00-18h00 Poster session 1 (Main Hall)
• 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 (schalkwyk, Main Hall)
  • note takers Mutono
• 09h15-10h00 Live Coding: Introduction to model implementation in R (Reshma, Main Hall)
  • Resulting Code
  • note takers Mutono
• 10h00-10h30 Coffee
• 10h30-11h30 R Tutorials: Lab 1 - ODE Models (schalkwyk, and Mentors, Comp. Lab)
• 11h30-12h30 Thinking about Data (Mutono, and Mentors, Main Hall)
  • note takers Reshma
• 14h00-15h00 Lecture: Study design (Reshma, Main Hall)
  • note takers: TBD
• 14h00-15h30 R Tutorials: Tutorial 4 - Visualizing Infectious Disease Data (Seth, and Mentors, Comp. Lab)
• 15h30-16h00 Tea (poster setup, group 2) (Mutono, and Mentors, Main Hall)
• 16h00-17h00 Tutorial 4, cont. & optionally Lab 3 - study design I & Lab 4 - study design II
• 17h00-18h00 Poster session 2 (Main Hall)
• 18h00-18h30 Dinner
• 19h00-20h00 Lecture: Guest Lecture Joseph Challenger
  • Moderator: (Jonathan, Main Hall)

Day 3

• 0730? whatsapp checkin
• 08h30-09h30 Lecture: Consequences of heterogeneity and modelling options (Jonathan, Main Hall)
  • note takers: Mutono, and Carl
• 09h30-11h00 (with coffee break) Comp. Session: Lab 2 - Consequences of heterogeneity (Jonathan, and Mentors, Comp. Lab)
  • note takers: Jonathan
  • run ICI3D::heterogeneityTutorial() at the R prompt
  • If you would like to look under the hood, the relevant code is available here
  • Summary (Carl)
• 10h00-10h30 Coffee
• 11h00-14h30 (with lunch break) Introduction to models and data: HIV in Harare (Reshma, and Carl, Comp. Lab)
  • note takers: Jonathan, and Elisha (also for tutorial, summary etc)
  • 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
• 14h30-15h30 Discussion: Formulating research questions (schalkwyk, and Seth, Section 1, Section 2)
  • section 1: Reshma, section 2: Rebecca
• 15h30-16h00 Tea
• 16h00-17h30 Lecture: Introduction to statistical philosophy (Jonathan, Main Hall)
  • note takers: Mutono
• 17h30-18h00 Projects: Topic Intro (Main Hall)
• 18h00-18h30 Dinner
• 19h00-20h00 Optional: Tutorials catch-up (Mentors, Comp. Lab)

Day 4

• 0730? whatsapp checkin
• 08h30-10h00 Discussion: Creating a model world to address a research question (Seth, and Mutono, Section 1, Section 2)
  • note takers: section 1 Carl
• 10h00-10h30 Coffee
• 10h30-11h15 Lecture: Introduction to likelihood (schalkwyk, Main Hall)
  • note takers: Carl, and Mutono
• 11h15-12h30 Comp. Session: Lab 5 - Introduction to likelihood (schalkwyk, and Mentors, Comp. Lab)
  • note takers: Zinhle, and Mutono
  • Summary (schalkwyk)
• 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: Reshma
• 15h30-16h00 Tea
• 16h00-17h00 Lecture: Introduction stochastic simulation models (Reshma, Main Hall)
• 17h00-18h00 Discussion: Ex 1 & 2: Stochastic models
• 18h00-18h30 Dinner
• 18h30-19h00 Finish Model Diagram
• 19h00-21h00 Social Event: Drumming (Main Hall)

Day 5

• 0730? whatsapp checkin
• 08h30-10h00 Discussion: Description of proposed model and assumptions (Mutono, schalkwyk, and Mentors, Section 1, Section 2)
  • note takers: section 1 Reshma, section 2 Mutono
• 10h00-10h30 Coffee
• 10h30-11h15 Lecture: Fitting I (schalkwyk, Main Hall)
  • note takers: Mutono
• 11h15-12h15 Mentor presentations (Seth, Main Hall)
  • note takers: TBD
  • Tumelo: TALK
  • Jeanette: TALK
  • Mphatso: TALK
• 12h30-13h00 faculty meeting
• 12h15-13h45 Lunch (note slight shift)
• 13h45-15h00 Comp. Session: Lab 6 - MLE fitting of an SIR model to prevalence data (schalkwyk, and Mentors, Comp. Lab)
  • 15h30 Summary (Seth)
• 15h00-15h30 Projects: Topic Qs (Jonathan, Main Hall)
  • note takers: Reshma, and Carl
• 15h30-16h00 Tea
• 16h00-17h00 Mid-Clinic Feeback session (Faikah, Main Hall)
• 17h00-18h00 Project selection (Main Hall)
  • note takers: Reshma, and Carl
• 18h00-18h30 Dinner
• 19h30-21h30 Social Event: Movie Night (Main Hall)

Day 6

• 0730? whatsapp checkin
• 09h00-10h30 Live Coding: Participatory coding for stochastic model (Jonathan, Main Hall)
  • note takers: Carl
• 10h30-11h00 Coffee
• 11h00-11h30 Projects: Group Assignments (Mutono, Comp. Lab)
• 11h30-12h30 Optional: Tutorials catch-up (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: Social Outing TBD

Day 8 (Monday, 23 June)

• 08h30-08h45 Discussion: Feedback responses; Review Schedule & goals (Reshma, Main Hall)
• 08h45-09h30 Lecture: Life cycle of a modeling project (Carl, Main Hall)
  • note takers: Reshma
• 09h30-10h00 Group Work: MMED project work (Group Breakouts)
• 10h00-10h30 Coffee
• 10h30-11h30 Introduction to github (Carl, and Mentors, Comp. Lab)
  • note takers: TBD
• 11h30-12h30 Group Work: MMED project work (Group Breakouts)
• 12h30-14h00 Lunch
• 14h00-15h30 Lecture: Likelihood fitting and dynamical models II (Seth, 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) (Carl, Main Hall)
  • note takers: TBD
• 10h00-10h30 Coffee
• 10h30-11h30 Comp. Session: Lab 7 & Lab 8 MCMC model fitting (Carl, and Mentors, Comp. Lab)
  • note takers: 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 (Mutono, Main Hall)
  • note takers: Jonathan
• 14h45-15h30 Comp. Session: Tutorial 5: Data cleaning, data (Mutono, and Mentors, Comp. Lab)
  • Summary (Mentors)
  • note takers: Jonathan
• 15h30-16h00 Tea
• 16h00-17h30 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• 18h00-18h30 Dinner

Day 10

• 08h30-09h30 Lecture: Model assessment (Jonathan, Main Hall)
  • note takers: Reshma
• 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, Main Hall)
  • note takers: Reshma
  • One-study code; Many-study code
  • Get a more direct summary title for this
• 12h30-14h00 Lunch
• 14h00-15h30 Group Work: MMED project work (Group Breakouts)
• 15h30-16h00 Tea
• 16h00-17h30 Group Work: MMED project work + mentoring sessions (Group Breakouts)
• 18h00-18h30 Dinner
• 19h00-20h00 Guest Lecture: Mmamapudi Kubjane (Main Hall)

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: Reshma
• 15h30-16h00 Tea
• 16h00-17h30 Discussion: Modelling for policy (Seth, Main Hall)
  • note takers: 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
• 13h30-15h30 Group Work: Project presentations (Mutono, Main Hall)
  • note takers: Jonathan
• 15h30-16h00 Tea
• 16h00-17h00 Discussion: Feedback session II (Faikah, Main Hall)
• 17h15-17h45 Closing Remarks (Reshma, Main Hall)
  • note takers: TBD
• 18h00-18h30 Dinner