The MMED program includes a number of parallel sessions for participants with different backgrounds. Track A is designed for those with a mathematical background, particularly those who have extensive training and/or experience with differential equation models of infectious disease dynamics. Track B is designed for those with a background in epidemiology and/or statistics, particularly those who are involved in data collection for infectious disease systems.
Schedule
Week 1
Monday
- 8:00 – 8:30 Registration and welcome, AIMS lobby
- 8:30 – 9:00 Introductions and Motivation for Workshop
- 9:00 – 10:00 Lecture: Public Health, Epidemiology, and Models
- 10:00 – 10:30 Coffee break
- 10:30 – 10:45 Organizational session: MMED Road Map and programme overview
- 10:45 – 11:30 Lecture: Introduction to Thinking About Data I
- 11:30 – 12:30 Lecture: Introduction to dynamic modeling of infectious diseases
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 15:20 Exercise: Dynamical Fever and Model Worlds (in pairs) and discussion
- 15:20 – 15:30 Discussion: Dynamical Fever and Model Worlds
- 15:30 – 16:00 Tea and poster set-up
- 16:00 – 17:00 Parallel sessions
- Track A: Introduction to infectious disease data
- Track B: Foundations of dynamic modeling
- 17:00 – 18:00 Poster session I
- 18:00 – 18:30 Dinner
- 19:00 – 20:30 Social Activity
Tuesday
- 8:30 – 9:15 Lecture: (Hidden) assumptions of simple ODE models
- 9:15 – 10:00 Lecture and Computer Session: Introduction to model implementation
- 10:00 – 10:30 Coffee break
- 10:30 – 12:30 Computer Session: R Tutorials I-III
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 14:45 Parallel sessions
- Track A: Lecture: Introduction to Thinking About Data II
- Track B: Lecture: Basic stochastic simulation models
- 14:45 – 15:30 Parallel sessions
- Track A: Computer Session: R Tutorials I-III, Lab 1: ODE models in R, or Tutorial 4: Visualizing Infectious Disease Data in R (as needed)
- Track B: Computer Session: Basic stochastic simulation models cnt’d
- 15:30 – 16:00 Tea and poster set-up
- 16:00 – 17:00 Computer Session: R Tutorials continued
- 17:00 – 18:00 Poster session II
- 18:00 – 18:30 Dinner
- 19:00 – 20:00 Real-world example (optional lecture)
Wednesday
- 8:30 – 9:15 Lecture: Consequences of heterogeneity, and modeling options
- 9:15 – 10:00 Computer Session: Lab: consequences of heterogeneity
- 10:00 – 10:30 Coffee break
- 10:30 – 11:00 Lecture: Work with models as a group on projector
- 11:00 – 12:30 Computer Session: Harare data in groups of <4.
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 14:30 Computer Session: Harare/other data in same groups.
- 14:30 – 15:30 Discussion: Harare data and spreadsheet work
- 15:30 – 16:00 Tea and poster set-up
- 16:00 – 17:00 Parallel sessions
- Track A: Formulating Research Questions A
- Track B: Formulating Research Questions B
- 17:00 – 18:00 Poster session III
- 18:00 – 18:30 Dinner
- 19:00 – 20:00 Real-world example (optional lecture)
Thursday
- 8:30 – 10:00 Parallel sessions
- Track A: Lecture and Computer Session: Study Design and Analysis in Epidemiology: Where does modeling fit? and Lab: Study Design in Epidemiology
- Track B: Exercise: Creating a model world to address a research question
- 10:00 – 10:30 Coffee break
- 10:30 – 12:00 Lecture: Introduction to statistical philosophy
- 12:00 – 12:30 Discussion: MMED research projects
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 15:30 Lecture: Participatory coding for Variability, Sampling Distributions, and Simulation Lecture
- 15:30 – 16:00 Tea
- 16:00 – 16:45 Lecture: Introduction to Likelihood
- 16:45 – 18:00 Computer Session: Lab 5: Introduction to Likelihood Lab
- 18:00 – 18:30 Dinner
- 19:30 – 21:00 Social activity: Drumming
Friday
- 8:30 – 10:00 Parallel sessions
- Track A: Lecture and Computer Session: Study Design and Analysis in Epidemiology II: RCT’s and Lab: Study Design for Clinical Trials
- Track B: Exercise: Description of proposed model and assumptions
- 10:00 – 10:30 Coffee break
- 10:30 – 11:15 Lecture: Likelihood fitting and dynamic models, Part 1: Dynamic Model Fitting and Inference Robustness
- 11:15 – 12:30 Computer session: MLE fitting of an SIR model to prevalence data
- Additional info: Parameter transformation
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 15:30 Mentor presentations
- 15:30 – 16:00 Tea
- 16:00 – 17:00 MMED Projects
- 17:00 – 18:00 Mid-session Feedback
- 18:00 – 18:30 Dinner
- 19:30 – 21:30 Social Activity
Saturday
- 9:00 – 10:30 Lecture: Participatory coding of a dynamical model
- 10:30 – 11:00 First chance to sign up for project groups and Coffee break
- 11:00 – 12:30 Exercise: Working with Git and GitHub
- 12:30 – 14:00 Social Activity: Group lunch at Kalky’s
- 14:00 – Free/working afternoon
Sunday
- Free day – optional group trip to Cape Point
Week 2
Monday
- 8:30 – 9:15 Lecture: Doing Science
- 9:15 – 9:30 Organizational Session: Schedule and goals for the second week
- 9:30 – 10:00 Work Session: Project groups meet for the first time
- 10:00 – 10:30 Coffee break
- 10:30 – 11:30 Computer Session: Introduction to GitHub
- 11:30 – 12:30 Computer Session: GitHub repos for group projects
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 15:30 Lecture: Likelihood fitting and dynamic models II
- 15:30 – 16:00 Tea
- 16:00 – 17:30 Work Session & Mentoring Session
- 18:00 – 18:30 Dinner
- 19:00 – 20:00 Real-world example (optional lecture)
Tuesday
- 8:30 – 10:00 Lecture: Introduction to Monte Carlo Markov Chains
- 10:00 – 10:30 Coffee break
- 10:30 - 11:30 Computer session: MCMC fitting Labs 7-8
- 11:30 – 12:30 Work Session
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 15:30 Lecture: Working with databases: management and manipulation in R
- 15:30 – 16:00 Tea
- 16:00 – 17:30 Work Session & Mentoring Session
- 18:00 – 18:30 Dinner
- 19:00 – 20:00 Real-world example (optional lecture)
Wednesday
- 8:30 – 10:00 Reading Session (all groups)
- 10:00 – 10:30 Coffee break
- 10:30 – 12:30 Work Session (All instructors)
- 10:45 – 11:15 Optional Session: Resolving merge conflicts
- 11:30 – 12:00 Optional Session: Data cleaning
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 15:30 Work Session
- 14:00 – 15:30 Optional Session: Model assessment
- 15:30 – 16:00 Tea
- 16:00 – 17:30 Work Session & Mentoring Session
- 18:00 – 18:30 Dinner
- 19:00 – 20:00 Real-world example (optional lecture)
Thursday
- 8:30 – 10:00 Lecture: Modeling for policy
- 10:00 – 10:30 Coffee break
- 10:30 – 12:30 Work Session (Mentors)
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 15:30 Work Session
- 15:30 – 16:00 Tea
- 16:00 – 17:30 Work Session & Mentoring Session
- 18:00 – 18:30 Dinner
Friday
- 8:30 – 10:00 Work Session
- 10:00 – 10:30 Coffee break
- 10:30 – 12:30 Work Session
- 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
- 14:00 – 15:45 Final presentations
- 15:45 – 16:00 Tea
- 16:05 – 17:05 Final Feedback Session
- 17:15 – 17:45 Closing session
- 18:00 – 18:30 Dinner
- 21:00 – 23:00 Social Activity
Saturday
- Clinic officially ends on Friday, but there will be an optional group trip on Saturday.