The MMED 2016 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.

The schedule below is preliminary and subject to change. Materials linked from this page are also subject to change and should not be considered final until the conclusion of the relevant session.

Note that the schedule below is preliminary and subject to change. Some links may not work at this time.

Monday, 30 May

• 8:00 – 8:25 Registration and welcome, AIMS lobby
  • Please gather in the main lecture hall by 8:30.
• 8:30 – 9:00 Introductions (all participants) and Motivation for Workshop (Dushoff and Hargrove)
• 9:00 – 10:00 Lecture: Public Health, Epidemiology, and Models (Porco) - Slides
• 10:00 – 10:30 Coffee break
• 10:30 – 10:45 Organizational session: MMED Road Map and programme overview (Bellan) - General roadmap, Track A roadmap, Track B roadmap
• 10:45 – 11:45 Lecture: Introduction to dynamic modeling of infectious diseases (Bellan) - Slides
• 11:45 – 12:30 Lecture: Introduction to Thinking About Data I (Delva) - Slides
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • If you still need wifi access, please visit the IT office (Room 110) between 13:30 and 14:00 to get this set up.
• 14:00 – 15:20 Exercise: Dynamical Fever and Model Worlds (in pairs) and discussion (Moderator: Brook)
• 15:20 – 15:30 Discussion: Dynamical Fever and Model Worlds (Welte)
• 15:30 – 16:00 Tea and poster set-up
• 16:00 – 17:00 Parallel sessions
  • Track A: Introduction to infectious disease data (Bruce) - Slides
  • Track B: Foundations of dynamic modeling (Dushoff) - Slides; Code; Spreadsheet
• 17:00 – 18:00 Poster session I
• 18:00 – 18:30 Dinner
• 19:00 – 19:30 Social Activity: Ice breakers
• 19:30 – 20:30 Social Activity: Card games: Bullsh!t and Casino

Tuesday, 31 May

• 8:30 – 9:15 Lecture: Mathematical assumptions of simple ODE models (Brook) - Slides
• 9:15 – 10:00 Lecture and Computer Session: Introduction to model implementation (Dushoff) - Live coding example: Code; Plot
• 10:00 – 10:30 Coffee break
• 10:30 – 12:30 Computer Session: R Tutorials I-III (All instructors); BScH break-out group (Bellan, Borchering)
  • When you have completed R Tutorials I-III, work on one of the following: Lab 1: ODE models (required) in R and Tutorial 4: Visualizing Infectious Disease Data in R (recommended)
  • All R tutorials and labs are linked from this page
• 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 (Delva) Slides
  • Track B: Lecture: Basic stochastic simulation models (Borchering) - Slides
• 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: - R Tutorial spillover SIR, Basic stochastic simulation models (continued)
• 15:30 – 16:00 Tea and poster set-up
• 16:00 – 17:00 Computer Session: R Tutorials (continued) & Mentoring session: John Hargrove, Steve Bellan, Alex Welte (sign up on sheet on back of lecture room door)
• 17:00 – 18:00 Poster session II
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional lecture): Faculty Research Presentations
  • Ngonghala - Poverty & disease dynamics Slides
  • Bellan - Early HIV infectivity Slides

Wednesday, 1 June

• 8:30 – 9:15 Lecture: Consequences of heterogeneity, and modeling options (Dushoff) - Slides
• 9:15 – 10:00 Computer Session: Lab: consequences of heterogeneity - Slides
• 10:00 – 10:30 Coffee break
• 10:30 – 11:00 Lecture: Introduction to models and data: HIV in Harare (Hargrove)
• 11:00 – 12:30 Computer Session: Harare data in groups of <4. (All instructors)
  • Download the exercise from this page.
  • If you finish all five steps for the Harare data before lunch, move on to working on data from other countries.
  • Additional info: Distributed Delay Models of Survival (Boxcar Models) - Download
• 13:00 Deadline to sign up to go to Kalky’s for lunch Sat afternoon (sheet on back of lecture door)
• 13:00 Deadline to sign up to go to Cape Point Sunday (all day) (sheet on back of lecture door)
• 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. (All instructors)
• 14:30 – 15:30 Discussion: Introduction to models and data: HIV in Harare (Hargrove)
• 15:30 – 16:00 Tea and poster set-up
• 16:00 – 17:00 Parallel sessions
  • Track A: Formulating Research Questions A (Welte)
  • Track B: Formulating Research Questions B (Bellan)
• 17:00 – 18:00 Poster session III
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional lecture): Faculty Research Presentations (Borchering, Welte)
  • Borchering - Impact of resource abundance on pathogen invasion risk Slides

Thursday, 2 June

• 8:30 – 10:00 Parallel sessions
  • Track A: Lecture and Computer Session: Study Design and Analysis in Epidemiology: Where does modeling fit? (Bellan) and Lab: Study Design in Epidemiology
  • Track B: Exercise: Creating a model world to address a research question (Dushoff) - Assignment and examples
• 10:00 – 10:30 Coffee break
• 10:30 – 12:00 Lecture: Introduction to statistical philosophy (Dushoff) - Slides, Additional material
• 12:00 – 12:30 Discussion: MMED research projects (Bruce)
  • Potential project groups
• 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 (Bellan)
• 15:30 – 16:00 Tea
• 16:00 – 16:45 Lecture: Introduction to Likelihood (Ngonghala)
• 16:45 – 18:00 Computer Session: Lab: Introduction to Likelihood
• 18:00 – 18:30 Dinner
• 19:30 – 21:00 Social activity: Drumming

Friday, 3 June

• 8:30 – 10:00 Parallel sessions
  • Track A: Lecture and Computer Session: Study Design and Analysis in Epidemiology II: RCT’s (Porco) and Lab: Study Design for Clinical Trials
  • Track B: Exercise: Description of proposed model and assumptions (Brook)
• 10:00 – 10:30 Coffee break
• 10:30 – 11:15 Lecture: Likelihood fitting and dynamic models, Part 1: Dynamic Model Fitting and Inference Robustness (Bellan) slides
• 11:15 – 12:30 Computer session: Lab: MLE fitting of an SIR model to prevalence data
  • Additional info: Parameter transformation - Download
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 15:30 Mentor presentations (Moderator: Dushoff)
• 15:30 – 16:00 Tea
  • 15:30-15:40 Group photo
• 16:00 – 17:00 MMED Projects (Moderator: Dushoff)
• 17:00 – 18:00 Mid-session Feedback (Moderator: Hitchcock)
• 18:00 – 18:30 Dinner
• 19:30 – 21:30 Social Activity: Movie night (Outbreak)

Saturday, 4 June

• 9:00 – 10:30 Lecture: Participatory coding of a dynamical model (Bellan, with Dushoff)
  • Code from this session is available from the tutorials page.
  • The model diagram developed during this session will be added after the session.
• 10:30 – 11:00 First chance to sign up for project groups and Coffee break
• 11:00 – 12:30 Exercise: Epidemic simulation and model implementation (Brook) Instructions, R Tutorial, Data template, Epidemic card data
• 12:30 – 14:00 Social Activity: Group lunch at Kalky’s
• 14:00 – Free/working afternoon

Sunday,5 June

• Free day – optional group trip to Cape Point
  • We will leave at 10:00. Please meet in the AIMS lobby by 9:55.
• Be sure to submit your project preferences via the Google form by noon.
  • If you are going on the Cape Point trip, this means you should submit your preferences before departure!

Monday, 6 June

• 8:30 – 9:15 Lecture: Doing Science (Williams) Slides
• 9:15 – 9:30 Organizational Session: Schedule and goals for the second week (Borchering)
• 9:30 – 10:00 Work Session: Project groups meet for the first time (All instructors)
• 10:00 – 10:30 Coffee break
• 10:30 – 11:30 Computer Session: Exercise: Working with Git and GitHub (Bellan)
• 11:30 – 12:30 Computer Session: GitHub repos for group projects (All instructors)
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 15:30 Lecture: Approaches to dynamic fitting (Dushoff) Slides
• 15:30 – 16:00 Tea
• 16:00 – 17:30 Work Session & Mentoring Session (All instructors)
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional lecture): Faculty Research Presentations (Delva, Brook)
  • Delva - Mind the age gap Slides

Tuesday, 7 June

• 8:30 – 10:00 Lecture: Introduction to Markov Chain Monte Carlo (MCMC) (Bellan)
  • Movies from this lecture are available in the /home/bellan/Public/MCMCmovs folder on the AIMS network. You can nagivate to it by typing file:///home/bellan/Public/MCMCmovs in your browser
• 10:00 – 10:30 Coffee break
• 10:30 - 11:30 Computer session: MCMC fitting Labs 7-8 in R Tutorials (All instructors)
• 11:30 – 12:30 Work Session (All instructors)
• 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 (Porco) - Slides
• 15:30 – 16:00 Tea
• 16:00 – 17:30 Work Session & Mentoring Session (All instructors)
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional lecture): Faculty Research Presentations
  • Porco - Thoughts on measles modeling Slides
  • Ndifon - Immune system: from principles to epidemiology Slides

Wednesday, 8 June

• 8:30 – 10:00 Reading Session (all groups): HIV in Mozambique (Williams)
  • Williams, BG, E Gouws, P Somse, M Mmelesi, C Lwamba, T Chikoko, E Fazito, M Turay, E Kiwango, P Chikukwa, H Damisoni, M Gboun. (2015) Epidemiological Trends for HIV in Southern Africa: Implications for Reaching the Elimination Targets Current HIV/AIDS Reports 12(1) doi: 10.1007/s11904-015-0264-x
  • EL Korenromp, B Gobet, E Fazito, J Lara, L Bollinger, & J Stover. (2015) Impact and Cost of the HIV/AIDS National Strategic Plan for Mozambique, 2015-2019 — Projections with the Spectrum/Goals Model PLOS One 10(11): e0142908. doi:10.1371/ journal.pone.0142908
  • Slides
• 10:00 – 10:30 Coffee break
• 10:00 – 10:30 VOTE for weekend trip by END OF LUNCH
• 10:30 – 12:30 Work Session (All instructors)
  • 11:15 – 12:00 Optional Session: Data cleaning (cancelled) - Slides, Tutorial
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 15:30 Work Session (All instructors)
  • 14:00 – 15:30 Optional Session: Model assessment (Dushoff) Slides
• 15:30 – 16:00 Tea
• 16:00 – 17:30 Work Session & Mentoring Session (All instructors)
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional lecture): Guest Faculty Research Lecture (Sheetal Silal, UCT)

Thursday, 9 June

• 8:30 – 10:00 Lecture: Modeling for policy (Williams)
• 10:00 – 10:30 Coffee break
• 10:30 – 12:30 Work Session (Mentors)
  • Sign up for weekend trip by 12:00
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 15:30 Work Session (All instructors)
• 15:30 – 16:00 Tea
• 16:00 – 17:30 Work Session & Mentoring Session (All instructors)
• 18:00 – 18:30 Dinner

Friday, 10 June

• 8:30 – 10:00 Work Session (All instructors)
• 10:00 – 10:30 Coffee break
• 10:30 – 12:30 Work Session (All instructors)
  • 10:30 – 11:30 Mentoring 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 (Moderator: Hitchcock)
• 17:15 – 17:45 Closing session
• 18:00 – 18:30 Dinner
• 21:00 – 23:00 Social Activity – cancelled

Saturday, 11 June

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