Clinic Schedule

This is an archived version of the schedule from the MMED 2016 clinic. Some links may not work at this time.

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.

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.