Clinic Schedule

This is an archived version of the schedule from the MMED 2015 clinic (June 1-12, 2015, African Institute for Mathematical Sciences, Muizenberg, Cape Town, RSA). Some links may not work at this time.

The MMED 2015 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, 1 June

• 8:00 – 8:30 Registration and welcome, AIMS lobby
  • If you have a laptop, please see Waseem in the IT office (Room 110) during registration to get set up with wifi access.
  • Please gather in the main lecture hall by 8:30.
• 8:30 – 9:00 Introductions (all participants) and Motivation for Workshop (Pulliam and Hargrove)
• 9:00 – 10:00 Lecture: Public Health, Epidemiology, and Models (Dushoff) - Slides
• 10:00 – 10:30 Coffee break
• 10:30 – 10:45 Organizational session: MMED Road Map and programme overview (Pulliam)
• 10:45 – 11:30 Lecture: Introduction to Thinking About Data I (Scott) - Slides
• 11:30 – 12:30 Lecture: Introduction to dynamic modeling of infectious diseases (Bellan) - Slides
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
  • If you still need wifi access, please see Jan in 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: Welte)
• 15:20 – 15:30 Discussion: Dynamical Fever and Model Worlds (Pulliam)
• 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, Additional material
• 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, 2 June

• 8:30 – 9:15 Lecture: Mathematical assumptions of simple ODE models (Pulliam) - Slides
• 9:15 – 10:00 Lecture and Computer Session: Introduction to spreadsheet models (Scott) - Slides
  • Practice spreadsheet: Measles example
• 10:00 – 10:30 Coffee break
• 10:30 – 12:30 Computer Session: R Tutorials I-III (All instructors); BScH break-out group (Bellan, Scott)
  • 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 (Scott)
  • Track B: Lecture: Basic stochastic simulation models (Welte) - 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: Basic stochastic simulation models cnt’d (Welte) - Spreadsheet: Download Excel file, Download Open Office file
• 15:30 – 16:00 Tea and poster set-up
• 16:00 – 17:00 Computer Session: R Tutorials continued (All instructors) & Mentoring session
• 17:00 – 18:00 Poster session II
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional lecture): Faculty Research Lecture #1 (Snoep)

Wednesday, 3 June

• 8:30 – 9:15 Lecture: Consequences of heterogeneity, and modeling options (Porco) - Slides
• 9:15 – 10:00 Computer Session: Lab: consequences of heterogeneity (All instructors) - Slides
• 10:00 – 10:30 Coffee break
• 10:30 – 11:00 Lecture: Work with spreadsheets as a group on projector (Hargrove)
• 11:00 – 12:30 Computer Session: Harare data in groups of <4. (All instructors)
  • Spreadsheets and data sets are available for download from this page.
  • If you finish all five spreadsheets 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
• 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: Harare data and spreadsheet work (Hargrove)
• 15:30 – 16:00 Tea and poster set-up
• 16:00 – 17:00 Parallel sessions
  • Track A: Formulating Research Questions A (Bellan)
  • Track B: Formulating Research Questions B (Pulliam)
• 17:00 – 18:00 Poster session III
• 18:00 – 18:30 Dinner
• 19:00 – 20:00 Real-world example (optional lecture): Faculty Research Lecture #2 (Ndifon)

Thursday, 4 June

• 8:30 – 10:00 Exercise: Creating a model world to address a research question (Pulliam) - 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 (Pulliam)
  • Potential project groups
• 12:30 – 14:00 Lunch break (Lunch is served from 12:30 to 13:00.)
• 14:00 – 15:30 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: Lecture and Computer Session: Use of models in study design for dynamic systems: Trachoma elimination (Porco) - Lab
• 15:30 – 16:00 Tea
• 16:00 – 16:45 Lecture: Introduction to Likelihood (Bellan)
• 16:45 – 18:00 Computer Session: Lab 5: Introduction to Likelihood Lab (All instructors)
• 18:00 – 18:30 Dinner
• 19:30 – 21:00 Social activity: Drumming

Friday, 5 June

• 8:30 – 10:00 Lecture and Computer Session: Modeling measurement uncertainty and within-host processes (Ndifon) - Slides, Code
• 10:00 – 10:30 Coffee break
• 10:30 – 11:15 Lecture: Likelihood fitting and dynamic models, Part 1: Dynamic Model Fitting and Inference Robustness (Pulliam) - Slides
• 11:15 – 12:30 Computer session: MLE fitting of an SIR model to prevalence data (All instructors) - Lab
  • 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
• 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, 6 June

• 9:00 – 10:30 Exercise: Description of proposed model and assumptions (Dushoff and Hargrove)
• 10:30 – 11:00 First chance to sign up for project groups and Coffee break
• 11:00 – 12:30 Lecture: Participatory coding for Variability, Sampling Distributions, and Simulation Lecture (Bellan)
• 12:30 – 14:00 Social Activity: Group lunch at Kalky’s
• 14:00 – Free/working afternoon

Sunday, 7 June

• Free day – optional group trip to Cape Point
  • We will leave at 10:00. Please meet in the AIMS lobby by 9:55.

Monday, 8 June

• 8:30 – 9:15 Lecture: Doing Science (Williams)
• 9:15 – 9:30 Organizational Session: Schedule and goals for the second week (Pulliam)
• 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: Introduction to GitHub (Mentors)
• 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: Likelihood fitting and dynamic models II (Dushoff)
• 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): Statistical power and validity of Ebola vaccine trials in Sierra Leone (Bellan)

Tuesday, 9 June

• 8:30 – 10:00 Lecture: Introduction to Monte Carlo Markov Chains (MCMC) (Bellan)
  • Movies from this lecture are available in the Desktop/Public/MCMCmovs folder on the AIMS network.
• 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 Lecture #4 (Hargrove)
• 20:00 - 22:00 Social Activities: Casino Lesson & Other Card Games (Optional)

Wednesday, 10 June

• 9:00 – 10:15 Reading Session (all groups): Gandhi 2006 (Williams)
• 10:15 – 10:45 Coffee break
• 10:45 – 12:30 Work Session (All instructors)
  • 10:45 – 11:15 Optional Session: Resolving merge conflicts (Pearson)
  • 11:30 – 12:00 Optional Session: Data cleaning (Pulliam) - Slides
• 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: Live coding of a dynamical model (Bellan, with Pulliam)
  • Code from this session is available from the tutorials page.
  • The model diagram developed during this session is available here.
• 15:30 – 16:00 Tea
• 16:00 – 17:30 Work Session & Mentoring Session (All instructors)
• 17:30 – 18:00 Dinner
  • There will be load shedding from 18:00 – 20:30.
  • Travis’s research lecture has been tentatively rescheduled for 14:00 on Thursday.

Thursday, 11 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 to go to Mzoli’s by 13:00. (You will need to be logged into GitHub to sign up.)
• 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, 12 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
• 20:30 – 21:30 Social Activity: Dance party (or ghost stories, or…?)
  • Load shedding has been cancelled.

Saturday, 13 June

• Clinic officially ends on Friday, but there will be an optional group trip to Mzoli’s Place on Saturday. We will leave from AIMS at 11:00, so please be in the lobby by 10:55.