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Return to the Schedule.

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.

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.

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.