Computing & Software
The following list links to the publicly available software (if any) used by each module. There will not be a SISMID Computer Laboratory. Participants are strongly encouraged to bring their own laptops to this year’s Institute. They are equally strongly encouraged to download and install the software before coming to the Institute.
This is a tentative list and subject to change; please check back here for updates.
Module 1 | Infectious Diseases and Immunology: |
R R/deSolve R/GillespieSSA R/PBSddesolve R/lhs NetLogo SaSAT (Windows only) (optional) Tinn-R (Windows only) (optional) R manual |
Module 2 | Mathematical Models of Infectious Disease: | |
Module 3 | Probability and Statistical Inference: | R |
Module 4 | MCMC Methods for Infectious Disease Studies: |
R BEAST Tracer FigTree R manual BEAST manual |
Module 5 | Design and Analysis of Vaccine Clinical Trials: | R |
Module 6 | Evaluating Indirect Effects of Vaccination: |
R BEAST TranStat R manual BEAST manual |
Module 7 | Stochastic Simulation Methods for Infectious Diseases: |
R Microsoft Visual C#/C++ Instructor Programs and Data |
Module 8 | Evaluating Surrogates of Protection: |
R |
Module 9 | Inference for Graphs and Network Theory in Infectious Diseases: |
R R/statnet R/networksis Python (Enthought Distribution) |
Module 10 | Causal Inference in Infectious Disease Epidemiology: |
R |
Module 11 | Evolutionary Inference and Infectious Disease Phylodynamics: |
PhyML MrBayes BEAST & BEAUTi Tracer FigTree HYPHY RDP Instructor Programs and Data |