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 Late Addition NetLogo SaSAT (Windows only) (optional) Tinn-R (Windows only) (optional) R manual
Module 2	Mathematical Models of Infectious Disease:	R R/deSolve Pejman Rohani Notes
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 Late Addition
Module 8	Evaluating Surrogates of Protection:	R
Module 9	Inference for Graphs and Network Theory in Infectious Diseases:	R R/statnet R/networksis Late Addition Python (Enthought Distribution) Late Addition
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 Late Addition