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. Participants will have free online access while they are on the University of Washington campus. Participants will also receive USB drives with copies of software and datasets when they arrive at the Institute.

This is a tentative list and subject to change; please check back here for updates. Latest update: 07/01/2014 7:54:18 PDT

Module 1 Probability and Statistical Inference: No Module Software
Module 2 Mathematical Models of Infectious Diseases: No Module Software
Module 3 Causal Inference: R 3.1.0
Module 4 Introduction to R: R 3.1.0
Module 5 MCMC I for Infectious Diseases: No Module Software
Module 6 Infectious Diseases, Immunology and Within-Host Models: No Module Software
Module 7 Stochastic Epidemic Models with Inference: Module 7 Handout
Transtat 3.0
Module 8 Evaluating Immune Correlates of Protection: Module 8 Handout
Module 8.1 Chan Slides
Module 8.3 Chan Slides
Module 8.5 Chan Slides
Module 8.8 Chan Slides
No Module Software
Module 9 Network Theory in Infectious Diseases: Module 9 Handout
No Module Software
Module 10 MCMC II for Infectious Diseases: Module 10 Handout
No Module Software
Module 11 Stochastic Simulation Methods: Module 11 Handout (external website)
GLEAMviz 5.0
GLEAMviz Software Manual

Module 12 Spatial Statistics in Epidemiology and Public Health: Module 12 Handout
R 3.1.0
Module 13 Introduction to Metagenomic Data Analysis: R 3.1.0
R cluster 1.15.2
R clusterSim 0.43-4
R edgeR 3.6.2
R ggplot2 1.0.0
R kernlab 0.9-19
R metagenomeSeq 1.7.15
R phyloseq 1.8.2
R randomForest 4.6-7
R reshape 0.8.5
R ROCR 1.0-5

Module 14 Evolutionary Dynamics and Molecular Epidemiology of Viruses: No Module Software