Also suggested by Jason Matheny was the Spatiotemporal Epidemiological Modeler (STEM). As the name indicates, it is “designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases.” One nice feature is that it has a Wiki of useful information for installing the software (in either Windows or Linux). Indeed, one of the project’s goals is to make STEM extensible in order to avoid unnecessary assumptions that would limit its power. The developers have published a paper about the modeling platform.
I have not installed it, but it apparently has uses GIS information about counties around the world and allows researchers to insert their own epidemiology models, although it also comes with some models preinstalled.
