Spatiotemporal Epidemiological Modeler

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.

eMedCheck 2.1

Version 2.1 of eMedCheck is now available. eMedCheck is an electronic medication screening form that can be run on a PDA. Using this software, POD staff record basic information about each family member. The software uses decision rules to determine which medication each person should receive. It also records the results for later analysis.

Varun Santosh, a graduate student here at the University of Maryland, has done most of the work developing this application.

Version 2.1 features updates to the user interface, including this screen for entering the number of people in the family:

Pandemic influenza planning

The same group at the University of Tübingen has a new version of InfluSim, which can “predict the course of an influenza epidemic in a fully susceptible population.”

The new version is a 20MB zip file that I downloaded and then extracted to a folder on my computer’s desktop. I then ran the executable and started using the program. The model allows the user to change a wide variety of parameters about the population, the disease, and treatment policies. The outputs include the number of people infected, the number of days of work lost, the number of hospital beds required, and the costs.

The extensive help includes a warning that the program “should not be used to predict the exact course of the next influenza pandemic.” Instead, its goal is help users understand how assumptions about the virus and the interventions used affect the epidemic. Waiting a few seconds after changing a parameter yields new results (shown as numbers and as graphs). The quick (though not instantaneous) display of new results should be useful to those who want to gain that insight.

More Models: SimPox

Jason Matheny at the Johns Hopkins University Applied Physics Laboratory sent me a list of more computer models for public health emergency preparedness planning. I will posting my comments on these in future posts here.

First up is SimPox from a research team at the Department of Medical Biometry, University of Tübingen. SimPox runs as a Java applet. It simulates the spread of smallpox in a population. The user can change parameters about the disease (including its infectivity and latent period), the population (the initial fraction immune), and the intervention measures (such as surveillance and vaccination) and see charts with the predicted number of people affected each day of the smallpox attack. This includes the number of roaming cases, the number of cases detected, and the number isolated. If multiple simulations runs are used, then the results for each day can be are shown as a standard error around the mean, the minimum and maximum (over the simulation runs), and the individual simulation results (trajectories). The program also provides a text report with all of the parameter settings and numerical results, which one could copy and paste to save or print.