The Spatiotemporal Epidemiological Modeler (STEM) Project

About STEM

STEM Banner

The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases. These models can aid in understanding and potentially preventing the spread of such diseases.

Policymakers responsible for strategies to contain disease and prevent epidemics need an accurate understanding of disease dynamics and the likely outcomes of preventive actions. In an increasingly connected world with extremely efficient global transportation links, the vectors of infection can be quite complex. STEM facilitates the development of advanced mathematical models, the creation of flexible models involving multiple populations (species) and interactions between diseases, and a better understanding of epidemiology.

STEM is designed to make it easy for developers and researchers to plug in their choice of models. It comes with spatiotemporal Susceptible/Infectious/Recovered (SIR) and Susceptible/Exposed/Infectious/Recovered (SEIR) models pre-coded with both deterministic and stochastic variations. STEM simulates the models using numerical ordinary differential equation solvers (two solver options are currently available) and outputs the results to a range of sources, for instance a map view or the file system.

more....

Project Status

June 14, 2009 - Stable v0.5.0 of STEM is available for download

January 28'th, 2009 - v0.4.0 of STEM is available for download

September 9'th, 2008 - v0.3.0a of STEM is available

Getting Started

Resources

News
 06-Nov 09:  Re: Events
 06-Nov 09:  Re: STEM Milestone M2 is now Available!!
 06-Nov 09:  Re: STEM Milestone M2 is now Available!!
 06-Nov 09:  Re: MAPPING
 06-Nov 09:  Re: MAPPING
more...
Videos and presentations
STEM Tutorial (English) 
STEM Tutorial (Spanish) 
Downloadable Scenarios
Please Readme first  Installation Instructions
Mexico USA pandemic flu scenario  
Global Geographic Models  Contains generic model building blocks organized by Continent. Geography, transportation, and People (no disease models).
Super-Continent Examples  Contains Demo Models using Continent Definitions included in Global Geographic Models Package above (required). See Readme.txt
Upcoming talks
Kaufman J, Edlund S, Bromberg M, Chodick G, Lessler J, Mesika Yossi, Ram R, Douglas J, Kaufman Z, Levanthal A, Marom R, Shalev V. 2009.Temporal and spatial effects of lunar calendar holidays on influenza A transmission in Israel. 
Epidemics 2, Athens, Greece, December 2009.

Recent Publications
Kaufman J, Edlund S, Douglas J.Infectious disease modeling: creating a community to respond to biological threats. 
Statistical Communications in Infectious Diseases, Vol 1, Issue 1, Article 1. The Berkeley Electronic Press. http://www.bepress/scid/vol1/iss1/art1

Edlund S, Bromberg M, Chodick G, Douglas J, Ford D, Kaufman Z, Lessler J, Marom R, Mesika Y, Ram R, Shalev V, Kaufman J. 2009.A spatiotemporal model for influenza. 
HIC 2009, Frontiers of Health Informatics, Canberra, Australia, August 19-21, 2009.

Edlund S, Kaufman J, Douglas J, Bromberg M, Kaufman A, Chodick G, Marom R, Shalev V, Lessler J, Mesika Y, Ram R, Leventhal A. 2009A study of two spatiotemporal models for seasonal influenza. 
in preparation.

more...
Acknowledgements
Development of STEM is supported in part by USAF/SG Development of STEM is being supported in part by the U.S. Air Force Surgeon General’s Office (USAF/SG) and administered by the Air Force District of Washington (AFDW) under Contract Number FA7014-07-C-0004. The Air Force has not accepted the products depicted and issuance of a contract does not constitute Federal endorsement of the IBM Almaden Research Center.  
 
The STEM Development team would also like to acknowledge the IBM Research Division and the Eclipse Foundation