The Spatiotemporal Epidemiological Modeler (STEM) Project
About STEM
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.
Resources
STEM Project Resources
-
Existing STEM Bugs on Bugzilla.
Submit a new bug - Developers Documentation Guide
- Newsgroup (See About the newsgroups if you have access problems)
- Wiki
- Access the STEM source code
- STEM IRC Chat Channel irc://irc.freenode.net/#eclipse-stem
News
07-Feb 12: STEM Release 1.3.0 is up 02-Feb 12: STEM Release Candidate 4 Now Up 01-Feb 12: STEM Release Candidate 3 is up 31-Jan 12: Food borne Disease Model: Demo Scenario is up 26-Jan 12: STEM RC2 is up. Videos and presentations
STEM Tutorial (English)STEM Tutorial (Spanish)
STEM Tutorial (Hebrew)
STEM Tutorial (Japanese)
5 min. STEM Video (English)
Downloadable Scenarios
Please Read-me first Installation InstructionsDocumentation To Learn more about the downloadable scenarios please see the tutorials on the STEM wiki
(New)Food borne disease Model This first demo mode of foodborne disease models beef production from cattle. The food production graph, created with pajek, is inserted into Argentina in this example scenario.
Evacuation demo The evacuation demonstration project aims to demonstrate how interventions can be used in STEM to control an outbreak.
Chickenpox !! The ChickenPox example scenario shows how to use the new aging (demographic) population model. The initial conditions in this example start the population far from equilibrium.
Asia Mosquito Density Model Demonstrates how the earth science data can be used to generate seasonal mosquito density estimates in Asia. Requires installation of the optional 2010 Earth Science Data Feature from the STEM update site and the Global Geography and Global Earth Science models (below).
Automated Experiment Example Demonstrates the automated experiment feature in STEM and how it is used to fit unknown EPI parameters to a reference incidence data set
Global Earth Science Models for release 1.2.1 and later Continent-level models of Earth Science Data including elevation, rainfall, temperature, and vegetation coverage. OBSERVE: You need to access the STEM update site and install the "STEM Earth Science Data for 2010" plugin to use these models.
Multi-Population Example Demonstrates a simplified multi-population disease model with anopheles mosquitos and humans
Pajek Import Example Demonstrates a simplified multi-population disease model where the entire graph is created using the new Pajek Import facility
Square Lattice Example Demonstrates both population migration and disease spread on a Square Lattice
Mexico USA pandemic flu scenario An example H1N1 Simulation
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
Past and upcoming talks
Edlund, S., Davis, M., Pieper, J., Kershenbaum, A., Waraporn, N., and Kaufman, J.H.A global study of malaria climate susceptibility.Edlund, S., Davis. M., Kaufman, J.The Spatiotemporal Epidemiological Modeler.
Edlund, S. et. al.The Spatio-Temporal Epidemiological Modeler
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.
Recent Publications
Edlund, S., Davis. M., Kaufman, J.The Spatiotemporal Epidemiological Modeler.Kaufman J, Edlund S, Douglas J.Infectious disease modeling: creating a community to respond to biological threats.
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.
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.
Acknowledgements
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