Modeling in Space and Time

A Framework for Visualization and Collaboration
Chapter
Part of the Integrated Series in Information Systems book series (ISIS, volume 27)

Chapter Overview

This chapter describes the Spatiotemporal Epidemiological Modeler (STEM), now being developed as an open source computer software system for defining and visualizing simulations of the spread of infectious disease in space and time. Part of the Eclipse Technology Project, http://www.eclipse.org/ stem, STEM is designed to offer the research community the power and extensibility to develop, validate, and share models on a common collaborative platform. Its innovations include a common representational framework that supports users in creating and configuring the components that constitute a model. This chapter defines modeling terms (canonical graph, decorators, etc.) and key concepts (e.g., labels, disease model computations) are discussed. Figures illustrate the types of visualizations STEM provides, including geographical views via GIS and Google Earth™ and report generated graphics.

Keywords

Open source tools Modeling Visualization Infectious disease transmission Collaboration 

References

  1. Ash, C., and Roberts, L. (2006). “Influenza: The state of our ignorance,” Science, 312 (April 21, 2006), 379. http://www.sciencemag.org.
  2. Cummings, DA., Irizarry, R.A., Endy, T.P., Nisalak, A., and Burke, D. (2004). “Travelling waves in dengue hemorrhagic fever incidence in Thailand,” Nature, 427:344–347.PubMedCrossRefGoogle Scholar
  3. Epstein, J.M., and Cummings, D. (2002). Toward a Containment Strategy for Smallpox Bioterror: An Individual-Based Computational Approach, CSED Working Paper 31 (December 2002). Washington, DC: Brookings Institution.Google Scholar
  4. Ford, DA., Kaufman, J.H., and Eiron, I. (2006). “An extensible spatial and temporal epidemiological modeling system,” International Journal of Health Geographics, 5(4) (January 17, 2006). http://www.ij-healthgeographic.
  5. Gross, J.L., and Yellen, J. (2003). Handbook of Graph Theory. Boca Baton, FL: CRC Press.CrossRefGoogle Scholar
  6. Haberman, R. (1998). Mathematical Models: Mechanical Vibrations, Population Dynamics, & Traffic Flow (Classics in Applied Mathematics). Philadelphia, PA: Society for Industrial & Applied Mathematics.CrossRefGoogle Scholar
  7. Liu, W-M., Hethcote, H.W., and Levin, SA. (1987). “Dynamical behavior of epidemiological models with nonlinear incidence rates,” Journal of Mathematical Biology, 25:359–380.PubMedCrossRefGoogle Scholar
  8. Myers, LA., Newman, ME.J., Martin, M., and Schrag, S. (2003). “Applying network theory to epidemics: Control measures for mycoplasma pneumonia outbreaks.” Emerging Infectious Diseases, 9(2):204–210. (February 2003). http://www.cdc.gov/ncidod/EID/vol9no2/02-0188.
  9. Schaffer, W.M., and Bronnikova, T.V. (2001). Ecology/Mathematics 380: Modeling Micro-parasitic Infections. See for example and references therein. Available at: http://www.bill.srnr.arizona.edu/classes/195b/195b.epmodel
  10. Widgren, S. (2004). Graph Theory in Veterinary Epidemiology - Modelling an Outbreak of Classical Swine Fever. Thesis. Institution for Ruminant Medicine and Veterinary Epidemiology, Swedish University of Agricultural Science.Google Scholar

Suggested Reading

  1. Anderson, R.M. (1982). Population Dynamics of Infectious Diseases: Theory and Applications. New York: Chapman and Hall.CrossRefGoogle Scholar
  2. Barrett, C.L., Eubank, S.G., and Smith, J.P. (2005). “If smallpox strikes Portland,” Scientific American 292:42–49, How modeling might be used to plan for and develop responses to epidemic events.PubMedCrossRefGoogle Scholar
  3. Enserink, M. (2003a). Science 301:294–296.Google Scholar
  4. Enserink, M. (2003b). Science 301:299.Google Scholar
  5. Normile D., Enserink, M. (2003c). Science 301:297–299.Google Scholar

Online Resources

  1. Eclipse Platform Technical Overview: http://www.eclipse.org/articles.
  2. Open Services Gateway initiative (OSGi) Alliance: http://www.osgi.org.
  3. Spatiotemporal Epidemiological Model (STEM): http://www.eclipse.org/stem.

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Daniel A. Ford
    • 1
  • James H. Kaufman
    • 1
  • Yossi Mesika
    • 2
  1. 1.Healthcare Informatics Research, Department of Computer ScienceIBM Almaden Research CenterSan JoseUSA
  2. 2.Healthcare and Life Sciences, IBM Haifa Research LabHaifa University CampusMount CarmelIsrael

Personalised recommendations