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Open Access Highly Accessed Software

FRED (A Framework for Reconstructing Epidemic Dynamics): an open-source software system for modeling infectious diseases and control strategies using census-based populations

John J Grefenstette1*, Shawn T Brown2, Roni Rosenfeld3, Jay DePasse2, Nathan TB Stone2, Phillip C Cooley4, William D Wheaton4, Alona Fyshe3, David D Galloway1, Anuroop Sriram3, Hasan Guclu1, Thomas Abraham3 and Donald S Burke1

Author Affiliations

1 Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

2 Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA

3 School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA

4 RTI International, Research Triangle Park, Durham, North Carolina, USA

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BMC Public Health 2013, 13:940  doi:10.1186/1471-2458-13-940

Published: 8 October 2013

Abstract

Background

Mathematical and computational models provide valuable tools that help public health planners to evaluate competing health interventions, especially for novel circumstances that cannot be examined through observational or controlled studies, such as pandemic influenza. The spread of diseases like influenza depends on the mixing patterns within the population, and these mixing patterns depend in part on local factors including the spatial distribution and age structure of the population, the distribution of size and composition of households, employment status and commuting patterns of adults, and the size and age structure of schools. Finally, public health planners must take into account the health behavior patterns of the population, patterns that often vary according to socioeconomic factors such as race, household income, and education levels.

Results

FRED (a Framework for Reconstructing Epidemic Dynamics) is a freely available open-source agent-based modeling system based closely on models used in previously published studies of pandemic influenza. This version of FRED uses open-access census-based synthetic populations that capture the demographic and geographic heterogeneities of the population, including realistic household, school, and workplace social networks. FRED epidemic models are currently available for every state and county in the United States, and for selected international locations.

Conclusions

State and county public health planners can use FRED to explore the effects of possible influenza epidemics in specific geographic regions of interest and to help evaluate the effect of interventions such as vaccination programs and school closure policies. FRED is available under a free open source license in order to contribute to the development of better modeling tools and to encourage open discussion of modeling tools being used to evaluate public health policies. We also welcome participation by other researchers in the further development of FRED.

Keywords:
Pandemic influenza; Simulator; Agent-based model; Synthetic population; Influenza modeling