EpiFire: An open source C++ library and application for contact network epidemiology
1 Section of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX, 78712, USA
2 Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
3 Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
4 Department of Epidemiology and Public Health, Yale University Medical School, New Haven, CT, 06520, USA
5 Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
BMC Bioinformatics 2012, 13:76 doi:10.1186/1471-2105-13-76Published: 4 May 2012
Contact network models have become increasingly common in epidemiology, but we lack a flexible programming framework for the generation and analysis of epidemiological contact networks and for the simulation of disease transmission through such networks.
Here we present EpiFire, an applications programming interface and graphical user interface implemented in C++, which includes a fast and efficient library for generating, analyzing and manipulating networks. Network-based percolation and chain-binomial simulations of susceptible-infected-recovered disease transmission, as well as traditional non-network mass-action simulations, can be performed using EpiFire.
EpiFire provides an open-source programming interface for the rapid development of network models with a focus in contact network epidemiology. EpiFire also provides a point-and-click interface for generating networks, conducting epidemic simulations, and creating figures. This interface is particularly useful as a pedagogical tool.