EpiFire: An open source C++ library and application for contact network epidemiology.

BMC Bioinformatics
Thomas HladishLauren Ancel Meyers

Abstract

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.

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Citations

Apr 10, 2013·Computer Methods and Programs in Biomedicine·Lilia L Ramírez-RamírezMatt McPherson
Sep 21, 2016·International Journal of Environmental Research and Public Health·Tiago França Melo de LimaClodoveu Augusto Davis Junior
Oct 31, 2015·PLoS Computational Biology·Christian L Vestergaard, Mathieu Génois
Apr 19, 2017·Emerging Infectious Diseases·David J MuscatelloC Raina MacIntyre
Oct 20, 2017·PLoS Computational Biology·Spencer J FoxLauren Ancel Meyers
Nov 13, 2020·Proceedings of the National Academy of Sciences of the United States of America·Akihiro NishiSean D Young

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Software Mentioned

Qt
gcc
Mac OS X
MassAction
_ Sim
Sim
igraph
NetworkX
Git
EpiFire GUI

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