Implementation and applications of EMOD, an individual-based multi-disease modeling platform

Anna Bershteyn, Jaline Gerardin, Daniel Bridenbecker, Christopher W. Lorton, Jonathan Bloedow, Robert S. Baker, Guillaume Chabot-Couture, Ye Chen, Thomas Fischle, Kurt Frey, Jillian S. Gauld, Hao Hu, Amanda S. Izzo, Daniel J. Klein, Dejan Lukacevic, Kevin A. McCarthy, Joel C. Miller, Andre Lin Ouedraogo, T.A. Perkins, Jeffrey SteinkrausQuirine A. Ten Bosch, Hung Fu Ting, Svetlana Titova, Bradley G. Wagner, Philip A. Welkhoff, Edward A. Wenger, Christian N. Wiswell

Research output: Contribution to journalArticleAcademicpeer-review

51 Citations (Scopus)

Abstract

Individual-based models provide modularity and structural flexibility necessary for modeling of infectious diseases at the within-host and population levels, but are challenging to implement. Levels of complexity can exceed the capacity and timescales for students and trainees in most academic institutions. Here we describe the process and advantages of a multi-disease framework approach developed with formal software support. The epidemiological modeling software, EMOD, has undergone a decade of software development. It is structured so that a majority of code is shared across disease modeling including malaria, HIV, tuberculosis, dengue, polio and typhoid. In additional to implementation efficiency, the sharing increases code usage and testing. The freely available codebase also includes hundreds of regression tests, scientific feature tests and component tests to help verify functionality and avoid inadvertent changes to functionality during future development. Here we describe the levels of detail, flexible configurability and modularity enabled by EMOD and the role of software development principles and processes in its development.
Original languageEnglish
Journal Pathogens and Disease
Volume76
Issue number5
DOIs
Publication statusPublished - 1 Jul 2018
Externally publishedYes

Keywords

  • epidemiological modeling
  • mathematical modeling
  • software

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