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 Alex Perkins, Jeffrey Steinkraus, Quirine A Ten Bosch, Hung-Fu Ting, Svetlana Titova, Bradley G Wagner, Philip A Welkhoff, Edward A Wenger, Christian N Wiswell, Institute for Disease Modeling
Author Information
Anna Bershteyn: Institute for Disease Modeling, Bellevue, WA, USA.
Jaline Gerardin: Institute for Disease Modeling, Bellevue, WA, USA.
Daniel Bridenbecker: Institute for Disease Modeling, Bellevue, WA, USA.
Christopher W Lorton: Institute for Disease Modeling, Bellevue, WA, USA.
Jonathan Bloedow: Institute for Disease Modeling, Bellevue, WA, USA.
Robert S Baker: Institute for Disease Modeling, Bellevue, WA, USA.
Guillaume Chabot-Couture: Institute for Disease Modeling, Bellevue, WA, USA.
Ye Chen: Institute for Disease Modeling, Bellevue, WA, USA.
Thomas Fischle: Institute for Disease Modeling, Bellevue, WA, USA.
Kurt Frey: Institute for Disease Modeling, Bellevue, WA, USA.
Jillian S Gauld: Institute for Disease Modeling, Bellevue, WA, USA.
Hao Hu: Institute for Disease Modeling, Bellevue, WA, USA.
Amanda S Izzo: Institute for Disease Modeling, Bellevue, WA, USA.
Daniel J Klein: Institute for Disease Modeling, Bellevue, WA, USA.
Dejan Lukacevic: Institute for Disease Modeling, Bellevue, WA, USA.
Kevin A McCarthy: Institute for Disease Modeling, Bellevue, WA, USA.
Joel C Miller: Institute for Disease Modeling, Bellevue, WA, USA.
Andre Lin Ouedraogo: Institute for Disease Modeling, Bellevue, WA, USA.
T Alex Perkins: Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
Jeffrey Steinkraus: Institute for Disease Modeling, Bellevue, WA, USA.
Quirine A Ten Bosch: Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
Hung-Fu Ting: Institute for Disease Modeling, Bellevue, WA, USA.
Svetlana Titova: Institute for Disease Modeling, Bellevue, WA, USA.
Bradley G Wagner: Institute for Disease Modeling, Bellevue, WA, USA.
Philip A Welkhoff: Institute for Disease Modeling, Bellevue, WA, USA.
Edward A Wenger: Institute for Disease Modeling, Bellevue, WA, USA.
Christian N Wiswell: Institute for Disease Modeling, Bellevue, WA, USA.
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.
