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 Steinkraus; Quirine A. Ten Bosch; Hung Fu Ting; Svetlana Titova; Bradley G. Wagner; Philip A. Welkhoff; Edward A. Wenger; Christian N. Wiswell

doi:10.1093/femspd/fty059

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 journal › Article › Academic › peer-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 language	English
Journal	Pathogens and Disease
Volume	76
Issue number	5
DOIs	https://doi.org/10.1093/femspd/fty059
Publication status	Published - 1 Jul 2018
Externally published	Yes

Keywords

epidemiological modeling
mathematical modeling
software

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Bershteyn, A., Gerardin, J., Bridenbecker, D., Lorton, C. W., Bloedow, J., Baker, R. S., Chabot-Couture, G., Chen, Y., Fischle, T., Frey, K., Gauld, J. S., Hu, H., Izzo, A. S., Klein, D. J., Lukacevic, D., McCarthy, K. A., Miller, J. C., Ouedraogo, A. L., Perkins, T. A., ... Wiswell, C. N. (2018). Implementation and applications of EMOD, an individual-based multi-disease modeling platform. Pathogens and Disease, 76(5). https://doi.org/10.1093/femspd/fty059

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

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.",

keywords = "epidemiological modeling, mathematical modeling, software",

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

year = "2018",

month = jul,

day = "1",

doi = "10.1093/femspd/fty059",

language = "English",

volume = "76",

journal = " Pathogens and Disease",

issn = "2049-632X",

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Bershteyn, A, Gerardin, J, Bridenbecker, D, Lorton, CW, Bloedow, J, Baker, RS, Chabot-Couture, G, Chen, Y, Fischle, T, Frey, K, Gauld, JS, Hu, H, Izzo, AS, Klein, DJ, Lukacevic, D, McCarthy, KA, Miller, JC, Ouedraogo, AL, Perkins, TA, Steinkraus, J, Ten Bosch, QA, Ting, HF, Titova, S, Wagner, BG, Welkhoff, PA, Wenger, EA & Wiswell, CN 2018, 'Implementation and applications of EMOD, an individual-based multi-disease modeling platform', Pathogens and Disease, vol. 76, no. 5. https://doi.org/10.1093/femspd/fty059

TY - JOUR

T1 - Implementation and applications of EMOD, an individual-based multi-disease modeling platform

AU - Bershteyn, Anna

AU - Gerardin, Jaline

AU - Bridenbecker, Daniel

AU - Lorton, Christopher W.

AU - Bloedow, Jonathan

AU - Baker, Robert S.

AU - Chabot-Couture, Guillaume

AU - Chen, Ye

AU - Fischle, Thomas

AU - Frey, Kurt

AU - Gauld, Jillian S.

AU - Hu, Hao

AU - Izzo, Amanda S.

AU - Klein, Daniel J.

AU - Lukacevic, Dejan

AU - McCarthy, Kevin A.

AU - Miller, Joel C.

AU - Ouedraogo, Andre Lin

AU - Perkins, T.A.

AU - Steinkraus, Jeffrey

AU - Ten Bosch, Quirine A.

AU - Ting, Hung Fu

AU - Titova, Svetlana

AU - Wagner, Bradley G.

AU - Welkhoff, Philip A.

AU - Wenger, Edward A.

AU - Wiswell, Christian N.

PY - 2018/7/1

Y1 - 2018/7/1

N2 - 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.

AB - 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.

KW - epidemiological modeling

KW - mathematical modeling

KW - software

U2 - 10.1093/femspd/fty059

DO - 10.1093/femspd/fty059

M3 - Article

C2 - 29986020

AN - SCOPUS:85067530391

SN - 2049-632X

VL - 76

JO - Pathogens and Disease

JF - Pathogens and Disease

IS - 5

ER -

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

Abstract

Keywords

UN SDGs

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