Implementation and applications of EMOD, an individual-based multi-disease modeling platform.
| Title: | Implementation and applications of EMOD, an individual-based multi-disease modeling platform. |
|---|---|
| Authors: | Bershteyn A; Institute for Disease Modeling, Bellevue, WA, USA.; Gerardin J; Institute for Disease Modeling, Bellevue, WA, USA.; Bridenbecker D; Institute for Disease Modeling, Bellevue, WA, USA.; Lorton CW; Institute for Disease Modeling, Bellevue, WA, USA.; Bloedow J; Institute for Disease Modeling, Bellevue, WA, USA.; Baker RS; Institute for Disease Modeling, Bellevue, WA, USA.; Chabot-Couture G; Institute for Disease Modeling, Bellevue, WA, USA.; Chen Y; Institute for Disease Modeling, Bellevue, WA, USA.; Fischle T; Institute for Disease Modeling, Bellevue, WA, USA.; Frey K; Institute for Disease Modeling, Bellevue, WA, USA.; Gauld JS; Institute for Disease Modeling, Bellevue, WA, USA.; Hu H; Institute for Disease Modeling, Bellevue, WA, USA.; Izzo AS; Institute for Disease Modeling, Bellevue, WA, USA.; Klein DJ; Institute for Disease Modeling, Bellevue, WA, USA.; Lukacevic D; Institute for Disease Modeling, Bellevue, WA, USA.; McCarthy KA; Institute for Disease Modeling, Bellevue, WA, USA.; Miller JC; Institute for Disease Modeling, Bellevue, WA, USA.; Ouedraogo AL; Institute for Disease Modeling, Bellevue, WA, USA.; Perkins TA; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.; Steinkraus J; Institute for Disease Modeling, Bellevue, WA, USA.; Ten Bosch QA; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.; Unit for Mathematical Modeling of Infectious Diseases, Institut Pasteur, Paris, France.; Ting HF; Institute for Disease Modeling, Bellevue, WA, USA.; Titova S; Institute for Disease Modeling, Bellevue, WA, USA.; Wagner BG; Institute for Disease Modeling, Bellevue, WA, USA.; Welkhoff PA; Institute for Disease Modeling, Bellevue, WA, USA.; Wenger EA; Institute for Disease Modeling, Bellevue, WA, USA.; Wiswell CN; Institute for Disease Modeling, Bellevue, WA, USA. |
| Corporate Authors: | Institute for Disease Modeling |
| Source: | Pathogens and disease [Pathog Dis] 2018 Jul 01; Vol. 76 (5). |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Oxford University Press Country of Publication: United States NLM ID: 101595366 Publication Model: Print Cited Medium: Internet ISSN: 2049-632X (Electronic) Linking ISSN: 2049632X NLM ISO Abbreviation: Pathog Dis Subsets: MEDLINE |
| Imprint Name(s): | Publication: 2015- : Oxford Oxford University Press; Original Publication: [Malden, MA] : Wiley-Blackwell, [2013]- |
| MeSH Terms: | Disease Susceptibility* ; Models, Theoretical* ; Software*; Computational Biology/*methods; Communicable Diseases/epidemiology ; Communicable Diseases/etiology ; Algorithms ; Humans ; Software Design |
| 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.; (© FEMS 2018.) |
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| Contributed Indexing: | Keywords: epidemiological modeling; mathematical modeling; software |
| Entry Date(s): | Date Created: 20180710 Date Completed: 20190930 Latest Revision: 20190930 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC6067119 |
| DOI: | 10.1093/femspd/fty059 |
| PMID: | 29986020 |
| Database: | MEDLINE |
Journal Article