Epidemiological Agent-Based Modelling Software (Epiabm)

Kit Gallagher; Ioana Bouros; Nicholas Fan; Elizabeth Hayman; Luke Heirene; Patricia Lamirande; Annabelle Lemenuel-Diot; Ben Lambert; David Gavaghan; Richard Creswell

doi:10.5334/jors.449

Epidemiological Agent-Based Modelling Software (Epiabm)

Volume 12 (2024): Issue 1

By: Kit Gallagher , Ioana Bouros , Nicholas Fan, Elizabeth Hayman , Luke Heirene , Patricia Lamirande , Annabelle Lemenuel-Diot , Ben Lambert , David Gavaghan and Richard Creswell

Open Access

|Mar 2024

Abstract

Epiabm is an open-source software package for epidemiological agent-based modelling, re-implementing the well-known CovidSim model from the MRC Centre for Global Infectious Disease Analysis at Imperial College London. It has been developed as part of the first-year training programme in the EPSRC SABS:R³ Centre for Doctoral Training at the University of Oxford. The model builds an age-stratified, spatially heterogeneous population and offers a modular approach to configure and run epidemic scenarios, allowing for a broad scope of investigative and comparative studies. Two simulation backends are provided: a pedagogical Python backend (with full functionality) and a high performance C++ backend for use with larger population simulations. Both are highly modular, and include a comprehensive testing suite (including 100% coverage on unit tests alongside a range of functional and integration tests), as well as complete online documentation for ease of understanding and extensibility. Epiabm is publicly available through GitHub at github.com/SABS-R3-Epidemiology/epiabm.

References

Adam D. Special report: The simulations driving the world’s response to COVID-19. Nature. Apr. 2020; 580(7803): 316–318. DOI: 10.1038/d41586-020-01003-6
Open DOI Search in Google Scholar Back to article
Birrell P, et al. Real-time nowcasting and forecasting of COVID-19 dynamics in England: the first wave. Philosophical Transactions of the Royal Society B: Biological Sciences. 2021; 376(1829). DOI: 10.1098/rstb.2020.0279
Open DOI Search in Google Scholar Back to article
Crick T, Hall BA, Ishtiaq S. Reproducibility in Research: Systems, Infrastructure, Culture. Journal of Open Research Software. Nov. 2017; 5. DOI: 10.5334/jors.73
Open DOI Search in Google Scholar Back to article
Danon L, et al. A spatial model of COVID-19 transmission in England and Wales: early spread, peak timing and the impact of seasonality. Philosophical Transactions of the Royal Society B: Biological Sciences. May 2021; 376(1829). DOI: 10.1098/rstb.2020.0272
Open DOI Search in Google Scholar Back to article
Davies NG, et al. Effects of non-pharmaceutical interventions on COVID-19 cases, deaths, and demand for hospital services in the UK: a modelling study. The Lancet Public Health. 2020; 5(7): e375–e385. ISSN: 2468–2667. DOI: 10.1016/S2468-2667(20)30133-X
Open DOI Search in Google Scholar Back to article
Eglen SJ. CODECHECK certificate 2020-010. en (2020). DOI: 10.5281/ZENODO.3865490
Open DOI Search in Google Scholar Back to article
Ferguson NM, et al. Report 9: Impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand; 2020. DOI: 10.25561/77482
Open DOI Search in Google Scholar Back to article
Ferguson NM, Nedjati Gilani G, Laydon, D. COVID-19 CovidSim microsimulation model. Computer Software. R Foundation for Statistical Computing; Apr. 2020.
Search in Google Scholar Back to article
Ferguson NM, et al. Strategies for mitigating an influenza pandemic. Nature. Apr. 2006. 442(7101): 448–452. DOI: 10.1038/nature04795
Open DOI Search in Google Scholar Back to article
He S, Peng Y, Sun K. SEIR modeling of the COVID-19 and its dynamics. Nonlinear Dynamics. June 2020; 101(3): 1667–1680. DOI: 10.1007/s11071-020-05743-y
Open DOI Search in Google Scholar Back to article
Hunter E, Mac Mamee B, Kelleher JD. A Comparison of Agent-Based Models and Equation Based Models for Infectious Disease Epidemiology; 2018. DOI: 10.18564/jasss.3414
Open DOI Search in Google Scholar Back to article
Keeling MJ, et al. Predictions of COVID-19 dynamics in the UK: Shortterm forecasting and analysis of potential exit strategies. PLOS Computational Biology. Jan. 2021. 17(1): 1–20. DOI: 10.1371/journal.pcbi.1008619
Open DOI Search in Google Scholar Back to article
Lyra W, et al. COVID-19 pandemics modeling with modified determinist SEIR, social distancing, and age stratification. The effect of vertical confinement and release in Brazil. PLOS ONE. Sept. 2020. 15(9): e0237627, Samy AM (ed.). DOI: 10.1371/journal.pone.0237627
Open DOI Search in Google Scholar Back to article
Shen C, Taleb NN, Bar-Yam Y. Review of Ferguson et al. ‘Impact of non-pharmaceutical interventions…’ New England Complex Systems Institute; Mar. 2020.
Search in Google Scholar Back to article
Stodden V, Miguez S. Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research. Journal of Open Research Software. July 2014; 2(1). DOI: 10.5334/jors.ay
Open DOI Search in Google Scholar Back to article
Wooldridge M. The Software that Led to the Lockdown. July 2020.
Search in Google Scholar Back to article
Wu JT, Cowling BJ. The use of mathematical models to inform influenza pandemic preparedness and response. Experimental Biology and Medicine. Aug. 2011; 236(8): 955–961. DOI: 10.1258/ebm.2010.010271
Open DOI Search in Google Scholar Back to article

Articles in this issue

DOI: https://doi.org/10.5334/jors.449 | Journal eISSN: 2049-9647

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Language: English

Submitted on: Nov 24, 2022

Accepted on: Feb 2, 2024

Published on: Mar 5, 2024

Published by: Ubiquity Press

In partnership with: Paradigm Publishing Services

Publication frequency: 1 issue per year

Keywords:

Agent-based modelling,

epidemiology,

COVID-19,

Python,

C++

© 2024 Kit Gallagher, Ioana Bouros, Nicholas Fan, Elizabeth Hayman, Luke Heirene, Patricia Lamirande, Annabelle Lemenuel-Diot, Ben Lambert, David Gavaghan, Richard Creswell, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 12 (2024): Issue 1