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Model integration in computational biology : the role of reproducibility, credibility and utility

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Karr, Jonathan, Sheriff, Rahuman S. Malik, Osborne, James, Gonzalez-Parra, Gilberton, Forgoston, Eric, Bowness, Ruth, Liu, Yaling, Thompson, Robin N., Garira, Winston , Barhak, Jacob, Rice, John, Torres, Marcella, Dobrovolny, Hana Maria, Tang, Tingting, Waites, William , Glazier, James A., Faeder, James and Kulesza, Alexander (2022) Model integration in computational biology : the role of reproducibility, credibility and utility. Frontiers in Systems Biology, 2 . 822606. doi:10.3389/fsysb.2022.822606 ISSN 2674-0702.

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Official URL: https://doi.org/10.3389/fsysb.2022.822606

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Abstract

During the COVID-19 pandemic, mathematical modeling of disease transmission has become a cornerstone of key state decisions. To advance the state-of-the-art host viral modeling to handle future pandemics, many scientists working on related issues assembled to discuss the topics. These discussions exposed the reproducibility crisis that leads to inability to reuse and integrate models. This document summarizes these discussions, presents difficulties, and mentions existing efforts towards future solutions that will allow future model utility and integration. We argue that without addressing these challenges, scientists will have diminished ability to build, disseminate, and implement high-impact multi-scale modeling that is needed to understand the health crises we face.

Item Type: Journal Article
Subjects: Q Science > Q Science (General)
R Medicine > RA Public aspects of medicine > RA0421 Public health. Hygiene. Preventive Medicine
Divisions: Faculty of Science, Engineering and Medicine > Science > Mathematics
Library of Congress Subject Headings (LCSH): Communicable diseases -- Transmission -- Mathematical models, Communicable diseases -- Transmission -- Computer simulation, Epidemics -- Mathematical models, Epidemics -- Computer simulation, Reproducible research
Journal or Publication Title: Frontiers in Systems Biology
Publisher: Frontiers Media
ISSN: 2674-0702
Official Date: 7 March 2022
Dates:
DateEvent
7 March 2022Published
4 February 2022Accepted
Volume: 2
Article Number: 822606
DOI: 10.3389/fsysb.2022.822606
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access (Creative Commons)
Date of first compliant deposit: 7 February 2022
Date of first compliant Open Access: 8 March 2022
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
P41EB023912National Institute of Biomedical Imaging and Bioengineeringhttp://dx.doi.org/10.13039/100000070
MR/V027956/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
UNSPECIFIEDEuropean Molecular Biology Laboratoryhttp://dx.doi.org/10.13039/100013060
Fellowship[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
188553[NSF] National Science Foundation (US)http://dx.doi.org/10.13039/100000001
186890[NSF] National Science Foundation (US)http://dx.doi.org/10.13039/100000001
1720625[NSF] National Science Foundation (US)http://dx.doi.org/10.13039/100000001
U24 EB028887National Institutes of Healthhttp://dx.doi.org/10.13039/100000002
R01 GM122424National Institutes of Healthhttp://dx.doi.org/10.13039/100000002
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