STM Article Repository

Yu, Jessica S. and Bagheri, Neda and Mac Gabhann, Feilim (2024) Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions. PLOS Computational Biology, 20 (3). e1011917. ISSN 1553-7358

[thumbnail of journal.pcbi.1011917.pdf] Text
journal.pcbi.1011917.pdf - Published Version

Download (1MB)

Abstract

Computational models enable scientists to understand observed dynamics, uncover rules underlying behaviors, predict experimental outcomes, and generate new hypotheses. There are countless modeling approaches that can be used to characterize biological systems, further multiplied when accounting for the variety of model design choices. Many studies focus on the impact of model parameters on model output and performance; fewer studies investigate the impact of model design choices on biological insight. Here we demonstrate why model design choices should be deliberate and intentional in context of the specific research system and question. In this study, we analyze agnostic and broadly applicable modeling choices at three levels—system, cell, and environment—within the same agent-based modeling framework to interrogate their impact on temporal, spatial, and single-cell emergent dynamics. We identify key considerations when making these modeling choices, including the (i) differences between qualitative vs. quantitative results driven by choices in system representation, (ii) impact of cell-to-cell variability choices on cell-level and temporal trends, and (iii) relationship between emergent outcomes and choices of nutrient dynamics in the environment. This generalizable investigation can help guide the choices made when developing biological models that aim to characterize spatial-temporal dynamics.

Item Type: Article
Subjects: GO for ARCHIVE > Biological Science
Depositing User: Unnamed user with email support@goforarchive.com
Date Deposited: 08 Apr 2024 13:19
Last Modified: 08 Apr 2024 13:19
URI: http://eprints.go4mailburst.com/id/eprint/2212

Actions (login required)

View Item
View Item