Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1371/journal.pcbi.1009777
Licence creative commons licence
Title (Primary) McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems
Author Bogdanowski, A.; Banitz, T. ORCID logo ; Muhsal, L.K.; Kost, C.; Frank, K. ORCID logo
Source Titel PLoS Computational Biology
Year 2022
Department OESA; iDiv
Volume 18
Issue 1
Page From e1009777
Language englisch
Topic T5 Future Landscapes
Supplements https://doi.org/10.1371/journal.pcbi.1009777.s001
https://doi.org/10.1371/journal.pcbi.1009777.s002
https://doi.org/10.1371/journal.pcbi.1009777.s003
https://doi.org/10.1371/journal.pcbi.1009777.s004
https://doi.org/10.1371/journal.pcbi.1009777.s005
Abstract Individual-based modeling is widely applied to investigate the ecological mechanisms driving microbial community dynamics. In such models, the population or community dynamics emerge from the behavior and interplay of individual entities, which are simulated according to a predefined set of rules. If the rules that govern the behavior of individuals are based on generic and mechanistically sound principles, the models are referred to as next-generation individual-based models. These models perform particularly well in recapitulating actual ecological dynamics. However, implementation of such models is time-consuming and requires proficiency in programming or in using specific software, which likely hinders a broader application of this powerful method. Here we present McComedy, a modeling tool designed to facilitate the development of next-generation individual-based models of microbial consumer-resource systems. This tool allows flexibly combining pre-implemented building blocks that represent physical and biological processes. The ability of McComedy to capture the essential dynamics of microbial consumer-resource systems is demonstrated by reproducing and furthermore adding to the results of two distinct studies from the literature. With this article, we provide a versatile tool for developing next-generation individual-based models that can foster understanding of microbial ecology in both research and education.
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=25697
Bogdanowski, A., Banitz, T., Muhsal, L.K., Kost, C., Frank, K. (2022):
McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems
PLoS Comput. Biol. 18 (1), e1009777 10.1371/journal.pcbi.1009777