{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T04:14:04Z","timestamp":1769832844941,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009777","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,2,10]],"date-time":"2022-02-10T00:00:00Z","timestamp":1644451200000}}],"reference-count":45,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2022,1,24]],"date-time":"2022-01-24T00:00:00Z","timestamp":1642982400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"osnabr\u00fcck university, evocell"},{"name":"osnabr\u00fcck university, evocell"},{"name":"osnabr\u00fcck university, evocell"},{"name":"osnabr\u00fcck university, evocell"},{"DOI":"10.13039\/501100001659","name":"german research foundation","doi-asserted-by":"crossref","award":["SFB 944, P19, KO 3909\/2-1, KO 3909\/4-1"],"award-info":[{"award-number":["SFB 944, P19, KO 3909\/2-1, KO 3909\/4-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"name":"helmholtz research program terrestrial environments"},{"name":"helmholtz research program terrestrial environments"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>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 <jats:italic>McComedy<\/jats:italic>, 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 <jats:italic>McComedy<\/jats:italic> 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.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1009777","type":"journal-article","created":{"date-parts":[[2022,1,24]],"date-time":"2022-01-24T18:40:30Z","timestamp":1643049630000},"page":"e1009777","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9634-7054","authenticated-orcid":true,"given":"Andr\u00e9","family":"Bogdanowski","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8541-789X","authenticated-orcid":true,"given":"Thomas","family":"Banitz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8269-260X","authenticated-orcid":true,"given":"Linea Katharina","family":"Muhsal","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7870-7343","authenticated-orcid":true,"given":"Christian","family":"Kost","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2769-0692","authenticated-orcid":true,"given":"Karin","family":"Frank","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,1,24]]},"reference":[{"issue":"5","key":"pcbi.1009777.ref001","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/nrmicro1643","article-title":"The role of ecological theory in microbial ecology","volume":"5","author":"JI Prosser","year":"2007","journal-title":"Nature Reviews Microbiology"},{"issue":"11","key":"pcbi.1009777.ref002","doi-asserted-by":"crossref","first-page":"2557","DOI":"10.1038\/ismej.2016.45","article-title":"Challenges in microbial ecology: building predictive understanding of community function and dynamics","volume":"10","author":"S Widder","year":"2016","journal-title":"The ISME Journal"},{"issue":"5739","key":"pcbi.1009777.ref003","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1126\/science.1118176","article-title":"Microbiology. 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