{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T02:16:17Z","timestamp":1775873777694,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,10,19]],"date-time":"2024-10-19T00:00:00Z","timestamp":1729296000000},"content-version":"vor","delay-in-days":26,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Union's Horizon 2020","award":["951773"],"award-info":[{"award-number":["951773"]}]},{"name":"European Union's Horizon Europe Research and Innovation Program","award":["101136379"],"award-info":[{"award-number":["101136379"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1720625"],"award-info":[{"award-number":["1720625"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2303695"],"award-info":[{"award-number":["2303695"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01-CA232137-01"],"award-info":[{"award-number":["U01-CA232137-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016460","name":"Jayne Koskinas Ted Giovanis Foundation for Health and Policy","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016460","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Multiscale models provide a unique tool for analyzing complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the intracellular level such as signaling, and at the extracellular level where cells communicate and coordinate with other cells. These models aim to understand the impact of genetic or environmental deregulation observed in complex diseases, describe the interplay between a pathological tissue and the immune system, and suggest strategies to revert the diseased phenotypes. The construction of these multiscale models remains a very complex task, including the choice of the components to consider, the level of details of the processes to simulate, or the fitting of the parameters to the data. One additional difficulty is the expert knowledge needed to program these models in languages such as C++ or Python, which may discourage the participation of non-experts. Simplifying this process through structured description formalisms\u2014coupled with a graphical interface\u2014is crucial in making modeling more accessible to the broader scientific community, as well as streamlining the process for advanced users. This article introduces three examples of multiscale models which rely on the framework PhysiBoSS, an add-on of PhysiCell that includes intracellular descriptions as continuous time Boolean models to the agent-based approach. The article demonstrates how to construct these models more easily, relying on PhysiCell Studio, the PhysiCell Graphical User Interface. A step-by-step tutorial is provided as Supplementary Material and all models are provided at https:\/\/physiboss.github.io\/tutorial\/.<\/jats:p>","DOI":"10.1093\/bib\/bbae509","type":"journal-article","created":{"date-parts":[[2024,10,19]],"date-time":"2024-10-19T06:43:53Z","timestamp":1729320233000},"source":"Crossref","is-referenced-by-count":7,"title":["Building multiscale models with PhysiBoSS, an agent-based modeling tool"],"prefix":"10.1093","volume":"25","author":[{"given":"Marco","family":"Ruscone","sequence":"first","affiliation":[{"name":"Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","place":["France"]},{"name":"INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","place":["France"]},{"name":"Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,","place":["France"]}]},{"given":"Andrea","family":"Checcoli","sequence":"additional","affiliation":[{"name":"Centre de Recherche des Cordeliers , Sorbonne Universit\u00e9 15 rue de l'\u00c9cole de M\u00e9decine, 75006 Paris ,","place":["France"]},{"name":"INSERM , U1138, 15 rue de l'\u00c9cole de M\u00e9decine, 75006 Paris ,","place":["France"]}]},{"given":"Randy","family":"Heiland","sequence":"additional","affiliation":[{"name":"Department of Intelligent Systems Engineering, Indiana University , 700 N Woodlawn Ave, Bloomington, IN 47408 ,","place":["USA"]}]},{"given":"Emmanuel","family":"Barillot","sequence":"additional","affiliation":[{"name":"Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","place":["France"]},{"name":"INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","place":["France"]},{"name":"Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,","place":["France"]}]},{"given":"Paul","family":"Macklin","sequence":"additional","affiliation":[{"name":"Department of Intelligent Systems Engineering, Indiana University , 700 N Woodlawn Ave, Bloomington, IN 47408 ,","place":["USA"]}]},{"given":"Laurence","family":"Calzone","sequence":"additional","affiliation":[{"name":"Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","place":["France"]},{"name":"INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","place":["France"]},{"name":"Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,","place":["France"]}]},{"given":"Vincent","family":"No\u00ebl","sequence":"additional","affiliation":[{"name":"Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","place":["France"]},{"name":"INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","place":["France"]},{"name":"Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,","place":["France"]}]}],"member":"286","published-online":{"date-parts":[[2024,10,18]]},"reference":[{"key":"2024101906432419300_ref1","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1039\/c0ib00075b","article-title":"Multi-scale modelling and 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