{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T22:27:45Z","timestamp":1780439265479,"version":"3.54.1"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2018,8,30]],"date-time":"2018-08-30T00:00:00Z","timestamp":1535587200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union Horizon 2020 research and innovation program","award":["668858, PrECISE project"],"award-info":[{"award-number":["668858, PrECISE project"]}]},{"name":"Chemotaxis project"},{"name":"INVADE"},{"name":"ITMO Cancer"},{"DOI":"10.13039\/100001006","name":"Breast Cancer Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001006","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016460","name":"Jayne Koskinas Ted Giovanis Foundation for Health and Policy","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100016460","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Due to the complexity and heterogeneity of multicellular biological systems, mathematical models that take into account cell signalling, cell population behaviour and the extracellular environment are particularly helpful. We present PhysiBoSS, an open source software which combines intracellular signalling using Boolean modelling (MaBoSS) and multicellular behaviour using agent-based modelling (PhysiCell).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>PhysiBoSS provides a flexible and computationally efficient framework to explore the effect of environmental and genetic alterations of individual cells at the population level, bridging the critical gap from single-cell genotype to single-cell phenotype and emergent multicellular behaviour. PhysiBoSS thus becomes very useful when studying heterogeneous population response to treatment, mutation effects, different modes of invasion or isomorphic morphogenesis events. To concretely illustrate a potential use of PhysiBoSS, we studied heterogeneous cell fate decisions in response to TNF treatment. We explored the effect of different treatments and the behaviour of several resistant mutants. We highlighted the importance of spatial information on the population dynamics by considering the effect of competition for resources like oxygen.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PhysiBoSS is freely available on GitHub (https:\/\/github.com\/sysbio-curie\/PhysiBoSS), with a Docker image (https:\/\/hub.docker.com\/r\/gletort\/physiboss\/). It is distributed as open source under the BSD 3-clause license.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty766","type":"journal-article","created":{"date-parts":[[2018,8,30]],"date-time":"2018-08-30T01:23:28Z","timestamp":1535592208000},"page":"1188-1196","source":"Crossref","is-referenced-by-count":117,"title":["PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5866-0322","authenticated-orcid":false,"given":"Gaelle","family":"Letort","sequence":"first","affiliation":[{"name":"Institut Curie, PSL Research University, Paris, France"},{"name":"INSERM, U900, Paris, France"},{"name":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7696-1241","authenticated-orcid":false,"given":"Arnau","family":"Montagud","sequence":"additional","affiliation":[{"name":"Institut Curie, PSL Research University, Paris, France"},{"name":"INSERM, U900, Paris, France"},{"name":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gautier","family":"Stoll","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Descartes\/Paris V, Sorbonne Paris Cit\u00e9, Paris, France"},{"name":"Gustave Roussy Cancer Campus, Villejuif, France"},{"name":"INSERM, U1138, Paris, France"},{"name":"Equipe 11 Labellis\u00e9e par la Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Randy","family":"Heiland","sequence":"additional","affiliation":[{"name":"Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel","family":"Barillot","sequence":"additional","affiliation":[{"name":"Institut Curie, PSL Research University, Paris, France"},{"name":"INSERM, U900, Paris, France"},{"name":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Macklin","sequence":"additional","affiliation":[{"name":"Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrei","family":"Zinovyev","sequence":"additional","affiliation":[{"name":"Institut Curie, PSL Research University, Paris, France"},{"name":"INSERM, U900, Paris, France"},{"name":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurence","family":"Calzone","sequence":"additional","affiliation":[{"name":"Institut Curie, PSL Research University, Paris, France"},{"name":"INSERM, U900, Paris, France"},{"name":"CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,8,30]]},"reference":[{"key":"2023013107273597700_bty766-B1","doi-asserted-by":"crossref","first-page":"E1617","DOI":"10.1073\/pnas.1617037114","article-title":"Modeling the two-way feedback between contractility and matrix realignment reveals a nonlinear mode of cancer cell invasion","volume":"114","author":"Ahmadzadeh","year":"2017","journal-title":"Proc. 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