PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling

Bioinformatics
Gaelle LetortLaurence Calzone

Abstract

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). 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...Continue Reading

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Citations

Jan 18, 2020·The Journal of Cell Biology·Alexandra ColinMarie-Hélène Verlhac
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Feb 11, 2021·PLoS Computational Biology·Juan Jiménez-SánchezVíctor M Pérez-García
Nov 20, 2020·Physical Biology·Nicola Mulberry, Leah Edelstein-Keshet
Jun 3, 2021·International Journal of Molecular Sciences·Gianluca SelvaggioFlorence Janody
Nov 30, 2021·PLoS Computational Biology·Ernesto A B F LimaThomas E Yankeelov
Dec 11, 2021·Microcirculation : the Official Journal of the Microcirculatory Society, Inc·Min Song, Stacey D Finley

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Software Mentioned

PhysiCell
OpenMP
VirtualLeaf
GitHub
BioFVM
CellSys
Chaste
MaBoSS
_ CreateInitTxtFile
MecaGen

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