RT Journal Article
SR Electronic
T1 PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.01.06.468363
DO 10.1101/2022.01.06.468363
A1 Miguel Ponce-de-Leon
A1 Arnau Montagud
A1 Vincent Noël
A1 Gerard Pradas
A1 Annika Meert
A1 Emmanuel Barillot
A1 Laurence Calzone
A1 Alfonso Valencia
YR 2022
UL http://biorxiv.org/content/early/2022/01/06/2022.01.06.468363.abstract
AB Motivation Cancer progression is a complex phenomenon that spans multiple scales from molecular to cellular and intercellular. Simulations can be used to perturb the underlying mechanisms of those systems and to generate hypotheses on novel therapies. We present a new version of PhysiBoSS, a multiscale modelling framework designed to cover multiple temporal and spatial scales, that improves its integration with PhysiCell, decoupling the cell agent simulations with the internal Boolean model in an easy-to-maintain computational framework.Results PhysiBoSS 2.0 is a redesign and reimplementation of PhysiBoSS, conceived as an add-on that expands the PhysiCell agent-based functionalities with intracellular cell signalling using MaBoSS having a decoupled, maintainable and model-agnostic design. PhysiBoSS 2.0 successfully reproduces simulations reported in the former PhysiBoSS and expands its functionalities such as using user-defined models and cells’ specifications, having mechanistic submodels of substrate internalisation with ODEs and enabling the study of drug synergies.Availability and implementation PhysiBoSS 2.0 is open-source and publicly available on GitHub (https://github.com/PhysiBoSS/PhysiBoSS) under the BSD 3-clause license. Additionally, a nanoHUB tool has been set up to ease the use of PhysiBoSS 2.0 (https://nanohub.org/tools/pba4tnf/).Contact alfonso.valencia{at}bsc.esSupplementary information Supplementary Information, figures, and tables are available at Bioinformatics online.Competing Interest StatementThe authors have declared no competing interest.