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

ABSTRACT: MOTIVATION: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). RESULTS: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. AVAILABILITY AND IMPLEMENTATION: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. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Letort G

PROVIDER: S-EPMC6449758 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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

Letort Gaelle G Montagud Arnau A Stoll Gautier G Heiland Randy R Barillot Emmanuel E Macklin Paul P Zinovyev Andrei A Calzone Laurence L

Bioinformatics (Oxford, England) 20190401 7

<h4>Motivation</h4>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).<h4>Results</h4>PhysiBoSS provides a flexible and computationally effic ...[more]

PMID: 30169736

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Project description:IntroductionSystems modelling and simulation can improve understanding of complex systems to support decision making, better managing system challenges. Advances in technology have facilitated accessibility of modelling by diverse stakeholders, allowing them to engage with and contribute to the development of systems models (participatory modelling). However, despite its increasing applications across a range of disciplines, there is a growing need to improve evaluation efforts to effectively report on the quality, importance, and value of participatory modelling. This paper aims to identify and assess evaluation frameworks, criteria, and/or processes, as well as to synthesize the findings into a comprehensive multi-scale framework for participatory modelling programs.Materials and methodsA scoping review approach was utilized, which involved a systematic literature search via Scopus in consultation with experts to identify and appraise records that described an evaluation framework, criteria, and/or process in the context of participatory modelling. This scoping review is registered with the Open Science Framework.ResultsThe review identified 11 studies, which varied in evaluation purposes, terminologies, levels of examination, and time points. The review of studies highlighted areas of overlap and opportunities for further development, which prompted the development of a comprehensive multi-scale evaluation framework to assess participatory modelling programs across disciplines and systems modelling methods. The framework consists of four categories (Feasibility, Value, Change/Action, Sustainability) with 30 evaluation criteria, broken down across project-, individual-, group- and system-level impacts.Discussion & conclusionThe presented novel framework brings together a significant knowledge base into a flexible, cross-sectoral evaluation effort that considers the whole participatory modelling process. Developed through the rigorous synthesis of multidisciplinary expertise from existing studies, the application of the framework can provide the opportunity to understand practical future implications such as which aspects are particularly important for policy decisions, community learning, and the ongoing improvement of participatory modelling methods.

Dataset Information

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

Publications

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

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