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Integrating intracellular dynamics using CompuCell3D and bionetsolver

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Integrating intracellular dynamics using CompuCell3D and bionetsolver : Applications to multiscale modelling of cancer cell growth and invasion. / Andasari, Vivi; Roper, R.T.; Swat, M.H.; Chaplain, Mark A.J.

In: PLoS ONE, Vol. 7, No. 3, e33726, 26.03.2012.

Research output: Contribution to journalArticle

Harvard

Andasari, V, Roper, RT, Swat, MH & Chaplain, MAJ 2012, 'Integrating intracellular dynamics using CompuCell3D and bionetsolver: Applications to multiscale modelling of cancer cell growth and invasion' PLoS ONE, vol 7, no. 3, e33726., 10.1371/journal.pone.0033726

APA

Andasari, V., Roper, R. T., Swat, M. H., & Chaplain, M. A. J. (2012). Integrating intracellular dynamics using CompuCell3D and bionetsolver: Applications to multiscale modelling of cancer cell growth and invasion. PLoS ONE, 7(3), [e33726]. 10.1371/journal.pone.0033726

Vancouver

Andasari V, Roper RT, Swat MH, Chaplain MAJ. Integrating intracellular dynamics using CompuCell3D and bionetsolver: Applications to multiscale modelling of cancer cell growth and invasion. PLoS ONE. 2012 Mar 26;7(3). e33726. Available from: 10.1371/journal.pone.0033726

Author

Andasari, Vivi; Roper, R.T.; Swat, M.H.; Chaplain, Mark A.J. / Integrating intracellular dynamics using CompuCell3D and bionetsolver : Applications to multiscale modelling of cancer cell growth and invasion.

In: PLoS ONE, Vol. 7, No. 3, e33726, 26.03.2012.

Research output: Contribution to journalArticle

Bibtex - Download

@article{ba04dac10374451ba141e6db8b2f220d,
title = "Integrating intracellular dynamics using CompuCell3D and bionetsolver: Applications to multiscale modelling of cancer cell growth and invasion",
author = "Vivi Andasari and R.T. Roper and M.H. Swat and Chaplain, {Mark A.J.}",
year = "2012",
doi = "10.1371/journal.pone.0033726",
volume = "7",
number = "3",
journal = "PLoS ONE",
issn = "1932-6203",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Integrating intracellular dynamics using CompuCell3D and bionetsolver

T2 - Applications to multiscale modelling of cancer cell growth and invasion

A1 - Andasari,Vivi

A1 - Roper,R.T.

A1 - Swat,M.H.

A1 - Chaplain,Mark A.J.

AU - Andasari,Vivi

AU - Roper,R.T.

AU - Swat,M.H.

AU - Chaplain,Mark A.J.

PY - 2012/3/26

Y1 - 2012/3/26

N2 - In this paper we present a multiscale, individual-based simulation environment that integrates CompuCell3D for lattice-based modelling on the cellular level and Bionetsolver for intracellular modelling. CompuCell3D or CC3D provides an implementation of the lattice-based Cellular Potts Model or CPM (also known as the Glazier-Graner-Hogeweg or GGH model) and a Monte Carlo method based on the metropolis algorithm for system evolution. The integration of CC3D for cellular systems with Bionetsolver for subcellular systems enables us to develop a multiscale mathematical model and to study the evolution of cell behaviour due to the dynamics inside of the cells, capturing aspects of cell behaviour and interaction that is not possible using continuum approaches. We then apply this multiscale modelling technique to a model of cancer growth and invasion, based on a previously published model of Ramis-Conde etal. (2008) where individual cell behaviour is driven by a molecular network describing the dynamics of E-cadherin and ß-catenin. In this model, which we refer to as the centre-based model, an alternative individual-based modelling technique was used, namely, a lattice-free approach. In many respects, the GGH or CPM methodology and the approach of the centre-based model have the same overall goal, that is to mimic behaviours and interactions of biological cells. Although the mathematical foundations and computational implementations of the two approaches are very different, the results of the presented simulations are compatible with each other, suggesting that by using individual-based approaches we can formulate a natural way of describing complex multi-cell, multiscale models. The ability to easily reproduce results of one modelling approach using an alternative approach is also essential from a model cross-validation standpoint and also helps to identify any modelling artefacts specific to a given computational approach. © 2012 Andasari et al.

AB - In this paper we present a multiscale, individual-based simulation environment that integrates CompuCell3D for lattice-based modelling on the cellular level and Bionetsolver for intracellular modelling. CompuCell3D or CC3D provides an implementation of the lattice-based Cellular Potts Model or CPM (also known as the Glazier-Graner-Hogeweg or GGH model) and a Monte Carlo method based on the metropolis algorithm for system evolution. The integration of CC3D for cellular systems with Bionetsolver for subcellular systems enables us to develop a multiscale mathematical model and to study the evolution of cell behaviour due to the dynamics inside of the cells, capturing aspects of cell behaviour and interaction that is not possible using continuum approaches. We then apply this multiscale modelling technique to a model of cancer growth and invasion, based on a previously published model of Ramis-Conde etal. (2008) where individual cell behaviour is driven by a molecular network describing the dynamics of E-cadherin and ß-catenin. In this model, which we refer to as the centre-based model, an alternative individual-based modelling technique was used, namely, a lattice-free approach. In many respects, the GGH or CPM methodology and the approach of the centre-based model have the same overall goal, that is to mimic behaviours and interactions of biological cells. Although the mathematical foundations and computational implementations of the two approaches are very different, the results of the presented simulations are compatible with each other, suggesting that by using individual-based approaches we can formulate a natural way of describing complex multi-cell, multiscale models. The ability to easily reproduce results of one modelling approach using an alternative approach is also essential from a model cross-validation standpoint and also helps to identify any modelling artefacts specific to a given computational approach. © 2012 Andasari et al.

UR - http://www.scopus.com/inward/record.url?scp=84858853541&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0033726

DO - 10.1371/journal.pone.0033726

M1 - Article

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 3

VL - 7

ER -

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