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Chaste : Cancer, Heart and Soft Tissue Environment

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Cooper_2020_Chaste_JOSS_1848_CC.pdf (1.638Mb)
Date
13/03/2020
Author
Cooper, Fergus R.
Baker, Ruth E.
Bernabeu, Miguel O.
Bordas, Rafel
Bowler, Louise
Bueno-Orovio, Alfonso
Byrne, Helen M.
Carapella, Valentina
Cardone-Noott, Louie
Cooper, Jonathan
Dutta, Sara
Evans, Benjamin D.
Fletcher, Alexander G.
Grogan, James A.
Guo, Wenxian
Harvey, Daniel G.
Hendrix, Maurice
Kay, David
Kursawe, Jochen
Maini, Philip K.
McMillan, Beth
Mirams, Gary R.
Osborne, James M.
Pathmanathan, Pras
Pitt-Francis, Joe M.
Robinson, Martin
Rodriguez, Blanca
Spiteri, Raymond J.
Gavaghan, David J.
Keywords
QA75 Electronic computers. Computer science
QH301 Biology
QP Physiology
DAS
Metadata
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Abstract
Chaste (Cancer, Heart And Soft Tissue Environment) is an open source simulation package for the numerical solution of mathematical models arising in physiology and biology. To date, Chaste development has been driven primarily by applications that include continuum modelling of cardiac electrophysiology (‘Cardiac Chaste’), discrete cell-based modelling of soft tissues (‘Cell-based Chaste’), and modelling of ventilation in lungs (‘Lung Chaste’). Cardiac Chaste addresses the need for a high-performance, generic, and verified simulation framewor kfor cardiac electrophysiology that is freely available to the scientific community. Cardiac chaste provides a software package capable of realistic heart simulations that is efficient, rigorously tested, and runs on HPC platforms. Cell-based Chaste addresses the need for efficient and verified implementations of cell-based modelling frameworks, providing a set of extensible tools for simulating biological tissues. Computational modelling, along with live imaging techniques, plays an important role in understanding the processes of tissue growth and repair. A wide range of cell-based modelling frameworks have been developed that have each been successfully applied in a range of biological applications. Cell-based Chaste includes implementations of the cellular automaton model, the cellular Potts model, cell-centre models with cell representations as overlapping spheres or Voronoi tessellations, and the vertex model. Lung Chaste addresses the need for a novel, generic and efficient lung modelling software package that is both tested and verified. It aims to couple biophysically-detailed models of airway mechanics with organ-scale ventilation models in a package that is freely available to the scientific community.
Citation
Cooper , F R , Baker , R E , Bernabeu , M O , Bordas , R , Bowler , L , Bueno-Orovio , A , Byrne , H M , Carapella , V , Cardone-Noott , L , Cooper , J , Dutta , S , Evans , B D , Fletcher , A G , Grogan , J A , Guo , W , Harvey , D G , Hendrix , M , Kay , D , Kursawe , J , Maini , P K , McMillan , B , Mirams , G R , Osborne , J M , Pathmanathan , P , Pitt-Francis , J M , Robinson , M , Rodriguez , B , Spiteri , R J & Gavaghan , D J 2020 , ' Chaste : Cancer, Heart and Soft Tissue Environment ' , Journal of Open Source Software , vol. 5 , no. 47 , pp. 1848 . https://doi.org/10.21105/joss.01848
Publication
Journal of Open Source Software
Status
Peer reviewed
DOI
https://doi.org/10.21105/joss.01848
ISSN
2475-9066
Type
Journal article
Rights
Copyright © 2020 the Author(s). Authors of papers retain copyright and release the work under a Creative Commons Attribution 4.0 International License (CC-BY).
Description
Funding: UK Engineering and Physical Sciences Research Council [grant number EP/N509711/1 (J.K.)].
Collections
  • University of St Andrews Research
URL
https://joss.theoj.org/papers/10.21105/joss.01848
URI
http://hdl.handle.net/10023/20238

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