Chaste : Cancer, Heart and Soft Tissue Environment
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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.
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
Journal of Open Source Software
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DescriptionFunding: UK Engineering and Physical Sciences Research Council [grant number EP/N509711/1 (J.K.)].
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