Cargando…

Chaste: Cancer, Heart and Soft Tissue Environment

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 electrophysio...

Descripción completa

Detalles Bibliográficos
Autores principales: Cooper, Fergus R, Baker, Ruth E, Bernabeu, Miguel O, Bordas, Rafel, Bowler, Louise, Bueno-Orovio, Alfonso, Byrne, Helen M, Carapella, Valentina, Cardone-Noott, Louie, Jonatha, Cooper, 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614534/
https://www.ncbi.nlm.nih.gov/pubmed/37192932
http://dx.doi.org/10.21105/joss.01848
_version_ 1783605615773351936
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
Jonatha, Cooper
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
author_facet Cooper, Fergus R
Baker, Ruth E
Bernabeu, Miguel O
Bordas, Rafel
Bowler, Louise
Bueno-Orovio, Alfonso
Byrne, Helen M
Carapella, Valentina
Cardone-Noott, Louie
Jonatha, Cooper
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
author_sort Cooper, Fergus R
collection PubMed
description 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 framework for 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. Chaste is designed to be modular and extensible, providing libraries for common scientific computing infrastructure such as linear algebra operations, finite element meshes, and ordinary and partial differential equation solvers. This infrastructure is used by libraries for specific applications, such as continuum mechanics, cardiac models, and cell-based models. The software engineering techniques used to develop Chaste are intended to ensure code quality, re-usability and reliability. Primary applications of the software include cardiac and respiratory physiology, cancer and developmental biology
format Online
Article
Text
id pubmed-7614534
institution National Center for Biotechnology Information
language English
publishDate 2020
record_format MEDLINE/PubMed
spelling pubmed-76145342023-05-14 Chaste: Cancer, Heart and Soft Tissue Environment Cooper, Fergus R Baker, Ruth E Bernabeu, Miguel O Bordas, Rafel Bowler, Louise Bueno-Orovio, Alfonso Byrne, Helen M Carapella, Valentina Cardone-Noott, Louie Jonatha, Cooper 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 J Open Source Softw Article 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 framework for 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. Chaste is designed to be modular and extensible, providing libraries for common scientific computing infrastructure such as linear algebra operations, finite element meshes, and ordinary and partial differential equation solvers. This infrastructure is used by libraries for specific applications, such as continuum mechanics, cardiac models, and cell-based models. The software engineering techniques used to develop Chaste are intended to ensure code quality, re-usability and reliability. Primary applications of the software include cardiac and respiratory physiology, cancer and developmental biology 2020-03-13 2020-03-13 /pmc/articles/PMC7614534/ /pubmed/37192932 http://dx.doi.org/10.21105/joss.01848 Text en https://creativecommons.org/licenses/by/4.0/Authors of papers retain copyright and release the work under a Creative Commons Attribution 4.0 International License (CC-BY (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Cooper, Fergus R
Baker, Ruth E
Bernabeu, Miguel O
Bordas, Rafel
Bowler, Louise
Bueno-Orovio, Alfonso
Byrne, Helen M
Carapella, Valentina
Cardone-Noott, Louie
Jonatha, Cooper
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
Chaste: Cancer, Heart and Soft Tissue Environment
title Chaste: Cancer, Heart and Soft Tissue Environment
title_full Chaste: Cancer, Heart and Soft Tissue Environment
title_fullStr Chaste: Cancer, Heart and Soft Tissue Environment
title_full_unstemmed Chaste: Cancer, Heart and Soft Tissue Environment
title_short Chaste: Cancer, Heart and Soft Tissue Environment
title_sort chaste: cancer, heart and soft tissue environment
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614534/
https://www.ncbi.nlm.nih.gov/pubmed/37192932
http://dx.doi.org/10.21105/joss.01848
work_keys_str_mv AT cooperfergusr chastecancerheartandsofttissueenvironment
AT bakerruthe chastecancerheartandsofttissueenvironment
AT bernabeumiguelo chastecancerheartandsofttissueenvironment
AT bordasrafel chastecancerheartandsofttissueenvironment
AT bowlerlouise chastecancerheartandsofttissueenvironment
AT buenoorovioalfonso chastecancerheartandsofttissueenvironment
AT byrnehelenm chastecancerheartandsofttissueenvironment
AT carapellavalentina chastecancerheartandsofttissueenvironment
AT cardonenoottlouie chastecancerheartandsofttissueenvironment
AT jonathacooper chastecancerheartandsofttissueenvironment
AT duttasara chastecancerheartandsofttissueenvironment
AT evansbenjamind chastecancerheartandsofttissueenvironment
AT fletcheralexanderg chastecancerheartandsofttissueenvironment
AT groganjamesa chastecancerheartandsofttissueenvironment
AT guowenxian chastecancerheartandsofttissueenvironment
AT harveydanielg chastecancerheartandsofttissueenvironment
AT hendrixmaurice chastecancerheartandsofttissueenvironment
AT kaydavid chastecancerheartandsofttissueenvironment
AT kursawejochen chastecancerheartandsofttissueenvironment
AT mainiphilipk chastecancerheartandsofttissueenvironment
AT mcmillanbeth chastecancerheartandsofttissueenvironment
AT miramsgaryr chastecancerheartandsofttissueenvironment
AT osbornejamesm chastecancerheartandsofttissueenvironment
AT pathmanathanpras chastecancerheartandsofttissueenvironment
AT pittfrancisjoem chastecancerheartandsofttissueenvironment
AT robinsonmartin chastecancerheartandsofttissueenvironment
AT rodriguezblanca chastecancerheartandsofttissueenvironment
AT spiteriraymondj chastecancerheartandsofttissueenvironment
AT gavaghandavidj chastecancerheartandsofttissueenvironment