Chaste: Cancer, Heart and Soft Tissue Environment.
Chaste: Cancer, Heart and Soft Tissue Environment.
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DOI：
10.21105/joss.01848
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发表时间：
2020-03-13
影响因子：
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通讯作者：
Gavaghan DJ
中科院分区：
文献类型：
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作者：
Cooper FR;Baker RE;Bernabeu MO;Bordas R;Bowler L;Bueno-Orovio A;Byrne HM;Carapella V;Cardone-Noott L;Jonatha C;Dutta S;Evans BD;Fletcher AG;Grogan JA;Guo W;Harvey DG;Hendrix M;Kay D;Kursawe J;Maini PK;McMillan B;Mirams GR;Osborne JM;Pathmanathan P;Pitt-Francis JM;Robinson M;Rodriguez B;Spiteri RJ;Gavaghan DJ
Chaste（癌症、心脏和软组织环境）是一个开源的模拟软件包，用于生理学和生物学中出现的数学模型的数值求解。迄今为止，Chaste的发展主要是由应用程序驱动的，包括心脏电生理学的连续建模（“心脏Chaste”），软组织的离散细胞建模（“基于细胞的Chaste”）和肺部通气建模（“肺Chaste”）。Cardiac Chaste满足了科学界对心脏电生理学的高性能、通用和经验证的模拟框架的需求。Cardiac Chaste提供了一个能够进行真实心脏模拟的软件包，该软件包高效，经过严格测试，并在HPC平台上运行。Cell-based Chaste解决了基于细胞的建模框架的有效和验证实现的需求，为模拟生物组织提供了一套可扩展的工具。计算建模，沿着实时成像技术，在理解组织生长和修复过程中起着重要作用。已经开发了广泛的基于细胞的建模框架，每个框架都成功地应用于一系列生物学应用中。基于细胞的Chaste包括细胞自动机模型，细胞Potts模型，细胞中心模型与细胞表示为重叠的球体或Voronoi镶嵌，和顶点模型的实现。Lung Chaste解决了对经过测试和验证的新型、通用和高效肺部建模软件包的需求。它的目的是将气道力学的生物病理学详细模型与器官规模的通气模型结合在一起，科学界可以免费获得。Chaste被设计为模块化和可扩展的，为常见的科学计算基础设施提供库，如线性代数运算，有限元网格，以及普通和偏微分方程求解器。该基础设施被库用于特定应用，例如连续介质力学、心脏模型和基于细胞的模型。用于开发Chaste的软件工程技术旨在确保代码质量，可重用性和可靠性。该软件的主要应用包括心脏和呼吸生理学，癌症和发育生物学
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