Computational Biology, Department of Computer Science, University of Oxford, Oxford, United Kingdom.
PLoS Comput Biol. 2013;9(3):e1002970. doi: 10.1371/journal.pcbi.1002970. Epub 2013 Mar 14.
Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.
Chaste（癌症、心脏和软组织环境）是一个用于计算模拟生理学和生物学数学模型的开源 C++库。该代码的开发源于两个初始应用：心脏电生理学和癌症发展。它已经支持并执行了大量心脏电生理学研究，包括对现实人心腔几何结构的除颤进行高性能计算研究。还开发了用于肿瘤起始和生长的新模型。特别是，基于细胞的模拟为结直肠隐窝中干细胞的作用提供了新的见解。Chaste 不断发展，现在正应用于更广泛的问题。该代码提供了用于处理常见科学计算组件的模块，例如网格和用于常微分方程 (ODE)/偏微分方程 (PDE) 的求解器。这些组件的重复使用避免了研究人员在每个新项目中“重新发明轮子”的需要，从而加快了新应用的进展速度。Chaste 使用工业衍生技术（特别是测试驱动开发）进行开发，以确保代码质量、可重用性和可靠性。在本文中，我们提供了一些示例，说明了 Chaste 可以用于解决的问题类型，这些问题可以在桌面计算机上运行。我们重点介绍了一些使用或正在使用 Chaste 的科学研究，以及它们提供的见解。源代码（特定版本和开发版本）可在 http://www.cs.ox.ac.uk/chaste 以开源伯克利软件分发 (BSD) 许可证下载，其中包括邮件列表的详细信息以及文档和教程的链接。
