Chaste: A test-driven approach to software development for biological modelling
Chaste: A test-driven approach to software development for biological modelling
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DOI：
10.1016/j.cpc.2009.07.019
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发表时间：
2009-12-01
影响因子：
6.3
通讯作者：
Gavaghan, David J.
中科院分区：
文献类型：
--
作者：
Pitt-Francis, Joe;Pathmanathan, Pras;Gavaghan, David J.
ESTEE(癌症、心脏和软组织环境)是一个软件库和一套测试套件，用于生物学领域的计算模拟。目前的功能来自癌症、心脏生理学和软组织力学领域的建模。它是在LGPL2.1许可下发布的。Chaste是使用敏捷编程方法开发的。该项目始于2005年，当时的理由是，各种生理现象的建模既需要通用的数学建模框架，也需要通用的计算/模拟框架。CHESTE项目由综合生物学(IB)e-Science项目演变而来，该项目是一个跨机构项目，旨在开发合适的IT基础设施来支持生理组级计算建模，主要关注心脏和癌症建模。项目摘要项目标题：ChasteCatalogue IDENTIFIER。AEFD_v1_0计划摘要URL：http://cpc.cs.qub.ac.uk/summaries/AEFD-v1-0.htmlProgram可从：爱尔兰贝尔法斯特女王大学CPC计划图书馆获得。许可条款：LGPL 2.1号。分布式程序中线路数，包括测试数据等：5 407 321号分布式程序中的字节数，包括测试数据等：42 004 554分布格式：tar.gz编程语言：C++操作系统：unix代码是否已矢量化或并行化？：是的。使用MPI.RAM：<；90MB并行化，用于手稿第6节中描述的两个场景(平板上的单域重入或圆柱形地穴模拟)。分类：3.外部例程：Boost、CodeSynthel XSD、CxxTest、HDF5、METIS、MPI、PETSc、Triangle、Xerces问题的本质：CHESTE可用于解决由模拟生物系统引起的耦合的ODE和PDE系统。介绍了CHESTE在心脏电生理学和肠道隐窝动力学两个应用领域的应用。解决方法：将多物理与偏微分方程、常微分方程组和离散力学模拟相结合。运行时间：手稿中描述的最大心脏模拟在单个3 GHz内核上运行约6小时。有关平行缩放的讨论，请参阅手稿的结果部分(第6部分)。(C)2009爱思唯尔B.V.保留所有权利。
Chaste ('Cancer, heart and soft-tissue environment') is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a Suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling.Program summaryProgram title: ChasteCatalogue identifier. AEFD_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFD-v1-0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: LGPL 2.1No. of lines in distributed program, including test data, etc.: 5 407 321No. of bytes in distributed program, including test data, etc.: 42 004 554Distribution format: tar.gzProgramming language: C++Operating system: UnixHas the code been vectorised or paralielized?: Yes. Parallelized using MPI.RAM: < 90 Megabytes for two of the scenarios described in Section 6 of the manuscript (Monodomain re-entry on a slab or Cylindrical crypt simulation). Up to 16 Gigabytes (distributed across processors) for full resolution bidomain cardiac simulation.Classification: 3.External routines: Boost, CodeSynthesis XSD, CxxTest, HDF5, METIS, MPI, PETSc, Triangle, XercesNature of problem: Chaste may be used for solving coupled ODE and PDE systems arising from modelling biological systems. Use of Chaste in two application areas are described in this paper: cardiac electrophysiology and intestinal crypt dynamics.Solution method: Coupled multi-physics with PDE, ODE and discrete mechanics simulation.Running time: The largest cardiac simulation described in the manuscript takes about 6 hours to run on a single 3 GHz core. See results section (Section 6) of the manuscript for discussion on parallel scaling. (C) 2009 Elsevier B.V. All rights reserved.