Using CellML with OpenCMISS to Simulate Multi-Scale Physiology.
Using CellML with OpenCMISS to Simulate Multi-Scale Physiology.
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DOI：
10.3389/fbioe.2014.00079
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发表时间：
2014
影响因子：
5.7
通讯作者：
Bradley CP
中科院分区：
文献类型：
--
作者：
Nickerson DP;Ladd D;Hussan JR;Safaei S;Suresh V;Hunter PJ;Bradley CP
OpenCMISS是一个开源的建模环境，特别针对生物工程问题的解决方案。OpenCMISS由两个主要部分组成：一个计算库（OpenCMISS- iron）和一个字段操作和可视化库（OpenCMISS- zinc）。OpenCMISS是为解决通用并行环境下的多尺度、多物理场耦合问题而设计的。CellML是一种XML格式，设计用于编码基于生物物理的常微分方程系统以及线性和非线性代数方程。CellML的主要设计目标是允许数学模型以模块化和可重用的格式进行编码，以帮助建模研究的再现性和互操作性。在OpenCMISS中，我们利用CellML模型使用户能够配置其多尺度生理模型的各个方面。这避免了用户为了执行定制的计算实验而熟悉OpenCMISS内部代码的需要。这方面的例子有：嵌入在组织电传播模型中的细胞电生理模型；力学生长和变形模拟的材料本构关系各种问题域的时变边界条件；流体本构关系和集总参数模型。在本文中，我们提供了实现细节，描述了如何将CellML模型集成到OpenCMISS中的多尺度生理模型中。还描述了OpenCMISS为用户提供的外部接口，包括具体的例子，说明了这些工具为生理建模和仿真社区提供的可扩展性和可用性。最后，我们对OpenCMISS的未来扩展提出了一些想法，以利用其他社区开发的信息标准，如FieldML、SED-ML和BioSignalML。还讨论了从CellML模型生成的加速器代码（图形处理单元和现场可编程门阵列）的集成计划。
OpenCMISS is an open-source modeling environment aimed, in particular, at the solution of bioengineering problems. OpenCMISS consists of two main parts: a computational library (OpenCMISS-Iron) and a field manipulation and visualization library (OpenCMISS-Zinc). OpenCMISS is designed for the solution of coupled multi-scale, multi-physics problems in a general-purpose parallel environment. CellML is an XML format designed to encode biophysically based systems of ordinary differential equations and both linear and non-linear algebraic equations. A primary design goal of CellML is to allow mathematical models to be encoded in a modular and reusable format to aid reproducibility and interoperability of modeling studies. In OpenCMISS, we make use of CellML models to enable users to configure various aspects of their multi-scale physiological models. This avoids the need for users to be familiar with the OpenCMISS internal code in order to perform customized computational experiments. Examples of this are: cellular electrophysiology models embedded in tissue electrical propagation models; material constitutive relationships for mechanical growth and deformation simulations; time-varying boundary conditions for various problem domains; and fluid constitutive relationships and lumped-parameter models. In this paper, we provide implementation details describing how CellML models are integrated into multi-scale physiological models in OpenCMISS. The external interface OpenCMISS presents to users is also described, including specific examples exemplifying the extensibility and usability these tools provide the physiological modeling and simulation community. We conclude with some thoughts on future extension of OpenCMISS to make use of other community developed information standards, such as FieldML, SED-ML, and BioSignalML. Plans for the integration of accelerator code (graphical processing unit and field programmable gate array) generated from CellML models is also discussed.
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DOI：
10.1098/rsta.2008.0310
发表时间：
2009-05-28
影响因子：
5
作者：
Beard, Daniel A.;Britten, Randall;Yu, Tommy
通讯作者：
Yu, Tommy
影响因子：
1.3
作者：
Nickerson, D.;Nash, M.;Hunter, P.
通讯作者：
Hunter, P.
DOI：
10.1177/0037549703040939
发表时间：
2003-12-01
影响因子：
1.6
作者：
Cuellar, AA;Lloyd, CM;Hunter, PJ
通讯作者：
Hunter, PJ
DOI：
10.1098/rsta.2009.0025
发表时间：
2009-05-28
期刊：
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
影响因子：
--
作者：
Christie GR;Nielsen PM;Blackett SA;Bradley CP;Hunter PJ
通讯作者：
Hunter PJ
影响因子：
3
作者：
Miller, Andrew K.;Marsh, Justin;Nielsen, Poul F.
通讯作者：
Nielsen, Poul F.