On-lattice agent-based simulation of populations of cells within the open-source Chaste framework
On-lattice agent-based simulation of populations of cells within the open-source Chaste framework
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DOI：
10.1098/rsfs.2012.0081
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发表时间：
2013-04-06
期刊：
影响因子：
4.4
通讯作者：
Owen, Markus R.
中科院分区：
文献类型：
--
作者：
Figueredo, Grazziela P.;Joshi, Tanvi V.;Owen, Markus R.
多年来，基于代理的模型已经开发出，结合联合收割机细胞分裂和加强随机行走的细胞在一个规则的晶格，反应扩散方程的营养物质和生长因子;和常微分方程的亚细胞网络调节细胞周期。当连接到血管层时，这种多尺度模型框架已被应用于肿瘤生长和治疗。在这里，我们报告了一个基于代理的多尺度环境的创建，融合了这些模型的特点，在一个虚拟生理人（VPH）Exemplar项目。该项目实现了模型和相关数据的重用、集成、扩展和共享。多尺度模型的基于试剂的部分和反应扩散部分已经实施，可作为VPH工具包（http：//toolkit.vph-noe.eu/）的一部分，作为最新公开发布的Chaste（癌症、心脏和软组织环境; http：//www.cs.ox.ac.uk/chaste/）的一部分下载。除了对代码的所有方面进行额外验证外，还根据原始模型验证了环境功能。在这项工作中，我们提出了基于代理的环境，包括系统描述，概念模型，仿真模型的开发和过程中的验证和验证的仿真结果的实施细节。我们探索环境的潜在用途，提出了范例应用程序的“如果”的情况下，可以很容易地在环境中进行研究。这些例子涉及肿瘤生长、细胞对资源的竞争和肿瘤对缺氧（低氧水平）的反应。最后，我们总结了扩展当前系统的未来步骤。
Over the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors; and ordinary differential equations for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here, we report on the creation of an agent-based multi-scale environment amalgamating the characteristics of these models within a Virtual Physiological Human (VPH) Exemplar Project. This project enables reuse, integration, expansion and sharing of the model and relevant data. The agent-based and reaction-diffusion parts of the multi-scale model have been implemented and are available for download as part of the latest public release of Chaste (Cancer, Heart and Soft Tissue Environment; http://www.cs.ox.ac.uk/chaste/), part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the 'what if' scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia (low oxygen levels). We conclude our work by summarizing the future steps for the expansion of the current system.