Microvessel Chaste: An Open Library for Spatial Modeling of Vascularized Tissues
Microvessel Chaste: An Open Library for Spatial Modeling of Vascularized Tissues
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DOI：
10.1016/j.bpj.2017.03.036
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发表时间：
2017-05-09
影响因子：
3.4
通讯作者：
Pitt-Francis, Joe M.
中科院分区：
文献类型：
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作者：
Grogan, James A.;Connor, Anthony J.;Pitt-Francis, Joe M.
血管化组织的空间模型在计算生理学中有着广泛的应用。我们介绍了一个软件库组成的多尺度，多物理模型的应用，包括肿瘤生长，血管生成，成骨，冠状动脉灌注，氧气输送。这种模型的组合是耗时的，许多研究人员编写定制软件。成像的最新进展已经产生了单个细胞尺度的血管化组织的详细三维（3D）数据集。为了充分利用这些数据，越来越需要一种软件，允许用户友好的组成有效的，血管化组织的3D模型，并比较预测与体内或体外实验和替代计算公式。Microvessel Chaste可用于模拟血管生长和适应机械和化学刺激;营养物质，生长因子和药物的血管内和血管外运输;以及复杂3D几何形状中的细胞增殖。此外，它还可用于开发自定义软件，将建模与实验数据处理工作流程集成，并通过C++实现的求解器的全面Python接口提供便利。本文链接到两个可重复的示例问题，展示了如何使用库来构建具有真实血管网络的肿瘤生长和血管生成模拟。
Spatial models of vascularized tissues are widely used in computational physiology. We introduce a software library for composing multiscale, multiphysics models for applications including tumor growth, angiogenesis, osteogenesis, coronary perfusion, and oxygen delivery. Composition of such models is time consuming, with many researchers writing custom software. Recent advances in imaging have produced detailed three-dimensional (3D) datasets of vascularized tissues at the scale of individual cells. To fully exploit such data there is an increasing need for software that allows user-friendly composition of efficient, 3D models of vascularized tissues, and comparison of predictions with in vivo or in vitro experiments and alternative computational formulations. Microvessel Chaste can be used to build simulations of vessel growth and adaptation in response to mechanical and chemical stimuli; intra- and extravascular transport of nutrients, growth factors and drugs; and cell proliferation in complex 3D geometries. In addition, it can be used to develop custom software for integrating modeling with experimental data processing workflows, facilitated by a comprehensive Python interface to solvers implemented in C++. This article links to two reproducible example problems, showing how the library can be used to build simulations of tumor growth and angiogenesis with realistic vessel networks.