Swat Maciej H, Thomas Gilberto L, Belmonte Julio M, Shirinifard Abbas, Hmeljak Dimitrij, Glazier James A
Department of Physics, Biocomplexity Institute, Indiana University, Bloomington, Indiana, USA.
Methods Cell Biol. 2012;110:325-66. doi: 10.1016/B978-0-12-388403-9.00013-8.
The study of how cells interact to produce tissue development, homeostasis, or diseases was, until recently, almost purely experimental. Now, multi-cell computer simulation methods, ranging from relatively simple cellular automata to complex immersed-boundary and finite-element mechanistic models, allow in silico study of multi-cell phenomena at the tissue scale based on biologically observed cell behaviors and interactions such as movement, adhesion, growth, death, mitosis, secretion of chemicals, chemotaxis, etc. This tutorial introduces the lattice-based Glazier-Graner-Hogeweg (GGH) Monte Carlo multi-cell modeling and the open-source GGH-based CompuCell3D simulation environment that allows rapid and intuitive modeling and simulation of cellular and multi-cellular behaviors in the context of tissue formation and subsequent dynamics. We also present a walkthrough of four biological models and their associated simulations that demonstrate the capabilities of the GGH and CompuCell3D.
直到最近，关于细胞如何相互作用以产生组织发育、体内平衡或疾病的研究几乎完全是实验性的。现在，从相对简单的细胞自动机到复杂的浸入边界和有限元机制模型等多细胞计算机模拟方法，使得基于生物学观察到的细胞行为和相互作用（如运动、黏附、生长、死亡、有丝分裂、化学物质分泌、趋化性等），在计算机上对组织尺度的多细胞现象进行研究成为可能。本教程介绍基于格点的格拉齐尔 - 格拉纳 - 霍赫韦格（GGH）蒙特卡洛多细胞建模以及基于GGH的开源CompuCell3D模拟环境，该环境允许在组织形成及后续动态变化的背景下，快速直观地对细胞和多细胞行为进行建模与模拟。我们还展示了四个生物学模型及其相关模拟的演练过程，这些演练展示了GGH和CompuCell3D的功能。
