BSim 2.0: An Advanced Agent-Based Cell Simulator
BSim 2.0: An Advanced Agent-Based Cell Simulator
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DOI：
10.1021/acssynbio.7b00121
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发表时间：
2017-10-01
影响因子：
4.7
通讯作者：
di Bernardo, Mario
中科院分区：
文献类型：
--
作者：
Matyjaszkiewicz, Antoni;Fiore, Gianfranco;di Bernardo, Mario
与传统的连续体建模方法相比，基于智能体的模型（ABMs）提供了许多优势，允许将大量细节和真实感结合到模拟中，允许在宏观层面上对单细胞行为进行计算机跟踪，并将这些行为与突发效应联系起来。在这项研究中，我们提出了BSim 2.0，一个全新版本的BSim，一个计算ABM框架，用于模拟细菌在典型实验环境中的动力学，包括微流控化学调节器。这是通过新方法的实施，包括能够物理和化学相互作用的细胞荚膜几何，细胞生长的现实模型，延迟微分方程求解器和现实的环境几何来促进的。
Agent-based models (ABMs) provide a number of advantages relative to traditional continuum modeling approaches, permitting incorporation of great detail and realism into simulations, allowing in silico tracking of single-cell behaviors and correlation of these with emergent effects at the macroscopic level. In this study we, present BSim 2.0, a radically new version of BSim, a computational ABM framework for modeling dynamics of bacteria in typical experimental environments including microfluidic chemostats. This is facilitated through the implementation of new methods including cells capsular geometry that are able to physically and chemically interact with one another, a realistic model of cellular growth, a delay differential-equation solver, and realistic environmental geometries.