Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes
Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes
复制标题
具有相变基因的细菌菌落的时空建模与分析
DOI：
10.1145/2742546
复制
发表时间：
2015-05-01
影响因子：
0.9
通讯作者：
Shaw, Simon
中科院分区：
文献类型：
--
作者：
Parvu, Ovidiu;Gilbert, David;Shaw, Simon
本文定义了一种新的时空建模和分析方法，应用于系统生物学的案例研究，即细菌菌落生长的相位变化模式。我们采用有色随机Petri网来构建模型，并运行随机模拟来记录圆形殖民地随时间和空间的发展。仿真输出以2D形式可视化，扇形图案可自动检测和分析。考虑到矩形和圆形几何形状，空间使用2.5维建模，并测量了对空间施加不同几何形状的影响。最后，我们概述了解释的Petri网模型的有限差分近似偏微分方程（PDE）。结果之一是推导出“最佳”九点扩散模型。我们的多维建模和分析方法是未来可能进行更复杂的多尺度建模工作的先驱。
This article defines a novel spatial-temporal modelling and analysis methodology applied to a systems biology case study, namely phase variation patterning in bacterial colony growth. We employ coloured stochastic Petri nets to construct the model and run stochastic simulations to record the development of the circular colonies over time and space. The simulation output is visualised in 2D, and sector-like patterns are automatically detected and analysed. Space is modelled using 2.5 dimensions considering both a rectangular and circular geometry, and the effects of imposing different geometries on space are measured. We close by outlining an interpretation of the Petri net model in terms of finite difference approximations of partial differential equations (PDEs). One result is the derivation of the “best” nine-point diffusion model. Our multidimensional modelling and analysis approach is a precursor to potential future work on more complex multiscale modelling.