Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Valencia, Spain.
Centro Universitario EDEM, Escuela de Empresarios, La Marina de València, Valencia, Spain.
Methods Mol Biol. 2021;2229:41-90. doi: 10.1007/978-1-0716-1032-9_2.
The Chemical Langevin Equation approach allows simple stochastic simulation of gene circuits under many practical situations where the number of molecules of the species involved is not extremely low. Here, we describe methods and a computational framework to simulate a population of cells containing gene circuits of interest. These methods account for both intrinsic and extrinsic noise sources, and allow us to have both individual cell-related species and population-related ones. The protocol covers aspects related to proper description of the system and setting the software tools. It also helps to deal with the optimization of data storage and the simulation precision versus computational time issue. Finally, it also gives practical tests to assess the validity of the underlying technical assumptions.
化学朗之万方程方法允许在涉及的物种分子数量不是极低的许多实际情况下，对基因电路进行简单的随机模拟。在这里，我们描述了一种模拟含有感兴趣基因电路的细胞群体的方法和计算框架。这些方法考虑了内在和外在的噪声源，并允许我们同时具有与单个细胞相关的物种和与种群相关的物种。该方案涵盖了与系统的正确描述和设置软件工具相关的方面。它还有助于处理数据存储的优化以及模拟精度与计算时间之间的问题。最后，它还提供了实际测试来评估基础技术假设的有效性。
