Kierzek Andrzej M
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland.
Bioinformatics. 2002 Mar;18(3):470-81. doi: 10.1093/bioinformatics/18.3.470.
The availability of a huge amount of molecular data concerning various biochemical reactions provoked numerous attempts to study the dynamics of cellular processes by means of kinetic models and computer simulations. Biochemical processes frequently involve small numbers of molecules (e.g. a few molecules of a transcriptional regulator binding to one 'molecule' of a DNA regulatory region). Such reactions are subject to significant stochastic fluctuations. Monte Carlo methods must be employed to study the functional consequences of the fluctuations and simulate processes that cannot be modelled by continuous fluxes of matter. This provides the motivation to develop software dedicated to Monte Carlo simulations of cellular processes with the rigorously proven Gillespie algorithm.
STOCKS, software for the stochastic kinetic simulation of biochemical processes is presented. The program uses a rigorously derived Gillespie algorithm that has been shown to be applicable to the study of prokaryotic gene expression. Features dedicated to the study of cellular processes are implemented, such as the possibility to study a process in the range of several cell generations with the application of a simple cell division model. Taking expression of Escherichia coli beta-galactosidase as an example, it is shown that the program is able to simulate systems composed of reactions varying in several orders of magnitude by means of reaction rates and the numbers of molecules involved.
The software is available at ftp://ibbrain.ibb.waw.pl/stocksand http://www.ibb.waw.pl/stocks.
Parameters of the model of prokaryotic gene expression are available in example files of software distribution.
大量有关各种生化反应的分子数据的可得性引发了众多尝试，即通过动力学模型和计算机模拟来研究细胞过程的动态变化。生化过程常常涉及少量分子（例如，少数转录调节因子分子与一个DNA调节区域的“分子”结合）。此类反应会受到显著的随机波动影响。必须采用蒙特卡罗方法来研究波动的功能后果，并模拟那些无法用物质的连续通量进行建模的过程。这为开发专门用于使用经过严格验证的 Gillespie 算法进行细胞过程蒙特卡罗模拟的软件提供了动力。
展示了用于生化过程随机动力学模拟的软件 STOCKS。该程序使用了经过严格推导的 Gillespie 算法，该算法已被证明适用于原核基因表达的研究。实现了专门用于研究细胞过程的功能，例如通过应用简单的细胞分裂模型来研究几个细胞世代范围内的过程。以大肠杆菌β-半乳糖苷酶的表达为例，结果表明该程序能够通过反应速率和所涉及的分子数量来模拟由相差几个数量级的反应组成的系统。
该软件可从 ftp://ibbrain.ibb.waw.pl/stocks 和 http://www.ibb.waw.pl/stocks 获取。
原核基因表达模型的参数可在软件发行版的示例文件中获取。
