生物化学动力学网络体系的计算机模拟

生物网络体系中的化学动力学模拟已成为生物体系研究过程中的一个重要环节。目前,已有数种针对于不同生物网络体系的模拟算法。在这些算法的基础上,开发出相应的一些模拟软件。本文对国际上常用的28个模拟软件进行了分类和总结。根据软件所支持模拟算法的原理及适用范围,将该28个软件大致分成4类:均匀体系确定性模拟软件、均匀体系随机性模拟软件、均匀体系混合性随机软件和扩散反应体系模拟软件。结合各类模拟算法的局限性,针对如何根据实际体系来正确选择生物网络体系的化学动力学模拟算法和模拟软件给出了必要的讨论。

Computer simulation for biological dynamic networks

Computer simulation of biological dynamic networks has been an important approach in the research of biological systems. Recently, there are a few simulation algorithms aiming to different biological systems. On the basis of these simulation algorithms, some simulation softwares have been developed. In this paper, 28 commonly used simulation softwares are reviewed and summarized. According to the principles and applicability of simulation algorithms used by corresponding softwares, 28 simulation softwares are classified into 4 categories. Also, how to choose a simulation method correctly according to the different actual biological networks are briefly highlighted.