Voss Klaus, Heiner Monika, Koch Ina
Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) [GMD], Sankt Augustin, Germany.
Stud Health Technol Inform. 2011;162:56-76.
Computer assisted analysis and simulation of biochemical pathways can improve the understanding of the structure and the dynamics of cell processes considerably. The construction and quantitative analysis of kinetic models is often impeded by the lack of reliable data. However, as the topological structure of biochemical systems can be regarded to remain constant in time, a qualitative analysis of a pathway model was shown to be quite promising as it can render a lot of useful knowledge, e. g., about its structural invariants. The topic of this paper are pathways whose substances have reached a dynamic concentration equilibrium (steady state). It is argued that appreciated tools from biochemistry and also low-level Petri nets can yield only part of the desired results, whereas executable high-level net models lead to a number of valuable additional insights by combining symbolic analysis and simulation.
计算机辅助的生化途径分析与模拟能够显著增进对细胞过程的结构和动态变化的理解。动力学模型的构建和定量分析常常因缺乏可靠数据而受阻。然而，由于生化系统的拓扑结构可被视为随时间保持不变，路径模型的定性分析已显示出颇具前景，因为它能够提供许多有用的知识，例如关于其结构不变量的知识。本文的主题是其物质已达到动态浓度平衡（稳态）的途径。有人认为，来自生物化学的常用工具以及低级Petri网只能产生部分预期结果，而可执行的高级网络模型通过结合符号分析和模拟能够带来许多有价值的额外见解。
