Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra
Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra
复制标题
DOI：
10.1142/9789814447362_0045
复制
发表时间：
2000-12
影响因子：
--
通讯作者：
A. Regev;William Silverman;E. Shapiro
中科院分区：
文献类型：
--
作者：
A. Regev;William Silverman;E. Shapiro
尽管关于蛋白质网络的知识体系正在迅速积累，但目前还没有方便的方法来共享和操纵这些信息。我们建议，一个正式的计算机语言来描述蛋白质网络的生物分子过程是必不可少的，在这一领域的快速发展。我们建议使用π演算，过程代数，最初开发用于描述计算机过程的生物分子过程的模型。我们的生物化学过程模型在数学上是明确定义的，同时保持生物学上的忠实和透明。它是经得起计算机模拟，分析和形式化验证。我们已经开发了一个计算机模拟系统，PiFCP，执行和分析的π演算程序。该系统允许我们跟踪，调试和监控各种操作下的生化网络的行为。我们提出了一个π演算模型的RTK-MAPK信号转导通路，正式表示详细的分子和生化信息，并研究了各种PiFCP模拟。
Despite the rapidly accumulating body of knowledge about protein networks, there is currently no convenient way of sharing and manipulation of such information. We suggest that a formal computer language for describing the biomolecular processes underlying protein networks is essential for rapid advancement in this field. We propose to model biomolecular processes by using the pi-Calculus, a process algebra, originally developed for describing computer processes. Our model for biochemical processes is mathematically well-defined, while remaining biologically faithful and transparent. It is amenable to computer simulation, analysis and formal verification. We have developed a computer simulation system, the PiFCP, for execution and analysis of pi-calculus programs. The system allows us to trace, debug and monitor the behavior of biochemical networks under various manipulations. We present a pi-calculus model for the RTK-MAPK signal transduction pathway, formally represent detailed molecular and biochemical information, and study it by various PiFCP simulations.