Chinese Journal of Computers   Full Text
Title	Application of Petri Nets to Bioinformatics
Authors	LIN Chuang1) YANG Hong-Kun1) SHAN Zhi-Guang2)
Address	1)(Department of Computer Science and Technology, Tsinghua University, Beijing 100084) 2)(Informatization Research Department, State Information Center， Beijing 100045)
Year	2007
Issue	No.11(1889—1900)
Abstract &   Background	Abstract Bioinformatics is a rapidly developing discipline that takes advantage of mathematics and computer technology to construct and analyze biological models. Petri nets are efficient tools used in Bioinformatics recently, while their application needs to be further expanded. The survey which this paper provides of the application of Petri nets in Bioinformatics study includes three parts: Using place/transition system to qualitatively analyze structural properties of biological objects; using stochastic Petri nets to add stochastic properties to biological modeling and analysis; using hybrid Petri nets to represent and analyze biological systems with both discrete and continuous properties. Finally, the application of Petri nets in Bioinformatics is summarized and the research directions and open problems in this area are also discussed. keywords bioinformatics; Petri nets; biological networks; topological analysis; biological simulation background This work is supported by the National Natural Science Foundation of China under grant Nos.60673187, 60673054 and 90412012 and is finished in the QoS Group, Department of Computer Science and Technology, Tsinghua University. Bioinformatics is a rapidly developing discipline that takes advantage of mathematics and computer technology to construct and analyze biological models. This area is promoted by the needs of experimental biologists to utilize and interpret the vast ocean of data collected in "wet" laboratories. Recently, the application of high-throughput technologies in molecular and cellular biology has led to the renaissance of an old topic: simulations of biological systems, which are useful to develop silico models and to complement in vitro and in vivo biological experiments. On the other hand, efficient tools in computer science and technology have been Petri Nets which have intuitive graphical representation, rigorous mathematical formalism, and moreover, powerful simulation utilities. Based on these facts, researchers apply Petri Net theory in bioinformatics study to explore qualitative and quantitative behavior of specific biological systems. The survey which our paper provides of the application of Petri nets in Bioinformatics study includes three parts: using place/transition system to qualitatively analyze structural properties of biological objects; using stochastic Petri nets to add stochastic properties to biological modeling and analysis; using hybrid Petri nets to represent and analyze biological systems with both discrete and continuous properties. The current degree in applying Petri Nets to bioinformatics needs to be further expanded, for the application is mainly concentrated on the structural level but not on the functional level of biological systems. It’s not a long time since Petri nets were introduced in bioinformatics study, but they are becoming increasingly promising formalisms inherited from computer science.