Simulating Biological Pathways with a Continuous Petri Net Using Runge-Kutta Methods

Author

Kang, Sunku ; Lee, Byungwoo ; Yang, Jihoon ; Kim, Seonho ; Kim, Saejoon

Author_Institution

Samsung Dept. of Comput. Sci., Sogang Univ., Seoul

fYear

2007

fDate

11-13 Oct. 2007

Firstpage

26

Lastpage

31

Abstract

The application of Petri nets to analyze and simulate biological pathways has been developed vigorously. Some of the modifications of Petri nets appeared to perform quantitative analysis of biological pathways: hybrid Petri net, timed Petri net, stochastic Petri net and so on. For a quantitative analysis of biological pathways, we propose to adopt Runge-Kutta methods to act on a continuous Petri net. We show that Runge-Kutta methods are applicable to a continuous Petri net in glycolysis and apoptosis pathways with reliable and efficient simulation results.

Keywords

Petri nets; Runge-Kutta methods; biology computing; Runge-Kutta methods; apoptosis; biological pathway simulation; continuous Petri net; glycolysis; hybrid Petri net; stochastic Petri net; systems biology; timed Petri net; Analytical models; Biochemical analysis; Biological system modeling; Biology; Computational modeling; Computer simulation; Discrete event systems; Information technology; Petri nets; Stochastic processes;

fLanguage

English

Publisher

ieee

Conference_Titel

Frontiers in the Convergence of Bioscience and Information Technologies, 2007. FBIT 2007

Conference_Location

Jeju City

Print_ISBN

978-0-7695-2999-8

Type

conf

DOI

10.1109/FBIT.2007.62

Filename

4524074