Affiliations: Graduate School of Science and Engineering, Yamaguchi
University, Yamaguchi, Japan | Human Genome Center, Institute of Medical Science,
University of Tokyo, Minato-ku, Tokyo, Japan | Faculty of Education, Yamaguchi University, Yamaguchi,
Japan
Note: [] Corresponding author: Hiroshi Matsuno, Graduate School of
Science and Engineering, Yamaguchi University, Yoshida 1677-1, Yamaguchi,
753–8512, Japan. E-mail: matsuno@sci.yamaguchi-u.ac.jp
Abstract: Parameter determination is important in modeling and simulating
biological pathways including signaling pathways. Parameters are determined
according to biological facts obtained from biological experiments and
scientific publications. However, such reliable data describing detailed
reactions are not reported in most cases. This prompted us to develop a general
methodology of determining the parameters of a model in the case of that no
information of the underlying biological facts is provided. In this study, we
use the Petri net approach for modeling signaling pathways, and propose a
method to determine firing delay times of transitions for Petri net models of
signaling pathways by introducing stochastic decision rules. Petri net
technology provides a powerful approach to modeling and simulating various
concurrent systems, and recently have been widely accepted as a description
method for biological pathways. Our method enables to determine the range of
firing delay time which realizes smooth token flows in the Petri net model of a
signaling pathway. The availability of this method has been confirmed by the
results of an application to the interleukin-1 induced signaling pathway.
Keywords: Petri net, interleukin-1 (IL-1) signaling pathway, firing delay time, stochastic decision rule, conflict resolution
