Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets |
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Authors: | Li Chen Ge Qi-Wei Mitsuru Nakata Hiroshi Matsuno Satoru Miyano |
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Affiliation: | (1) Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan;(2) Faculty of Education, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan;(3) Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan |
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Abstract: | This paper first presents basic Petri net components representing molecular interactions and mechanisms of signalling pathways, and introduces a method to construct a Petri net model of a signalling pathway with these components. Then a simulation method of determining the delay time of transitions, by using timed Petri nets — i.e. the time taken in firing of each transition — is proposed based on some simple principles that the number of tokens flowed into a place is equivalent to the number of tokens flowed out. Finally, the availability of proposed method is confirmed by observing signalling transductions in biological pathways through simulation experiments of the apoptosis signalling pathways as an example. |
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Keywords: | Apoptosis modelling Petri net signalling pathway simulation |
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