caa a22 4500 445842784 CHVBK 20180317145350.0 cr unu---uuuuu 170323e20110901xx s 000 0 eng 10.1007/s11047-009-9164-6 doi (NATIONALLICENCE)springer-10.1007/s11047-009-9164-6 Hybrid Petri net based modeling for biological pathway simulation [Elektronische Daten] [Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano] Hybrid Petri net (HPN) is an extension of the Petri net formalism, which enables us to handle continuous information in addition to discrete information. Firstly, this paper demonstrates how biological pathways can be modeled by the integration of discrete and continuous elements, with an example of the λ phage genetic switch system including induction and retroregulation mechanisms. Although HPN allows intuitive modeling of biological pathways, some fundamental biological processes such as complex formation cannot be represented with HPN. Thus, this paper next provides the formal definition of hybrid functional Petri net with extension (HFPNe), which has high potential for modeling various kinds of biological processes. Cell Illustrator is a software tool developed on the basis of the definition of HFPNe. Hypothesis creation by Cell Illustrator is demonstrated with the example of the cyanobacterial circadian gene clock system. Finally, our ongoing tasks, which include the development of a computational platform for systems biology, are presented. Springer Science+Business Media B.V., 2009 Hybrid Petri net nationallicence Cell Illustrator nationallicence Pathway simulation nationallicence Matsuno Hiroshi Graduate School of Science and Engineering, Yamaguchi University, 1677-1, 753-8512, Yoshida, Yamaguchi, Japan aut Nagasaki Masao Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan aut Miyano Satoru Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan aut Natural Computing Springer Netherlands 10/3(2011-09-01), 1099-1120 1567-7818 10:3<1099 2011 10 11047 https://doi.org/10.1007/s11047-009-9164-6 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s11047-009-9164-6 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Matsuno Hiroshi Graduate School of Science and Engineering, Yamaguchi University, 1677-1, 753-8512, Yoshida, Yamaguchi, Japan aut NATIONALLICENCE 700 1- Nagasaki Masao Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan aut NATIONALLICENCE 700 1- Miyano Satoru Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan aut NATIONALLICENCE 773 0- Natural Computing Springer Netherlands 10/3(2011-09-01), 1099-1120 1567-7818 10:3<1099 2011 10 11047 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer