Constructing biological pathway models with hybrid functional petri nets.

In many research projects on modeling and analyzing biological pathways, the Petri net has been recognized as a promising method for representing biological pathways. From the pioneering works by Reddy et al., 1993, and Hofestädt, 1994, that model metabolic pathways by traditional Petri net, several enhanced Petri nets such as colored Petri net, stochastic Petri net, and hybrid Petri net have been used for modeling biological phenomena. Recently, Matsuno et al., 2003b, introduced the hybrid functional Petri net (HFPN) in order to give a more intuitive and natural modeling method for biological pathways than these existing Petri nets. Although the paper demonstrates the effectiveness of HFPN with two examples of gene regulation mechanism for circadian rhythms and apoptosis signaling pathway, there has been no detailed explanation about the method of HFPN construction for these examples. The purpose of this paper is to describe method to construct biological pathways with the HFPN step-by-step. The method is demonstrated by the well-known glycolytic pathway controlled by the lac operon gene regulatory mechanism.

[1]  H. Arnstein.  The molecular biology of the cell : B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts and J.D. Watson Garland Publishing; New York, London, 1983 xxxix + 1181 pages. $33.95 (hardback); $27.00, £14.95 (paperback, only in Europe) , 1986 .

[2]  Michael L. Mavrovouniotis,et al.  Petri Net Representations in Metabolic Pathways , 1993, ISMB.

[3]  Ralf Hofestädt,et al.  A petri net application to model metabolic processes , 1994 .

[4]  B. Alberts,et al.  Molecular Biology of the Cell, Third Edition , 1994 .

[5]  Jean-Marie Proth.  Petri nets for modelling and evaluating deterministic and stochastic manufacturing systems , 1997, Proceedings of the Seventh International Workshop on Petri Nets and Performance Models.

[6]  René David,et al.  Continuous and Hybrid Petri Nets , 1998, J. Circuits Syst. Comput..

[7]  P J Goss,et al.  Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[8]  R. Drath.  Hybrid object nets : An object oriented concept for modeling complex hybrid systems , 1998 .

[9]  R Hofestädt,et al.  Quantitative modeling of biochemical networks , 1998, Silico Biol..

[10]  G. Wheeler.  The modelling and analysis of IEEE802.6's configuration , 1999 .

[11]  H Matsuno,et al.  Hybrid Petri net representation of gene regulatory network. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[12]  Hartmann J. Genrich,et al.  Executable Petri net models for the analysis of metabolic pathways , 2001, International Journal on Software Tools for Technology Transfer.

[13]  W. Bentley,et al.  Stochastic kinetic analysis of the Escherichia coli stress circuit using σ32-targeted antisense , 2001 .

[14]  Claire J. Tomlin,et al.  Lateral Inhibition through Delta-Notch Signaling: A Piecewise Affine Hybrid Model , 2001, HSCC.

[15]  Atsushi Doi,et al.  Biopathways representation and simulation on hybrid functional Petri net , 2003, Silico Biol..

[16]  Monika Heiner,et al.  Steady state analysis of metabolic pathways using Petri nets , 2003, Silico Biol..

[17]  Hiroshi Matsuno,et al.  Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Net , 2002, Pacific Symposium on Biocomputing.

[18]  Masao Nagasaki,et al.  Genomic Object Net: I. A platform for modelling and simulating biopathways. , 2003, Applied bioinformatics.

[19]  Masao Nagasaki,et al.  Constructing biological pathway models with hybrid functional Petri net , 2004, Silico Biol..