Colored Stochastic Petri Nets for Modeling Complex Biological Systems

The stochastic modeling of biological systems is gaining more and more attention when stochastic fluctuations need to be described. On the other hand, the biological systems under investigation become much more complex than before. Traditional modeling methods like stochastic Petri nets do not easily scale and thus become difficult to tackle this situation. This paper aims to present a colored stochastic Petri net approach for systems biology to modeling complex biological systems. Specifically, this paper describes a type of biochemically-interpreted colored stochastic Petri nets and their extensions and analysis techniques for systems biology and illustrates their applications using Ca 2+ release sites that consist of a set of coupled Ca 2+ channels.

[1]  N. Thornberry,et al.  Inhibition of Human Caspases by Peptide-based and Macromolecular Inhibitors* , 1998, The Journal of Biological Chemistry.

[2]  Dominique Pontier,et al.  Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri nets. , 2003, Mathematical biosciences.

[3]  Foreword and Editorial International Journal of Hybrid Information Technology , 2022 .

[4]  C. Petri.  Kommunikation mit Automaten , 1962 .

[5]  Monika Heiner,et al.  Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments , 2009, Trans. Comp. Sys. Biology.

[6]  Doktor der Naturwissenschaften.  Colored Petri Nets for Systems Biology , 2012 .

[7]  Thomas Runge.  Application of Coloured Petri Nets in Systems Biology , 2004 .

[8]  Monika Heiner,et al.  Snoopy - a unifying Petri net framework to investigate biomolecular networks , 2010, Bioinform..

[9]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[10]  Peter Kemper,et al.  Markov chain models of coupled calcium channels: Kronecker representations and iterative solution methods. , 2008 .

[11]  David R. Gilbert,et al.  A Model Checking Approach to the Parameter Estimation of Biochemical Pathways , 2008, CMSB.

[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]  Lars Michael Kristensen,et al.  Coloured Petri Nets and CPN Tools for modelling and validation of concurrent systems , 2007, International Journal on Software Tools for Technology Transfer.

[14]  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.

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

[16]  Martin Schwarick,et al.  Snoopy - A Unifying Petri Net Tool , 2012, Petri Nets.

[17]  Michael Westergaard,et al.  CPN Tools for Editing, Simulating, and Analysing Coloured Petri Nets , 2003, ICATPN.

[18]  Marta Simeoni,et al.  Petri nets for modelling metabolic pathways: a survey , 2010, Natural Computing.

[19]  Russ B. Altman,et al.  Research Paper: Using Petri Net Tools to Study Properties and Dynamics of Biological Systems , 2004, J. Am. Medical Informatics Assoc..

[20]  Claudine Chaouiya,et al.  Petri net modelling of biological networks , 2007, Briefings Bioinform..

[21]  Martin Schwarick,et al.  MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly , 2011, 2011 Eighth International Conference on Quantitative Evaluation of SysTems.

[22]  LiuFei,et al.  Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing , 2013 .

[23]  Sunwon Park,et al.  Colored Petri net modeling and simulation of signal transduction pathways. , 2006, Metabolic engineering.

[24]  Monika Heiner,et al.  Petri Nets for Systems and Synthetic Biology , 2008, SFM.

[25]  A. Kupfer,et al.  Modelling and Simulation of the TLR4 Pathway with Coloured Petri Nets , 2006, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society.

[26]  Lars Michael Kristensen,et al.  Design/CPN - A Computer Tool for Coloured Petri Nets , 1997, TACAS.

[27]  John R. King,et al.  Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study , 2010, BMC Systems Biology.

[28]  Monika Heiner,et al.  Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets , 2001 .

[29]  Mor Peleg,et al.  Qualitative models of molecular function: linking genetic polymorphisms of tRNA to their functional sequelae , 2002, Proc. IEEE.

[30]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[31]  Peter Kemper,et al.  Markov chain models of coupled calcium channels: Kronecker representations and iterative solution methods , 2008, Physical biology.

[32]  D. Gillespie.  Approximate accelerated stochastic simulation of chemically reacting systems , 2001 .