A hybrid Petri net for modelling hybrid biochemical interactions

CEUR Workshop Proceedings

Volumn 643, Issue , 2010, Pages 66-79

  Herajy, Mostafa ^a   Heiner, Monika ^a  

^a BRANDENBURG UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Hybrid biochemical simulation; Hybrid Petri net; Systems biology

Indexed keywords

BIOCHEMICAL INTERACTIONS; BIOCHEMICAL SIMULATIONS; BIOCHEMICAL SYSTEMS; BIOLOGICAL MODELLING; HYBRID PETRI NET; STOCHASTIC SIMULATIONS; SYSTEMS BIOLOGY; VISUAL REPRESENTATIONS;

ALGORITHMS; BIOCHEMISTRY; BIOLOGICAL SYSTEMS; COMPUTER SIMULATION; STOCHASTIC MODELS; STOCHASTIC SYSTEMS; TOOLS;

PETRI NETS;

EID: 79958064220     PISSN: 16130073     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (24)

1. Alfonsi, A., Cances, E., Turinici, G., Ventura, B.D., Huisinga, W.: Exact simulation of hybrid stochastic and deterministic models for biochemical systems. Rr-5435, INRIA-Rocquencourt, 2004.
2. Alfonsi, A., Cances, E, Turinici, G., et al: Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems. In: ESAIM 14, pp 1-13. (2005).
3. Alla, H. and David, R.: Continuous and hybrid Petri nets. J. Circ. Syst. Comp. 8, 159-188 (1998).
4. Breitling, R., Gilbert, D., Heiner, M., Orton, R.: A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings in Bioinformatics 9, 404-421 (2008).
5. David, R., and Alla, H.: Discrete, Continuous, and Hybrid Petri Nets. Springer, 2010.
6. Gilbert, D., Heiner, M.: From Petri nets to differential equations - an integrative approach for biochemical network analysis. In: ICATPN, pp. 181-200. LNCS 4024 Springer (2006).
7. Gilbert, D., Heiner, M., Lehrack, S.: A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets. In: 5th International Conference on Computational Methods in Systems Biology pp. 200-216, Springer, Edinburgh (2007).
8. Gillespie, D.T.: A General method for numerical simulation of the stochastic time evolution of coupled chemical reactions. J. Comput Phys 22, 403-437 (1976).
9. Heiner, M., Gilbert, D., Donaldson, D.: Petri Nets for Systems and Synthetic Biology. In: Bernardo, M., Degano, P., Zavattaro, G. (Eds.): SFM 2008, LNCS, Vol. 5016, pp. 215-264, Springer, Heidelberg (2008).
10. Heiner, M., Lehrack, S., Gilbert, D, Marwan, W.: Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments. T. Comp. Sys. Biology 11: 138-163 (2009).
11. Heiner, M., Richter, R., Rohr, C., Schwarick, M.: Snoopy - A Tool to Design and Execute Graph-Based Formalisms. [Extended Version]. Petri Net Newsletter 74, 8-22 (2008).
12. Kiehl, T., et al: Hybrid Simulation of cellular behavior, J. Bioinformatics 20, 316-322 (2004).
13. Li, H., Cao, Y., Petzold, L., Gillespie D.: Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems, Biotechnology Progress, 24, 56-61 (2008).
14. Matsuno, H., et al: Biopathways Representation and Simulation on Hybrid Functional Petri Net. In Silico Biol. 3, 389-404 (2003).
15. Matsuno, H., Doi, A., Nagasaki, M., Miyano, S.: Hybrid Petri net representation of gene regulatory network. Pac Symp Biocomput., 341-52 (2000).
16. Murata, T.: Petri Nets: Properties, Analysis and Applications. Proc. the IEEE 77, 541-580 (1989).
17. Pahle, J.: Biochemical simulations: stochastic, approximate stochastic and hybrid approaches. Briefings in Bioinformatics 10, 53-64 (2009).
18. Pross, S., Bachmann, B.: A Petri Net Library for Modeling Hybrid Systems in OpenModelica. In: 7th Modelica Conference, pp. 454-462. Italy (2009).
19. Rohr, C., Marwan, W., Heiner, M.: Snoopy - a unifying Petri net framework to investigate biomolecular networks. J. Bioinformatics 26, 974-975 (2010).
20. Reddy, V., Mavrovouniotis, M., Liebman, M.: Petri Net Representations in Metabolic Pathways, In: ISMB-93, MIT Press, 328-336 (1993).
21. Ruediger, S., et al: Hybrid Stochastic and Deterministic Simulations of Calcium Blips J. Biophysical 93, 1847-1857 (2007)
22. Srivastava, R., You, L., Summers, J., Yin, J.: Stochastic vs. Deterministic Modeling of Intracellular Viral Kinetics. J. theor. Biol. 218, 309-321 (2002).
23. Trivedi, K.S., Kulkarni, V.G.: FSPNs: Fluid Stochastic Petri Nets. In: 14th International Conference on Application and Theory of Petri Nets, pp 24-31, (1993).
24. Troncale, S., Tahi, F., Campard, D., Vannier, J.P., Guespin, J.: Modeling and simulation with hybrid functional Petri nets of the role of Interleukin-6 in human early haematopoiesis. Pacic Symp Biocomput 11: 427-438 (2006).