Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks

Electronic Notes in Theoretical Computer Science

Volumn 151, Issue 3, 2006, Pages 111-129

  Shaw, Oliver ^a   Steggles, Jason ^a   Wipat, Anil ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Genetic Algorithms; Kinetic parameters; Petri nets; Stochastic simulation; Systems Biology

Indexed keywords

COMPUTER SIMULATION; GENETIC ALGORITHMS; MATHEMATICAL MODELS; PARAMETER ESTIMATION; PROBLEM SOLVING; STOCHASTIC CONTROL SYSTEMS;

KINETIC PARAMETERS; STOCHASTIC SIMULATION; SYSTEMS BIOLOGY;

PETRI NETS;

EID: 33745007060     PISSN: 15710661     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.entcs.2006.03.015     Document Type: Article

References (35)

1. Arkin A., Ross J., and McAdams H.H. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected E. coli cells. Genetics 149 (1998) 1633-1648
2. Billington J., Christensen S., van Hee K., Kindler E., Kummer O., Petrucci L., Post R., Stehno C., and Weber M. The Petri net markup language: Concepts, technology, and tools. In: van der Aalst W.M.P., and Best E. (Eds). Proceedings of the 24th International Conference on Applications and Theory of Petri Nets. (ICATPN 2003), Eindhoven, The Netherlands, June 23-27, 2003. Lecture Notes in Computer Science Volume 2679 (June 2003), Springer-Verlag 483-505
3. Endy D., and Brent R. Modelling cellular behaviour. Nature 409 6818 (2001) 391-395
4. Garey M.R., and Johnson D.S. Computers and Intractability (1979), Freeman
5. M.A. Gibson. Computational Methods for Stochastic Biological Systems. PhD thesis, California Inst. Technology, 2000
6. Gibson M.A., and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. Journal of Physical Chemistry 104 (2000) 1876-1889
7. Gibson M.A., and Bruck J. Computational Modeling of Genetic and Biochemical Networks (2001), The MIT Press
8. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81 25 (1977) 2340-2361
9. Gillespie D.T. Approximate accelerated stochastic simulation of chemically reacting systems. Journal of Chemical Physics 115 4 (2001) 1716-1733
10. Goldberg D.E. Genetic algorithms in search, optimization, and machine learning (1989), Addison-Wesley Pub. Co.
11. Goss P.J.E., and Peccoud J. Quantitative modelling of stochastic systems in molecular biology by using stochastic Petri nets. Proceedings of the National Academy of Sciences of the United States of America 95 12 (1998) 6750-6755
12. Holland J.H. Adaptation in natural and artificial systems (1975)
13. Hucka M., Finney A., et al. The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19 4 (2003) 524-531
14. Iyengar R., Wolkenhauer W., Kolch W., Cho K., and Kilngmuller U. Opening editorial. Systems Biology 1 1 (2004) 1
15. Kiehl T.R., Mattheyses R.M., and Simmons M.K. Hybrid simulation of cellular behavior. Bioinformatics 20 3 (2004) 316-322
16. Kirkpatrick S., Gelatt Jr. C.D., and Vecchi M.P. Optimization by simulated annealing. Science 220 (1983) 671-680
17. Kunst F., Ogasawara N., et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature (1997) 249-256
18. Marsan M.A., Balbo G., Chiola G., Conte G., Donatelli S., and Franceschinis G. An introduction to generalized stochastic Petri nets. Microelectronics and Reliability 31 4 (1991) 699-725
19. Marwan W. Theory of time-resolved somatic complementation and its use to explore the sporulation control network in physarum polycephalum. Genetics 164 (2003) 105-115
20. McAdams H.H., and Arkin A. Stochastic mechanisms in gene expression. Proceedings of the National Academy of Sciences of the United States of America 94 3 (1997) 814-819
21. McAdams H.H., and Shapiro L. Circuit simulation of genetic networks. Science 269 5224 (1995) 650-656
22. McAdams H.H., and Shapiro L. A bacterial cell-cycle regulatory network operating in time and space. Science 301 5641 (2003) 1874-1877
23. Mendes P., and Kell D.B. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14 10 (1998) 869-883
24. Mitrani I. Probablisitc Modelling (1998), Cambridge University Press
25. Molloy M.K. Performance analysis using stochastic petri nets. IEEE Transactions on Computers 31 9 (1982) 913-917
26. Murata T. Petri nets - properties, analysis and applications. Proceedings of the Ieee 77 4 (1989) 541-580
27. Peterson J.L. Petri Net Theory and the Modeling of Systems (1981), Prentice Hall, Inc., Englewood Cliffs, New Jersey
28. Petri Nets World. Petri nets world home page (2004). http://www.daimi.au.dk/petrinet/
29. Pinney J.W., Westhead D.R., and McConkey G.A. Petri net representations in systems biology. Biochem Soc Trans 31 6 (2003) 1513-1515
30. Reddy V.N., Liebman M.N., and Mavrovouniotis M.L. Qualitative analysis of biochemical reaction systems. Computers in Biology and Medicine 26 1 (1996) 9-24
31. SBML. The SBML homepage. at (2004). http://www.sbml.org
32. O.J. Shaw, A. Koelmans, L.J. Steggles, and A. Wipat, Applying Petri nets to systems biology using XML technology. In Proceedings of the Workshop on the Definition, Implementation and Application of a Standard Interchange Format for Petri Nets, Satellite event of the 25th International Conference on Application and Theory of Petri Nets, Bologna, Italy, pages 11-25, 2004
33. Srivastava R., Peterson M.S., and Bentley W.E. Stochastic kinetic analysis of the escherichia coli stress circuit using sigma(32)-targeted antisense. Biotechnology and Bioengineering 75 1 (2001) 120-129
34. Srivastava R., You L., Summers J., and Yin J. Stochastic vs. deterministic modeling of intracellular viral kinetics. J. Theor. Biol. 218 3 (2002) 309-321
35. Zolfraghari S., and Liang M. Comparative study of simulated annealing, genetic algorithms and tabu search for solving comprehensive machine-grouping problems. International Journal of Production Research 40 (2002) 2141-2158