Petri nets for systems and synthetic biology

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5016 LNCS, Issue , 2008, Pages 215-264

  Heiner, Monika ^a   Gilbert, David ^b   Donaldson, Robin ^b  

^a BRANDENBURG UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHITECTURAL DESIGN; BIOCHEMICAL ENGINEERING; COMMUNICATION SYSTEMS; COMPUTATIONAL METHODS; COMPUTER NETWORKS; COMPUTER SOFTWARE; COMPUTERS; GRAPH THEORY; MARINE BIOLOGY; METROPOLITAN AREA NETWORKS; MINE FLOODING; MODAL ANALYSIS; NETWORK PROTOCOLS; PETRI NETS; PIGMENTS; SIGNAL TRANSDUCTION; SOFTWARE DESIGN; STOCHASTIC MODELS; STOCHASTIC PROGRAMMING; TRANSIENT ANALYSIS;

(EXTENDED) PETRI NETS; APPLIED (CO); BEHAVIOUR ANALYSIS; BIOCHEMICAL NETWORKS; BIOCHEMICAL PATHWAYS; CASCADE (CO); COMPUTATIONAL SYSTEMS BIOLOGY; CONTINUOUS MODELING; ERK SIGNAL; EXTENDED MODEL; HEIDELBERG (CO); INTERNATIONAL (CO); SOFTWARE SYSTEMS; SPRINGER (CO); SYNTHETIC BIOLOGY;

FORMAL METHODS;

EID: 45749112203     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-68894-5_7     Document Type: Conference Paper

References (68)

1. Singhal, V., Aziz, A., Sanwal, K., Brayton, R.: Model checking continuous time Markov chains. ACM Trans. on Computational Logic 1(1), 162-170 (2000)
2. Angeli, D., De Leenheer, P., Sontag, E.D.: On the structural monotonicity of chemical reaction networks. In: Proc. 45th IEEE Conference on Decision and Control, pp. 7-12 (2006)
3. Adalsteinsson, D., McMillen, D., Elston, T.C.: Biochemical network stochastic simulator (bionetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics 5, 24 (2004)
4. Antoniotti, M., Policriti, A., Ugel, N., Mishra, B.: Model building and model checking for biochemical processes. Cell Biochemistry and Biophysics 38, 271-286 (2003)
5. BioNessie website. A biochemical pathway simulation and analysis tool. University of Glasgow (2008), http://www.bionessie.org
6. Bause, F., Kritzinger, P.S.: Stochastic Petri Nets. Vieweg (2002)
7. Hermanns, H., Baier, C., Haverkort, B., Katoen, J.-P.: Model-checking algorithms for continuous-time markov chains. IEEE Trans. on Software Engineering 29(6), 524-541 (2003)
8. Calzone, L., Chabrier-Rivier, N., Fages, F., Soliman, S.: Machine learning biochemical networks from temporal logic properties. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 68-94. Springer, Heidelberg (2006)
9. Chabrier, N., Fages, F.: Symbolic model checking of biochemical networks. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 149-162. Springer, Heidelberg (2003)
10. Clarke, E.M., Grumberg, O., Peled, D.A.: Model checking. MIT Press, Cambridge (2001) (third printing)
11. Chaouiya, C.: Petri net modelling of biological networks. Briefings in Bioinformatics 8(4), 210-219 (2007)
12. Charlie Website. A Tool for the Analysis of Place/Transition Nets. BTU Cottbus (2008), http://www-dssz.informatik.tu-cottbus.de/ software/charlie/ charlie.html
13. Chickarmane, V., Kholodenko, B.N., Sauro, H.M.: Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation. Journal of Theoretical Biology 244(1), 68-76 (2007)
14. Curry, E.: Stochastic Simulation of the Entrained Circadian Rhythm. Master thesis, School of Informatics, Univ. of Edinburgh (2006)
15. Calder, M., Vyshemirsky, V., Gilbert, D., Orton, R.: Analysis of signalling pathways using continuous time Markov chains. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 44-67. Springer, Heidelberg (2006)
16. David, R., Alla, H.: Discrete, Continuous, and Hybrid Petri Nets. Springer, Heidelberg (2005)
17. D'Aprile, D., Donatelli, S., Sproston, J.: CSL model checking for the ?GreatSPN tool. In: Aykanat, C., Dayar, T., Körpeoǧlu, İ. (eds.) ISCIS 2004. LNCS, vol. 3280, Springer, Heidelberg (2004)
18. Desel, J., Esparza, J.: Free Choice Petri Nets. Cambridge University Press, New York (1995)
19. Desel, J., Juhás, G.: What is a Petri Net? In: Ehrig, H., Juhás, G., Padberg, J., Rozenberg, G. (eds.) APN 2001. LNCS, vol. 2128, pp. 1-25. Springer, Heidelberg (2001)
20. Dormand, J.R., Prince, P.J.: A family of embedded runge-kutta formulae. J. Comp. Appl. Math. 6, 1-22 (1980)
21. Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Meseguer, J., Sonmez, K.: Pathway logic: Symbolic analysis of biological signaling. In: Proc. Seventh Pacific Symposium on Biocomputing, pp. 400-412 (2002)
22. Fages, F., Rizk, A.: On the analysis of numerical data time series in temporal logic. In: Calder, M., Gilmore, S. (eds.) CMSB 2007. LNCS (LNBI), vol. 4695, pp. 48-63. Springer, Heidelberg (2007)
23. Gilbert, D., Heiner, M.: From Petri nets to differential equations - an integrative approach for biochemical network analysis. In: Donatelli, S., Thiagarajan, P.S. (eds.) ICATPN 2006. LNCS, vol. 4024, pp. 181-200. Springer, Heidelberg (2006)
24. Gilbert, D., Heiner, M., Lehrack, S.: A unifying framework for modelling and analysing biochemical pathways using Petri nets. In: TR I-02, CS Dep., BTU Cottbus (2007)
25. Gilbert, D., Heiner, M., Lehrack, S.: A unifying framework for modelling and analysing biochemical pathways using Petri nets. In: Calder, M., Gilmore, S. (eds.) CMSB 2007. LNCS (LNBI), vol. 4695, pp. 200-216. Springer, Heidelberg (2007)
26. Gilbert, D., Heiner, M., Rosser, S., Fulton, R., Gu, X., Trybilo, M.: A Case Study in Model-driven Synthetic Biology. In: 2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC), IFIP WCC 2008, Milano (to appear, 2008)
27. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81(25), 2340-2361 (1977)
28. Goss, P.J.E., Peccoud, J.: Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc. Natl. Acad. Sci., USA, 95, 2340-2361 (1998)
29. Heiner, M., Donaldson, R., Gilbert, D.: Petri Nets for Systems Biology. In: Iyengar, M.S. (ed.) Symbolic Systems Biology: Theory and Methods, Jones and Bartlett Publishers, Inc (to appear, 2008)
30. Hucka, M., Finney, A., Sauro, H.M., Bolouri, H., Doyle, J.C., Kitano, H. et al.: The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. J. Bioinformatics 19, 524-531 (2003)
31. Heiner, M., Koch, I.: Petri Net Based Model Validation in Systems Biology. In: Cortadella, J., Reisig, W. (eds.) ICATPN 2004. LNCS, vol. 3099, pp. 216-237. Springer, Heidelberg (2004)
32. Heath, J., Kwiatkowska, M., Norman, G., Parker, D., Tymchyshyn, O.: Probabilistic model checking of complex biological pathways. In: Priami, C. (ed.) CMSB 2006. LNCS (LNBI), vol. 4210, pp. 32-47. Springer, Heidelberg (2006)
33. Hofestädt, R.: A Petri net application of metabolic processes. Journal of System Analysis, Modeling and Simulation 16, 113-122 (1994)
34. Heiner, M., Richter, R., Schwarick, M.: Snoopy - A Tool to Design and Animate/Simulate Graph-Based Formalisms. In: Proc. PNTAP 2008, ACM, New York (to appear, 2008)
35. Koch, I., Heiner, M.: Petri Nets. In: Junker, B.H., Schreiber, F. (eds.) Biological Network Analysis, 7, pp. 139-179. Wiley Book Series on Bioinformatics (2008)
36. Kierzek, A.M.: STOCKS: STOChastic kinetic simulations of biochemical systems with gillespie algorithm. Bioinformatics 18(3), 470-481 (2002)
37. Lautenbach, K.: Exact Liveness Conditions of a Petri Net Class (in German). Technical report, GMD Report 82, Bonn (1973)
38. Levchenko, A., Bruck, J., Sternberg, P.W.: Scaffold proteins biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl. Acad. Sci. USA 97(11), 5818-5823 (2000)
39. Li, C., Miyano, S., Matsuno, H.: Petri net based descriptions for systematic understanding of biological pathways. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. E89-A(11), 3166-3174 (2006)
40. Ajmone Marsan, M., Balbo, G., Conte, G., Donatelli, S., Franceschinis, G.: Modelling with Generalized Stochastic Petri Nets, 2nd edn. Wiley Series in Parallel Computing. John Wiley and Sons, Chichester (1995)
41. MC2 Website. MC2 - PLTL model checker. University of Glasgow (2008), http://www.brc.dcs.gla.ac.uk/software/mc2/
42. Matsuno, H., Fujita, S., Doi, A., Nagasaki, M., Miyano, S.: Towards Pathway Modelling and Simulation. In: van der Aalst, W.M.P., Best, E. (eds.) ICATPN 2003. LNCS, vol. 2679, pp. 3-22. Springer, Heidelberg (2003)
43. Max-Gruenebaum-Foundation, http://www.max-gruenebaum-stiftung.de
44. Murata, T.: Petri nets: Properties, analysis and applications. Proc.of the IEEE 77(4), 541-580 (1989)
45. Palsson, B.O.: Systems Biology: Properties of Reconstructed Networks. Cambridge University Press, Cambridge (2006)
46. Petri, C.A.: Communication with Automata (in German). Schriften des Instituts für Instrumentelle Mathematik, Bonn (1962)
47. Parker, D., Norman, G., Kwiatkowska, M.: PRISM 3.0.beta1 Users' Guide (2006)
48. Pnueli, A.: The temporal semantics of concurrent programs. Theor. Comput. Sci. 13, 45-60 (1981)
49. Priese, L., Wimmel, H.: Theoretcial Informatics - Petri Nets (in German). Springer, Heidelberg (2003)
50. Reisig, W.: Petri nets; An introduction. Springer, Heidelberg (1982)
51. Reddy, V.N., Mavrovouniotis, M.L., Liebman, M.L.: Petri Net Representations in Metabolic Pathways. In: Proc. of the Int. Conf. on Intelligent Systems for Molecular Biology (1993)
52. Salis, H., Kaznessis, Y.: Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. J. Chem. Phys. 122 (2005)
53. Snoopy Website. A Tool to Design and Animate/Simulate Graphs. BTU Cottbus (2008), http://www-dssz.informatik.tu-cottbus.de/ software/snoopy.html
54. 32-targeted antisense. Biotechnology and Bioengineering 75(1), 120-129 (2001)
55. Shampine, L.F., Reichelt, M.W.: The MATLAB ODE Suite. SIAM Journal on Scientific Computing 18, 1-22 (1997)
56. Starke, P.H., Roch, S.: INA - The Intergrated Net Analyzer. Humboldt University Berlin (1999), www.informatik.hu-berlin.de/ starke/ ina.html
57. Schröter, C., Schwoon, S., Esparza, J.: The Model Checking Kit. In: van der Aalst, W.M.P., Best, E. (eds.) ICATPN 2003. LNCS, vol. 2679, pp. 463-472. Springer, Heidelberg (2003)
58. Shaw, O.J., Steggles, L.J., Wipat, A.: Automatic parameterisation of stochastic Petri net models of biological networks. CS-TR-909, School of CS, Univ. of Newcastle upon Tyne (2005)
59. Schulz-Trieglaff, O.: Modelling the randomness in biological systems. Master thesis, School of Informatics, University of Edinburgh (2005)
60. Starke, P.H.: Some Properties of Timed Nets under the Earliest Firing Rule. In: Rozenberg, G. (ed.) APN 1989. LNCS, vol. 424, pp. 418-432. Springer, Heidelberg (1990)
61. Starke, P.H.: Analysis of Petri Net Models (in German). B.G. Teubner, Stuttgart, Stuttgart (1990)
62. Stewart, W.J.: Introduction to the Numerical Solution of Markov Chains. Princeton University Press, Princeton (1994)
63. Tovchigrechko, A.: Model checking using interval decision diagrams. PhD thesis, BTU Cottbus, Dep. of CS, (submitted 2006)
64. Turner, T.E., Schnell, S., Burrage, K.: Stochastic approaches for modelling in vivo reactions. Comp. Biology and Chemistry 28(3), 165-178 (2004)
65. Wilkinson, D.J.: Stochastic Modelling for System Biology, 1st edn. CRC Press, New York (2006)
66. Sujathab, A., Marwan, W., Starostzik, C.: Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri net modeling and simulation. J. of Theoretical Biology 236(4), 349-365 (2005)
67. Younes, H., Kwiatkowska, M., Norman, G., Parker, D.: Numerical vs. statistical probabilistic model checking. STTT 8(3), 216-228 (2006)
68. Younes, H.L.S., Simmons, R.G.: Probabilistic verification of descrete event systems using acceptance sampling. In: Brinksma, E., Larsen, K.G. (eds.) CAV 2002. LNCS, vol. 2404, pp. 223-235. Springer, Heidelberg (2002)