Design issues for qualitative modelling of biological cells with Petri nets

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

Volumn 5054 LNBI, Issue , 2008, Pages 48-62

  Krepska, Elzbieta ^a   Bonzanni, Nicola ^a   Feenstra, Anton ^a   Fokkink, Wan ^a   Kielmann, Thilo ^a   Bal, Henri ^a   Heringa, Jaap ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; CANNING; GRAPH THEORY; INFORMATION THEORY; MARINE BIOLOGY; MONTE CARLO METHODS; PETRI NETS;

BIOLOGICAL CELLS; BIOLOGICAL PROCESSING; C. ELEGANS; CONCURRENT SYSTEMS; DESIGN ISSUES; DEVELOPMENT PROCESSES; EXECUTION SEMANTICS; HEIDELBERG (CO); IN-SILICO; INTERNATIONAL (CO); MONTE CARLO SIMULATION (MCS); NOVEL CONCEPT; QUALITATIVE MODELLING; SYSTEMS BIOLOGY;

FORMAL METHODS;

EID: 47149100702     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-68413-8_4     Document Type: Conference Paper

References (33)

1. Alon, U.: An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC (2006)
2. Genrich, H., Küffner, R., Voss, K.: Executable Petri net models for the analysis of metabolic pathways. International Journal on Software Tools for Technology Transfer (STTT) 3(4), 394-404 (2001)
3. E-Cell, http://www.e-cell.org
4. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81(25), 2340-2361 (1977)
5. Srivastava, R., You, L., Summers, J., Yin, J.: Stochastic vs. deterministic modeling of intracellular viral kinetics. Journal of Theoretical Biology 218(3), 309-321 (2002)
6. Sackmann, A., Heiner, M., Koch, I.: Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinformatics 7, 482 (2006)
7. Chaouiya, C.: Petri net modelling of biological networks. Briefings in Bioinformatics 8(4), 210-219 (2007)
8. Wormbook, http://www.wormbook.org
9. Reddy, V., Mavrovouniotis, M., Liebman, M.: Qualitative analysis of biochemical
10. Reddy, V., Mavrovouniotis, M., Liebman, M.: Qualitative analysis of biochemical reaction system. Computers in Biology and Medicine 26(1), 9-24 (1996)
11. Fisher, J., Piterman, N., Hajnal, A., Henzinger, T.A.: Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Computational Biology 3(5), 92 (2007)
12. Petri, C.A.: Kommunikation mit Automaten. Schriften des UM Nr. 2, Institut für Instrumentelle Mathematik, Bonn (1962)
13. Murata, T.: Petri nets: Properties, analysis and applications. Proceedings of the IEEE 77(4), 541-580 (1989)
14. Kleijn, J.H., Koutny, M., Rozenberg, G.: Towards a Petri net semantics for membrane systems. In: Freund, R., Pǎun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2005. LNCS, vol. 3850, pp. 292-309. Springer, Heidelberg (2006)
15. Distributed ASCI Supercomputer DAS-3, http://www.informatik.hu-berlin.de/ top/pnml
16. Petri Net Markup Language, http://www.informatik.hu-berlin.de/top/pnml
17. TINA, http://www.laas.fr/tina/
18. Fisher, J., Henzinger, T.A., Mateescu, M., Piterman, N.: Bounded asynchrony: A biologically inspired notion of concurrency. Technical report, MTC (2007)
19. Clarke, D., Costa, D., Arbab, F.: Modelling coordination in biological systems. In: Margaria, T., Steffen, B. (eds.) ISoLA 2004. LNCS, vol. 4313, pp. 9-25. Springer, Heidelberg (2006)
20. Koch, I., Junker, B.H., Heiner, M.: Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21(7), 1219-1226 (2005)
21. Li, C., Ge, Q.W., Nakata, M., Matsuno, H., Miyando, S.: Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets. Journal of Biosciences 32, 113-127 (2007)
22. Goss, P., Peccoud, J.: Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 95(12), 6750-6755 (1998)
23. KEGG, http://www.genome.jp/kegg
24. Srivastava, R., Peterson, M.S., Bentley, W.E.: Stochastic kinetic analysis of the Escherichia coli stress circuit using σ-32-targeted antisense. Biotechnology and Bioengineering 75(1), 120-129 (2001)
25. Matsuno, H., Doi, A., Nagasaki, M., Miyano, S.: Hybrid Petri net representation of gene regulatory network. In: Proceedings of Pacific Symposium on Biocomputing, vol. 5, pp. 341-352 (2000)
26. Hofestädt, R., Thelen, S.: Quantitative modeling of biochemical networks. In Silico Biology 6, 39-53 (1998)
27. Matsuno, H., Li, C., Miyano, S.: Petri net based descriptions for systematic understanding of biological pathways. IEICE Transactions on Fundamentals of Electronics, Communications and Computer Science E89-A(11), 3166-3174 (2006)
28. Simao, E., Remy, E., Thieffry, D., Chaouiya, C.: Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E. Coli. Bioinformatics 21(2), 190-196 (2005)
29. Steggles, L., Banks, R., Wipat, A.: Modelling and analysing genetic networks: From Boolean networks to Petri nets. In: Priami, C. (ed.) CMSB 2006. LNCS (LNBI), vol. 4210, pp. 127-141. Springer, Heidelberg (2006)
30. Peleg, M., Rubin, D., Altman, R.B.: Using Petri net tools to study properties and dynamics of biological systems. Journal of the American Medical Informatics Association (JAMIA) 12(2), 181-199 (2005)
31. Fisher, J., Henzinger, T.A.: Executable cell biology. Nature Biotechnology 25(11), 1239-1249 (2007)
32. Yoo, A.S., Bais, C., Greenwald, I.: Crosstalk between the EGFR and LIN-12/Notch pathways in C. elegans vulval development. Science 303(5658), 663-666 (2004)
33. Shaye, D.D., Greenwald, I.: Endocytosis-mediated downregulation of LIN-12/Notch upon Ras activation in Caenorhabditis elegans. Nature 420(6916), 686-690 (2002)