Multiscale modelling of coupled Ca2+ channels using coloured stochastic petri nets

IET Systems Biology

Volumn 7, Issue 4, 2013, Pages 106-113

  Liu, Fei ^a   Heiner, Monika ^b  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

^b BRANDENBURG UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COLOURED STOCHASTIC PETRI NETS; COMPLEX MODEL; CONTINUOUS TIME MARKOV CHAIN; GEOMETRICAL ARRANGEMENTS; HIGH LEVEL DESCRIPTION; MULTI-SCALE MODELLING; SPATIAL ARRANGEMENTS; SPATIAL SCALE;

BIOTECHNOLOGY; CELL CULTURE;

CALCIUM;

CALCIUM CHANNEL;

ARTICLE; BIOLOGY; CHEMICAL MODEL; CHEMISTRY; COLOR; COMPUTER PROGRAM; COMPUTER SIMULATION; METABOLISM; METHODOLOGY; PROBABILITY; REPRODUCIBILITY; STATISTICS;

CALCIUM CHANNELS; COLOR; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; MARKOV CHAINS; MODELS, CHEMICAL; REPRODUCIBILITY OF RESULTS; SOFTWARE; STOCHASTIC PROCESSES;

EID: 84879629991     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2012.0017     Document Type: Article

References (26)

1. Dallon, J.C.: 'Multiscale modeling of cellular systems in biology', Curr. Opin. Coll. Interface Sci., 2010, 15, (1-2), pp. 24-31
2. Liu, F.: 'Colored Petri nets for systems biology'. PhD thesis, Brandenburg University of Technology, Cottbus, 2012
3. Heiner, M., Gilbert, D.: 'BioModel engineering for multiscale systems biology', Prog. Biophys. Mol. Biol., 2013, 111, (2-3), pp. 119-128 doi 10.1016/j.pbiomolbio.2012.10.001
4. Baldan P., Cocco, N., Marin, A., Simeoni, M.: 'Petri nets for modelling metabolic pathways: a survey', Nat. Comput., 2010, 9, (4), pp. 955-989
5. Marwan, W., Wagler, A., Weismantel, R.: 'Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks', Nat. Comput., 2011, 10, (2), pp. 639-654
6. Genrich, H.J., Lautenbach, K.: 'The analysis of distributed systems by means of predicate/transition-nets'. Proc. Int. Symp. Semantics of Concurrent Computation (LNCS 70), Evian, France, July 1979, pp. 123-146
7. Jensen, K.: 'Coloured Petri nets and the invariant-method':, Theor. Comput. Sci., 1981, 14, (3), pp. 317-336
8. Berridge, M., Potter, B.: 'Inositol trisphosphate analogues induce different oscillatory patterns in Xenopus oocytes', Cell Regul., 1990, 1, pp. 675-681
9. Heiner, M., Gilbert, D., Donaldson, R.: 'Petri nets for systems and synthetic biology'. Proc. Int. Conf. Formal Methods for Computational Systems Biology (LNCS, 5016), Bertinoro, Italy, June 2008, pp. 215-264
10. Christensen, S., Jørgensen, J.B., Kristensen, L.M.: 'Design/CPN - a computer tool for coloured Petri nets'. Proc. Int. Workshop on Tools and Algorithms for Construction and Analysis of Systems (LNCS, 1217), Enschede, Netherlands, April 1997, pp. 209-223
11. Ratzer, A.V., Wells, L., Lassen, H.M., et al.: 'CPN tools for editing, simulating, and analysing coloured Petri nets'. Proc. Int. Conf. Applications and Theory of Petri Nets, Eindhoven, Netherlands, June 2003, pp. 450-462
12. Rohr, C., Marwan, W., Heiner, M.: 'Snoopy - a unifying Petri net framework to investigate biomolecular networks', Bioinformatics, 2010, 26, (7), pp. 974-975
13. Heiner, M., Herajy, M., Liu, F., Rohr, C., Schwarick, M.: 'Snoopy - a unifying Petri net tool'. Proc. Int. Conf. Application and Theory of Petri Nets and Concurrency (LNCS, 7347), Hamburg, Germany, June 2012, 2012, pp. 398-407
14. Sneyd, J., Falcke, M.: 'Models of the inositol trisphosphate receptor', Prog. Biophys. Mol. Biol., 2005, 89, (3), pp. 207-245
15. 2++ oscillations'. Proc. National Academy of Sciences USA, 1992, vol. 89, pp. 9895-9899
16. 2++ release channels', Phys. Rev., 2003, E 67, pp. 031905
17. DeRemigio, H., LaMar, M.D., Kemper, P., Smith, G.D.: 'Markov chain models of coupled calcium channels: Kronecker representations and iterative solution methods', Phys. Biol., 2008, 5, (3), pp. 1-14
18. 2++ signaling complexes and their analysis', Nat. Comput., 2011, 10, (3), pp. 1045-1075
19. 2++ channel models', J. Theor. Biol., 2005, 235, (1), pp. 121-150
20. DeRemigio, H., Smith, G.D.: 'The dynamics of stochastic attrition viewed as an absorption time on a terminating Markov chain', Cell Calcium, 2005, 38, (2), pp. 73-86
21. Groff, J.R., DeRemigio, H., Smith, G.D.: 'Markov chain models of ion channels and calcium release sites', in Laing, C., Lord, G.J. (Eds.): 'Stochastic methods in neuroscience' (Oxford University Press, 2009), pp. 29-64
22. 2++ dynamics', Biophys. J., 2003, 84, (1), pp. 42-56
23. Charlie - a tool for the analysis of place/transition Petri nets, available at: http://www-dssz.informatik.tu-cottbus.de/DSSZ/Software/Charlie, accessed March 2013
24. Schwarick, M., Rohr, C., Heiner, M.: 'MARCIE - model checking and reachability analysis done efficiently'. Proc. Int. Conf. Quantitative Evaluation of Systems, Aachen, Germany, September 2011, pp. 91-100
25. Liu, F., Heiner, M., Rohr, C.: 'Manual for colored Petri nets in Snoopy', Brandenburg University of Technology Cottbus, available at: http:// www-dssz.informatik.tu-cottbus.de/publications/btu-reports/Manual_for_ colored_Petri_nets_2012_03.pdf, 2012
26. Dictyostelium colony formation, available at: http://www.multiscalepn. brunel.ac.uk, accessed March 2013