Query-based verification of qualitative trends and oscillations in biochemical systems

Theoretical Computer Science

Volumn 411, Issue 20, 2010, Pages 2019-2036

  Ballarini, Paolo ^a   Guerriero, Maria Luisa ^b  

^a UNIVERSITÉ PARIS EST   (France)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Model checking; Qualitative quantitative analysis of biochemical systems; Stochastic methods

Indexed keywords

ABSTRACT MODELS; BIOCHEMICAL SYSTEMS; CLASSIFICATION PROCEDURE; STOCHASTIC METHODS; TEMPORAL LOGIC PROPERTIES;

MODEL CHECKING; STOCHASTIC SYSTEMS; TEMPORAL LOGIC;

STOCHASTIC MODELS;

EID: 77950461614     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2010.02.010     Document Type: Article

References (35)

1. Aziz A., Kanwal K., Singhal V., and Brayton V. Verifying continuous time Markov chains. Proc. 8th International Conference on Computer Aided Verification, CAV'96. LNCS vol. 1102 (1996), Springer 269-276
2. C. Baier, On algorithmic verification methods for probabilistic systems, Habilitation thesis, Ph.D. Thesis, Fakultaet fuer Mathematik Informatik, Universitaet Mannheim, 1998.
3. Baier C., Cloth L., Haverkort B.R., Kuntz M., and Siegle M. Model checking Markov chains with actions and state labels. IEEE Trans. Softw. Eng. 33 (2007) 224
4. Baier C., Haverkort B., Hermann H., and Katoen J.-P. Model-checking algorithms for continuous-time Markov chains. IEEE Trans. Softw. Eng. 29 6 (2003) 524-541
5. P. Ballarini, M. Forlin, T. Mazza, D. Prandi, Efficient parallel statistical model checking of biochemical networks, in: Proceedings of Parallel and Distributed Methods in Verification, Electronic Proceedings in Theoretical Computer Science, 2009.
6. Ballarini P., Mazza T., Palmisano A., and Csikasz-Nagy A. An irreversibility study of the interactions between Cdk and APC in the budding yeast cell-cycle. Proc. of PASM'08. ENTCS vol. 232 (2009) 39-53
7. L. Cardelli, Artificial biochemistry. Technical report, The Microsoft Research - CoSBi, 2006.
8. Ciocchetta F., Gilmore S., Guerriero M.L., and Hillston J. Integrated simulation and model-checking for the analysis of biochemical systems. Proc. of PASM'08. ENTCS vol. 232 (2009) 17-38
9. Clarke E., Grumberg O., and Peled D. Model Checking (1999), The MIT Press
10. R. Donaldson, D. Gilbert, A Monte Carlo model checker for probabilistic LTL with numerical constraints, Technical Report TR-2008-282, University of Glasgow, Department of Computing Science, 2008.
11. Dunlap J.P., Loros J.L., and DeCoursey P.J. Chronobiology: Biological Timekeeping (2003), Sinauer
12. Fages F., Soliman S., and Chabrier-Rivier N. Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM. J. Biol. Phys. Chem. 4 2 (2004) 64-73
13. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 25 (1977) 2340-2361
14. Goldbeter A. Biochemical Oscillations and Cellular Rhythms: The Molecular Bases of Periodic and Chaotic Behaviour (1997), Cambridge University Press
15. Guerriero M.L. Qualitative and quantitative analysis of a Bio-PEPA model of the Gp130/JAK/STAT signalling pathway. Trans. Comput. Syst. Biol. 8 (2009) 90-115
16. Gunawan R., Cao Y., Petzold L., and Doyle F.J. Sensitivity analysis of discrete stochastic systems. Biophysical J. 88 4 (2005) 2530-2540
17. Hansson H.A., and Jonsson B. A framework for reasoning about time and reliability. Proc. Real-Time Systems Symposium (1989), IEEE Computer Society Press 102-111
18. Haverkort B.R., Cloth L., Hermanns H., and Katoen J.-P. Model checking performability properties. DSN '02: Proceedings of the 2002 International Conference on Dependable Systems and Networks (2002), IEEE Computer Society, Washington, DC, USA 103-112
19. Heath J.K., Kwiatkowska M., Norman G., Parker D., and Tymchyshyn O. Probabilistic model checking of complex biological pathways. Theoret. Comput. Sci. 319 (2008) 239-257
20. Heiner M., Gilbert D., and Donaldson R. Petri nets for systems and synthetic biology. SFM'08. LNCS vol. 5016 (2008) 215-264
21. Hinton A., Kwiatkowska M., Norman G., and Parker D. PRISM: A tool for automatic verification of probabilistic systems. Proc. of TACAS'06. LNCS vol. 3920 (2006) 441-444
22. In: Kitano H. (Ed). Foundations of Systems Biology (2002), MIT Press
23. Kwiatkowska M., Norman G., and Parker D. Probabilistic symbolic model checking with PRISM: A Hybrid approach. Proc. of TACAS'02. LNCS vol. 2280 (2002) 52-66
24. Kwiatkowska M., Norman G., and Parker D. Stochastic model checking. SFM'07. LNCS vol. 4486 (2007) 220-270
25. Monteiro P.T., Ropers D., Mateescu R., Freitas A.T., and de Jong H. Temporal logic patterns for querying dynamic models of cellular interaction networks. ECCB 24 (2008) 227-233
26. NuSMV Home Page. http://nusmv.irst.itc.it/.
27. Pnueli A. The temporal semantics of concurrent programs. Theoret. Comput. Sci. 13 (1981) 45-60
28. PRISM Home Page. http://www.prismmodelchecker.org.
29. Schlögl F. Chemical Reaction Models for Non-Equilibrium Phase Transitions. Z. Phys. 253 (1972) 147-161
30. Sible J.C., and Tyson J.J. Mathematical modeling as a tool for for investigating cell cycle control networks. Methods 41 (2007) 238-247
31. Stewart W.J. Introduction to numerical solution of Markov Chains (1994), Princeton
32. The BIOCHAM Home Page. http://contraintes.inria.fr/BIOCHAM/.
33. The MC2(PLTLc) Home Page. http://www.brc.dcs.gla.ac.uk/software/mc2/.
34. Vellela M., and Qian H. Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: The Schlögl model revisited. J. R. Soc. Interface (2008)
35. Volterra V. Variations and fluctuations of the number of individuals in animal species living together. Animal Ecology (1931)