MARCIE - Model checking and reachability analysis done efficiently

Proceedings of the 2011 8th International Conference on Quantitative Evaluation of Systems, QEST 2011

Volumn , Issue , 2011, Pages 91-100

  Schwarick, Martin ^a   Heiner, Monika ^a   Rohr, Christian ^b  

^a BRANDENBURG UNIVERSITY OF TECHNOLOGY   (Germany)

^b Magdeburg Centre for Systems Biology MaCS   (Germany)

Author keywords

Computation Tree Logic; Continuous Stochastic Logic; Continuous Time Markov Chain; Fast Adaptive Uniformization; Generalized Stochastic Petri Net; Interval Decision Diagram; Model Checking; Rewards; Stochastic Simulation

Indexed keywords

COMPUTATION TREE LOGIC; CONTINUOUS STOCHASTIC LOGIC; CONTINUOUS TIME MARKOV CHAIN; DECISION DIAGRAM; GENERALIZED STOCHASTIC PETRI NETS; REWARDS; STOCHASTIC SIMULATIONS; UNIFORMIZATION;

COMPUTATION THEORY; DECISION THEORY; MARKOV PROCESSES; MATRIX ALGEBRA; NUMERICAL ANALYSIS; PETRI NETS; RANDOM ACCESS STORAGE; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

MODEL CHECKING;

EID: 80055034906     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/QEST.2011.19     Document Type: Conference Paper

References (47)

1. P. M. Merlin and D. J. Farber, "Recoverability of communication protocols - implications of a theoretical study," IEEE Transactions on Communications, vol. 24, no. 9, pp. 1036-1043, 1976.
2. M. A. Marsan, G. Balbo, G. Conte, S. Donatelli, and G. Franceschinis, Modelling with Generalized Stochastic Petri Nets. Wiley Series in Parallel Computing, John Wiley and Sons, 1995, 2nd Edition.
3. G. Ciardo and K. S. Trivedi, "A Decomposition Approach for Stochastic Reward Net Models," Performance Evaluation, vol. 18, no. 1, pp. 37-59, 1993. (Pubitemid 23710402)
4. G. Ciardo and M. Tilgner, "On the use of Kronecker operators for the solution of generalized stocastic Petri nets," Institute for Computer Applications in Science and Engineering, ICASE Report 96-35, 1996.
5. R. E. Bryant, "Graph-Based Algorithms for Boolean Function Manipulation," vol. C-35, no. 8, pp. 677-691, 1986.
6. M. Heiner, M. Schwarick, and A. Tovchigrechko, "DSSZ-MC - A Tool for Symbolic Analysis of Extended Petri Nets," in Proc. Petri Nets 2009. LNCS 5606, Springer, 2009, pp. 323-332.
7. D. Gilbert, M. Heiner, and S. Lehrack, "A unifying framework for modelling and analysing biochemical pathways using Petri nets," in Proc. CMSB 2007. LNCS/LNBI 4695, Springer, 2007, pp. 200-216.
8. M. Heiner, D. Gilbert, and R. Donaldson, "Petri nets in systems and synthetic biology," in SFM. LNCS 5016, Springer, 2008, pp. 215-264.
9. L. Napione, D. Manini, F. Cordero, A. Horvath, A. Picco, M. D. Pierro, S. Pavan, M. Sereno, A. Veglio, F. Bussolino, and G. Balbo, "On the Use of Stochastic Petri Nets in the Analysis of Signal Transduction Pathways for Angiogenesis Process," in Proc. CMSB 2009. LNCS/LNBI 5688, Springer, 2009, pp. 281-295.
10. M. Heiner, S. Lehrack, D. Gilbert, and W. Marwan, "Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments."LNCS/ LNBI 5750, Springer, 2009, pp. 138-163.
11. A. Tovchigrechko, "Model checking using interval decision diagrams," Ph.D. dissertation, BTU Cottbus, Dep. of CS, 2008.
12. M. Schwarick and M. Heiner, "CSL model checking of biochemical networks with interval decision diagrams," in Proc. CMSB 2009. LNCS/LNBI 5688, Springer, 2009, pp. 296-312.
13. M. Schwarick and A. Tovchigrechko, "IDD-based model validation of biochemical networks," TCS 412, pp. 2884-2908, 2010.
14. M. Schwarick, "IDD-MC - a model checker for bounded Stochastic Petri nets," in Proc. 17th AWPN. CEUR-WS 643, 2010, pp. 80-87.
15. G. Ciardo, R. L. Jones, A. S. Miner, and R. Siminiceanu, "Logical and stochastic modeling with SMART," Perform. Eval., vol. 63, no. 1, pp. 578-608, 2006.
16. A. Hinton, M. Kwiatkowska, G. Norman, and D. Parker, "PRISM: A tool for automatic verification of probabilistic systems," in Proc. TACAS 2006. LNCS 3920, Springer, 2006, pp. 441-444.
17. A. Franzke, "Charlie 2.0 - a multi-threaded Petri net analyzer,"Diploma Thesis (in German), BTU Cottbus, Dep. of CS, 2009.
18. F. Bause, P. Kemper, and P. Kritzinger, "Abstract Petri Net Notation," Univ. Dortmund, Dep. of CS, Tech. Rep., 1994.
19. C. Rohr, W. Marwan, and M. Heiner, "Snoopy-a unifying Petri net framework to investigate biomolecular networks,"Bioinformatics, vol. 26, no. 7, pp. 974-975, 2010.
20. M. Schwarick, Manual: Marcie - An analysis tool for Generalized Stochastic Petri nets, BTU Cottbus, Dep. of CS, 2010.
21. A. Noack, "A ZBDD Package for Efficient Model Checking of Petri Nets (in German)," BTU Cottbus, Dep. of CS, Tech. Rep., 1999.
22. E. M. Clarke, E. A. Emerson, and A. P. Sistla, "Automatic verification of finite state concurrent systems using temporal logic specifications," ACM TOPLAS, vol. 8, no. 2, pp. 244-263, 1986.
23. W. Stewart, Introduction to the Numerical Solution of Markov Chains. Princeton Univ. Press, 1994.
24. A. Miner and D. Parker, Validation of Stochastic Systems: A Guide to Current Research. LNCS 2925, Springer, 2004, ch. Symbolic Representations and Analysis of Large Probabilistic Systems, pp. 296-338.
25. G. Ciardo, "Data representation and efficient solution: A decision diagram approach," in Proc. SFM. LNCS 4486, Springer, 2007, pp. 371-394.
26. D. Deavours and W. H. Sanders, "On-the-Fly solution techniques for Stochastic Petri nets and extensions," in IEEE Transactions on Software Engineering, 1997, pp. 132-141.
27. A. S. Miner and G. Ciardo, "Efficient Reachability Set Generation and Storage Using Decision Diagrams," in Proc. 20th ICATPN. LNCS 1639, Springer, 1999, pp. 6-25.
28. D. Parker, "Implementation of symbolic model checking for probabilistic systems," Ph.D. dissertation, University of Birmingham, 2002.
29. G. Ciardo, A. Blakemore, P. F. Chimento, J. K. Muppala, and K. S. Trivedi, "Automated generation and analysis of Markov reward models using stochastic reward nets." IMA Volumes in Mathematics and its Applications: Linear Algebra, Markov Chains, and Queueing Models / Meyer, C.; Plemmons, R.J, vol. 48, pp. 145-191, 1993.
30. T. Henzinger, M. Mateescu, and V. Wolf, "Sliding window abstraction for infinite Markov chains," in Proc. CAV. Springer, LNCS 5643, 2009, pp. 337-352.
31. F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, "Fast Adaptive Uniformization for the Chemical Master Equation,"in HIBI. IEEE Comp. Soc., 2009, pp. 118-127.
32. D. Gillespie, "Exact stochastic simulation of coupled chemical reactions," The Journal of Physical Chemistry, vol. 81(25), pp. 2340-2361, 1977.
33. W. Sandmann and C. Maier, "On the statistical accuracy of stochastic simulation algorithms implemented in Dizzy," in Proc. WCSB 2008, 2008, pp. 153-156.
34. R. German, Performance analysis of communication systems with non-Markovian stochastic Petri nets. Wiley, 2001.
35. M. Heiner, C. Rohr, M. Schwarick, and S. Streif, "A comparative study of stochastic analysis techniques," in Proc. CMSB 2010. ACM, 2010, pp. 96-106.
36. A. Aziz, K. Sanwal, V. Singhal, and R. Brayton, "Model checking continuous-time Markov chains," ACM Trans. on Computational Logic, vol. 1, no. 1, pp. 162-170, 2000.
37. C. Baier, H. Hermanns, and J.-P. Katoen, "Approximative Symbolic Model checking of Contiuous-Time Markov Chains," in Proc. 10th CONCUR. LNCS 1664, Springer, 1999, pp. 163-175.
38. C. Baier, B. Haverkort, H. Hermanns, and J.-P. Katoen, "Model checking continuous-time Markov chains by transient analysis,"in Proc. CAV 2000. LNCS 1855, Springer, 2000, pp. 358-372.
39. M. Kwiatkowska, G. Norman, and D. Parker, "Stochastic model checking," in SFM. LNCS 4486, Springer, 2007, pp. 220-270.
40. B. Haverkort, L. Cloth, H. Hermanns, J.-P. Katoen, and C. Baier, "Model Checking Performability Properties," IEEE CS Press, pp. 103-112, 2002.
41. L. Cloth and B. R. H. M. Haverkort, "Five performability algorithms. A comparison," in MAM 2006: Markov Anniversary Meeting, Charleston, SC, USA. Boson Books, 2006, pp. 39-54.
42. D. N. Jansen, J.-P. Katoen, M. Oldenkamp, M. Stoelingan, and I. Zapreev, "How fast and fat is your probabilistic model checker?" in HVC 2007. LNCS 4899, Springer, 2008, pp. 69-85.
43. J.-P. Katoen, I. S. Zapreev, E. M. Hahn, H. Hermanns, and D. N. Jansen, "The Ins and Outs of The Probabilistic Model Checker MRMC," in Proc. QEST. IEEE Computer Society, 2009, pp. 167-176.
44. F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, "Sabre: A tool for stochastic analysis of biochemical reaction networks."in Proc. QEST. IEEE Computer Society, 2010, pp. 217-218.
45. O. Ibe and K. Trivedi, "Stochastic Petri net models of polling systems," IEEE Journal on Selected Areas in Communications, vol. 8, no. 9, pp. 1649-1657, 1990.
46. O. Andrei and M. Calder, "A model and analysis of the AKAP scaffold," Electron. Notes Theor. Comput. Sci., vol. 268, pp. 3-15, December 2010.
47. R. Donaldson and D. Gilbert, "A Monte Carlo model checker for probabilistic LTL with numerical constraints," University of Glasgow, Dep. of CS, Tech. Rep., 2008.