IDD-based model validation of biochemical networks

Theoretical Computer Science

Volumn 412, Issue 26, 2011, Pages 2884-2908

  Schwarick, Martin ^a   Tovchigrechko, Alexej ^a  

^a BRANDENBURG UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Biochemical networks; CSL; CT; Interval decision diagrams; Model checking; Petri nets

Indexed keywords

BIOCHEMICAL NETWORK; COMPUTATION TREE LOGIC; CONTINUOUS STOCHASTIC LOGIC; CSL; CT; DECISION DIAGRAM; INTERVAL DECISION DIAGRAMS; MODEL VALIDATION; PETRI NET PROPERTIES; QUALITATIVE AND QUANTITATIVE ANALYSIS; STATE-SPACE EXPLOSION; STOCHASTIC PETRI NETS;

COMPUTATION THEORY; GRAPH THEORY; PETRI NETS; QUALITY CONTROL; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

MODEL CHECKING;

EID: 79955730053     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2010.06.030     Document Type: Conference Paper

References (43)

1. C. Baier, B. Haverkort, H. Hermanns, and J.-P. Katoen Model checking continuous-time Markov chains by transient analysis Proc. CAV 2000 LNCS vol. 1855 2000 Springer 358 372
2. P. Baldan, N. Cocco, A. Marin, and M. Simeoni Petri nets for modelling metabolic pathways: a survey J. Natural Comput. 2010
3. K.S. Brace, R.L. Rudell, and R.E. Bryant Efficient implementation of a BDD package Proceedings of the 27th ACM/IEEE Design Automation Conference ACM/IEEE 1990 IEEE Computer Society Press 40 45
4. R.E. Bryant Graph-based algorithms for Boolean function manipulation IEEE Transactions on Computers C-35 8 1986 677 691
5. 20 states and beyond Proceedings of the 5th Annual IEEE Symposium on Logic in Computer Science 1990 IEEE Computer Society Press 1 33
6. M. Calder, V. Vyshemirsky, R. Orton, and D. Gilbert Analysis of signalling pathways using the PRISM model checker Proc. CMSB 2005 LFCS 2005 University of Edinburgh 179 190
7. D. Cerotti, D. D'Aprile, S. Donatelli, and J. Sproston Verifying stochastic well-formed nets with CSL model checking tools Proc. ACSD 2006 2006 IEEE Computer Society 143 152
8. K.-H. Cho, S.-Y. Shin, H.-W. Kim, O. Wolkenhauer, B. McFerran, and W. Kolch Mathematical modeling of the influence of RKIP on the ERK signaling pathway CMSB 2003 LNCS vol. 2602 2003 Springer 127 141 (Pubitemid 36241647)
9. G. Ciardo, R.L. Jones, A.S. Miner, R.I. Siminiceanu, SMART: stochastic model analyzer for reliability and timing, in: Tools of Aachen 2001, International MultiConference on Measurement, Modelling and Evaluation of Computer-Communication Systems, 2001, pp. 2934.
10. E.M. Clarke, E.A. Emerson, and A.P. Sistla Automatic verification of finite state concurrent systems using temporal logic specifications ACM Trans. Program. Lang. Syst. 8 2 1986 244 263 (Pubitemid 16633197)
11. E.M. Clarke, O. Grumberg, and D. Peled Model Checking 2001 MIT Press
12. J.-M. Couvreur, E. Encrenaz, E. Paviot-Adet, D. Poitrenaud, and P.-A. Wacrenier Data decision diagrams for Petri net analysis Proceedings of the 23rd International Conference on Applications and Theory of Petri Nets LNCS vol. 2360 2002 Springer 1 101
13. M. Fujita, P.C. McGeer, and J.C.-Y. Yang Multi-terminal binary decision diagrams: an efficient datastructure for matrix representation Form. Methods Syst. Des. 10 23 1997 149 169 (Pubitemid 127506985)
14. D. Gilbert, and M. Heiner From Petri nets to differential equations an integrative approach for biochemical network analysis Proc. ICATPN 2006 LNCS vol. 4024 2006 Springer 181 200 (Pubitemid 44071794)
15. D. Gilbert, M. Heiner, S. Lehrack, A unifying framework for modelling and analysing biochemical pathways using Petri nets. TR I-02, CS Dep., BTU Cottbus, 2007.
16. D. Gilbert, M. Heiner, and S. Lehrack A unifying framework for modelling and analysing biochemical pathways using Petri nets Proc. CMSB 2007 LNCS/LNBI vol. 4695 2007 Springer 200 216
17. J. Heath, M. Kwiatkowska, G. Norman, D. Parker, and O. Tymchyshyn Probabilistic model checking of complex biological pathways Proc. CMSB 2006 LNBI vol. 4210 2006 Springer 32 47 (Pubitemid 44849977)
18. M. Heiner, D. Gilbert, and R. Donaldson Petri nets in systems and synthetic biology SFM LNCS vol. 5016 2008 Springer 215 264
19. M. Heiner, R. Richter, and M. Schwarick Snoopy a tool to design and animate/simulate graph-based formalisms Proc. PNTAP 2008, Associated to SIMUTools 2008 2008 ACM Digital Library
20. M. Heiner, M. Schwarick, and A. Tovchigrechko DSSZ-MC a tool for symbolic analysis of extended Petri nets Proc. Petri Nets 2009 LNCS vol. 5606 2009 Springer 323 332
21. C. Huang, and J. Ferrell Ultrasensitivity in the mitogen-activated protein kinase cascade Proc. Natl. Acad. Sci. 93 1996 10078 10083 (Pubitemid 26314577)
22. T. Kam, State Minimization of Finite State Machines Using Implicit Techniques. Ph.D. Thesis, University of California at Berkeley, 1995.
23. K. Lautenbach, H. Ridder, A completion of the S-invariance technique by means of fixed point algorithms. Technical Report 1095, Universitt Koblenz-Landau, 1995.
24. A. Levchenko, J. Bruck, and P.W. Sternberg Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties Proc. Natl. Acad. Sci. USA 97 11 2000 5818 5823 (Pubitemid 30367482)
25. Z. Manna, and A. Pnueli The Temporal Logic of Reactive and Concurrent Systems Specification 1992 Springer
26. S. Minato Zero-suppressed BDDs for set manipulation in combinatorial problems Proceedings of the 30th ACM/IEEE Design Automation Conference 1993 ACM Press 272 277 (Pubitemid 23673251)
27. A.S. Miner, and G. Ciardo Efficient reachability set generation and storage using decision diagrams Proceedings of the 20th International Conference on Application and Theory of Petri Nets LNCS vol. 1639 1999 Springer 6 25
28. J. Møller, J. Lichtenberg, Difference decision diagrams, Master's thesis, Department of Information Technology, Technical University of Denmark, Building 344, DK-2800 Lyngby, Denmark, 1998.
29. A. Noack, A ZBDD package for efficient model checking of Petri nets. Technical report, BTU Cottbus, Dep. of CS, 1999 (in German).
30. D. Parker, Implementation of symbolic model checking for probabilistic systems. Ph.D. Thesis, University of Birmingham, 2002.
31. D. Parker, G. Norman, M. Kwiatkowska, PRISM 3.0.beta1 Users' Guide, 2006.
32. L. Priese, and H. Wimmel Theoretical Informatics Petri Nets 2003 Springer (in German)
33. H. Ridder, Analysis of Petri net models with decision diagrams. Ph.D. Thesis, Universitt Koblenz-Landau, 1997 (in German).
34. C. Rohr, W. Marwan, and M. Heiner Snoopy a unifying Petri net framework to investigate biomolecular networks Bioinformatics 26 7 2010 974 975
35. M. Schwarick Transient analysis of stochastic Petri nets with interval decision diagrams Proc. 15th German Workshop on Algorithms and Tools for Petri Nets, AWPN 2008 CEUR Workshop Proceedings vol. 380 September 2008 CEUR-WS.org 43 48
36. M. Schwarick, and M. Heiner CSL model checking of biochemical networks with interval decision diagrams Proc. CMSB 2009 LNCS/LNBI vol. 5688 2009 Springer 296 312
37. Snoopy Website. A tool to design and animate/simulate graphs. BTU Cottbus. http://www-dssz.informatik.tu-cottbus.de/software/snoopy.html, 2008.
38. W.J. Stewart Introduction to the Numerical Solution of Markov Chains 1994 Princeton University Press
39. K. Strehl, L. Thiele, Symbolic model checking using interval diagram techniques. Technical report, Computer Engineering and Networks Lab (TIK), Swiss Federal Institute of Technology (ETH) Zurich, 1998.
40. R. Tarjan Depth-first search and linear graph algorithms SIAM J. Comput. 1 2 1972 146 160
41. A. Tovchigrechko, Model checking using interval decision diagrams. Ph.D. Thesis, BTU Cottbus, Dep. of CS, 2008.
42. A. Xie, and P.A. Beerel Efficient state classification of finite state Markov chains Design Automation Conference 1998 605 610
43. T. Yoneda, H. Hatori, A. Takahara, and S. Minato BDDs vs. Zero-suppressed BDDs: For CTL Symbolic Model Checking of Petri Nets LNCS vol. 1166 1996 435 449 (Pubitemid 126149775)