From model-checking to temporal logic constraint solving

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

Volumn 5732 LNCS, Issue , 2009, Pages 319-334

  Fages, François ^a   Rizk, Aurélien ^a  

^a INRIA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DEGREE OF SATISFACTION; ENGINEERING PROBLEMS; FREE VARIABLE; PARAMETER OPTIMIZATION PROBLEMS; SYSTEMS BIOLOGY; TEMPORAL LOGIC FORMULA; TEMPORAL LOGIC SPECIFICATIONS; TRUTH VALUES;

BIOLOGY; COMPUTER PROGRAMMING; CONSTRAINT THEORY; MODEL CHECKING; STRUCTURAL OPTIMIZATION;

TEMPORAL LOGIC;

EID: 70350424435     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-04244-7_26     Document Type: Conference Paper

References (35)

1. Abdulla, P.A., Cerans, K., Jonsson, B., Tsay, Y.-K.: General decidability theorems for infinite-state systems. Logic in Computer Science, pp. 313-321 (1996)
2. Emerson, E.A., Clarke, E.M.: Characterizing correctness properties of parallel programs using fixpoints. In: de Bakker, J.W., van Leeuwen, J. (eds.) ICALP 1980. LNCS, vol. 85, pp. 169-181. Springer, Heidelberg (1980)
3. Antoniotti, M., Policriti, A., Ugel, N., Mishra, B.: Model building and model checking for biochemical processes. Cell Biochemistry and Biophysics 38, 271-286 (2003)
4. Bagnara, R., Hill, P.M., Zaffanella, E.: The Parma Polyhedra Library: Toward a complete set of numerical abstractions for the analysis and verification of hardware and software systems. Science of Computer Programming 72(1-2), 3-21 (2008)
5. Batt, G., Ropers, D., de Jong, H., Geiselmann, J., Mateescu, R., Page, M., Schneider, D.: Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli. Bioinformatics 21(suppl. 1), 19-28 (2005)
6. Batt, G., Yordanov, B., Weiss, R., Belta, C.: Robustness analysis and tuning of synthetic gene networks. Bioinformatics 23(18), 2415-2422 (2007)
7. Bernot, G., Comet, J.-P., Richard, A., Guespin, J.: A fruitful application of formal methods to biological regulatory networks: Extending thomas' asynchronous logical approach with temporal logic. Journal of Theoretical Biology 229(3), 339-347 (2004)
8. Calder, M., Vyshemirsky, V., Gilbert, D., Orton, R.: Analysis of signalling pathways using the continuous time markow chains. In: Plotkin, G. (ed.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 44-67. Springer, Heidelberg (2006); CMSB 2005 Special Issue
9. Calzone, L., Chabrier-Rivier, N., Fages, F., Soliman, S.: Machine learning biochemical networks from temporal logic properties. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 68-94. Springer, Heidelberg (2006); CMSB 2005 Special Issue
10. Chabrier, N., Fages, F.: Symbolic model checking of biochemical networks. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 149-162. Springer, Heidelberg (2003)
11. Chan, W.: Temporal-logic queries. In: Emerson, E.A., Sistla, A.P. (eds.) CAV 2000. LNCS, vol. 1855, pp. 450-463. Springer, Heidelberg (2000)
12. Chen, K.C., Csikász-Nagy, A., Györffy, B., Val, J., Novàk, B., Tyson, J.J.: Kinetic analysis of a molecular model of the budding yeast cell cycle. Molecular Biology of the Cell 11, 396-391 (2000)
13. Clarke, E.M., Grumberg, O., Peled, D.A.: Model Checking. MIT Press, Cambridge (1999)
14. Delzanno, G., Podelski, A.: Constraint-based deductive model checking. STTT 3(3), 250-270 (2001)
15. Egerstedt, M., Mishra, B.: (2008)
16. Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Meseguer, J., Kemal Sönmez, M.: Pathway logic: Symbolic analysis of biological signaling. In: Proceedings of the seventh Pacific Symposium on Biocomputing, January 2002, pp. 400-412 (2002)
17. Fages, F., Rizk, A.: On temporal logic constraint solving for the analysis of numerical data time series. Theoretical Computer Science 408(1), 55-65 (2008)
18. Fages, F., Soliman, S.: From reaction models to influence graphs and back: a theorem. In: Fisher, J. (ed.) FMSB 2008. LNCS (LNBI), vol. 5054, pp. 90-102. Springer, Heidelberg (2008)
19. Fages, F., Soliman, S., Rizk, A.: BIOCHAM v2.8 user's manual. In: INRIA (2009), http://contraintes.inria.fr/BIOCHAM
20. Halbwachs, N., Proy, Y.e., Roumanoff, P.: Verification of real-time systems using linear relation analysis. In: Formal Methods in System Design, pp. 157-185 (1997)
21. Hansen, N., Ostermeier, A.: Completely derandomized self-adaptation in evolution strategies. Evolutionary Computation 9(2), 159-195 (2001)
22. Heath, J., Kwiatkowska, M., Norman, G., Parker, D., Tymchyshyn, O.: Probabilistic model checking of complex biological pathways. In: Priami, C. (ed.) CMSB 2006. LNCS (LNBI), vol. 4210, pp. 32-47. Springer, Heidelberg (2006)
23. Henzinger, T.A., Ho, P.-H., Wong-Toi, H.: HYTECH: A model checker for hybrid systems. In: Grumberg, O. (ed.) CAV 1997. LNCS, vol. 1254, pp. 460-463. Springer, Heidelberg (1997)
24. Janssen, M., Van Hentenryck, P., Deville, Y.: A constraint satisfaction approach for enclosing solutions to parametric ordinary differential equations. SIAM Journal on Numerical Analysis 40(5) (2002)
25. Kitano, H.: Towards a theory of biological robustness. Molecular Systems Biology 3, 137 (2007)
26. Larsen, K.G., Pettersson, P., Yi, W.: Uppaal in a nutshell. Int. Journal on Software Tools for Technology Transfer 1, 134-152 (1997)
27. Levchenko, A., Bruck, J., Sternberg, P.W.: Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. PNAS 97(11), 5818-5823 (2000)
28. Clarke, E.M., Emerson, E.A.: Design and synthesis of synchronization skeletons using branching-time temporal logic. In: Kozen, D. (ed.) Logic of Programs 1981. LNCS, vol. 131, pp. 52-71. Springer, Heidelberg (1982)
29. Pnueli, A.: The temporal logic of programs. In: FOCS, pp. 46-57 (1977)
30. Podelski, A.: Model checking as constraint solving. In: Palsberg, J. (ed.) SAS 2000. LNCS, vol. 1824, pp. 22-37. Springer, Heidelberg (2000)
31. Qiao, L., Nachbar, R.B., Kevrekidis, I.G., Shvartsman, S.Y.: Bistability and oscillations in the huang-ferrell model of mapk signaling. PLoS Computational Biology 3(9), 1819-1826 (2007)
32. Rizk, A., Batt, G., Fages, F., Soliman, S.: On a continuous degree of satisfaction of temporal logic formulae with applications to systems biology. In: Heiner, M., Uhrmacher, A.M. (eds.) CMSB 2008. LNCS (LNBI), vol. 5307, pp. 251-268. Springer, Heidelberg (2008)
33. Rizk, A., Batt, G., Fages, F., Soliman, S.: A general computational method for robustness analysis with applications to synthetic gene networks. BioInformat-ics 25(12), 169-178 (2009)
34. Tevfik, B., Richard, G., William, P.: Symbolic model checking of infinite state systems using presburger arithmetic. In: Grumberg, O. (ed.) CAV 1997. LNCS, vol. 1254, pp. 400-411. Springer, Heidelberg (1997)
35. Wolper, P., Boigelot, B.: Verifying systems with infinite but regular state space. In: Y. Vardi, M. (ed.) CAV 1998. LNCS, vol. 1427, pp. 88-97. Springer, Heidelberg (1998)