A probabilistic model for molecular systems

Fundamenta Informaticae

Volumn 67, Issue 1-3, 2005, Pages 13-27

  Barbuti, Roberto ^a   Cataudella, Stefano ^a   Maggiolo Schettini, Andrea ^a   Milazzo, Paolo ^a   Troina, Angelo ^a  

^a UNIVERSITY OF PISA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; SEMANTICS;

MOLECULAR REACTIONS; MOLECULAR SYSTEMS; PROBABILISTIC ALGORITHM;

PROBABILISTIC LOGICS;

EID: 33645301043     PISSN: 01692968     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (24)

1. R. Alur, C. Belta, F. Ivancic, V. Kumar, M. Mintz, G. Pappas, H. Rubin, and J. Schug. Hybrid Systems: Computation and Control, volume 2034 of LNCS, chapter Hybrid Modeling and Simulation of Biomolecular Networks, pages 19-32. Springer, 2001.
2. C. Baier and M. Kwiatowska. Model checking for a probabilistic branching time logic with fairness. Distributed Computing, 11(3):125-155, 1998.
3. Christel Baier, Boudewijn R. Haverkort, Holger Hermanns, and Joost-Pieter Katoen. Model checking continuous-time markov chains by transient analysis. In Proc. of CAV, volume 1885 of LNCS, pages 358-372. Springer, 2000.
4. A. Bianco and L. de Alfaro. Model checking of probabilistic and nondeterministic systems. In Proc. of Int. Conference on Foundation of Software Technologies and Theoretical Computer Science, volume 1026 of LNCS, pages 499-513. Springer, 1995.
5. L. Cardelli. Bioware languages. In Computer Systems. Theory, Technology and Applications. Papers for Roger Needham, pages 59-66. Springer, 2003.
6. N. Chabrier and F. Fages. Symbolic model checking of biochemical networks. In Comp. Methods in Systems Biology (CMSB), volume 2602 of LNCS, pages 149-162. Springer, 2003.
7. N. Chabrier-Rivier, F. Fages, and S. Soliman. The biochemical abstract machine biocham. In Comp. Methods in Systems Biology (CMSB) 2004, LNCS. Springer, to appear.
8. M. Curti, P. Degano, C. Priami, and C.T. Baldari. Modelling biochemical pathways through enhanced π-calculus. Theoretical Computer Science, 325(1): 111-140, 2004.
9. Vincent Danos and Cosimo Laneve. Formal molecular biology. Theoretical Computer Science, 325(1):69-110, 2004.
10. S. Geman and M. Johnson. Probabilistic grammars and their applications. International Encyclopedia of the Social & Behavioral Sciences, pages 12075-12082, Elsevier, 2002.
11. D. Gillespie. Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry, 81:2340-2361, 1977.
12. H. Hansson and B. Jonsson. A logic for reasoning about time and probability. Formal Aspects of Computing, 6(5):512-535, 1994.
13. D. Harel. A grand challenge: Full reactive modeling of a multi-cellular animal. Bulletin of the EATCS, European Association for Theoretical Computer Science, 81:226-235, 2003.
14. N. Kam, D. Harel, H. Kugler, R. Marelly, A. Pnueli, E.J.A. Hubbard, and M.J. Stern. Formal modeling of c. elegans development: A scenario-based approach. In Comp. Methods in Systems Biology (CMSB), volume 2602 of LNCS, pages 4-20. Springer, 2003.
15. M. Kwiatkowska. Model checking for probability and time: From theory to practice. In Proc. of LICS'03, pages 351-360. IEEE CS Press, 2003.
16. I. Marini, L. Bucchioni, P. Borella, A. Del Corso, and U. Mura. Sorbitol dehydrogenase from bovine lens: Purification and properties. Archives of Biochemistry and Biophysics, 340:383-391, 1997.
17. H. Matsuno, A. Doi, M. Nagasaki, and S. Miyano. Hybrid petri net representation of gene regulatory networ. In Pacific Symposium on Biocomputing, volume 5, pages 341-352, World Scientific Press, 2000.
18. M. Nagasaki, S. Miyano, S. Onami, and H. Kitano. Bio-calculus: Its concept and molecular interaction. Genome Informatics, 10:133-143, 1999.
19. L. Popova-Zeugmann, M. Heiner, and I. Koch. Modelling and analysis of biochemical networks with time petri nets. In 13th Int. Workshop on Concurrency Specification and Programming (CS&P'04), number 170 in Informatik-Berichte, pages 136-143. Humboldt-Universitaet, 2004.
20. C. Priami, A. Regev, E.Y. Shapiro, and W. Silverman. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters, 80:25-31, 2001.
21. PRISM Model Checker, web site, 2004. http://www.cs.bham.ac.uk/~dxp/prism.
22. A. Regev. Computational Systems Biology: a Calculus for Biomolecular Knowledge. PhD thesis, Tel Aviv University, 2002.
23. A. Regev, W. Silverman, and E.Y. Shapiro. Representation and simulation of biochemical processes using the pi-calculus process algebra. In Pacific Symposium on Biocomputing, pages 459-470, World Scientific Press, 2001.
24. SICStus prolog. web site, 2004. http://www.sics.se/sicstus/.