Verification and testing of biological models

Proceedings - Winter Simulation Conference

Volumn , Issue , 2010, Pages 620-630

  Clark, Allan ^a   Gilmore, Stephen ^a   Hillston, Jane ^a   Kemper, Peter ^b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b Dept of Economics and Thomas Jefferson Program in Public Policy at the College of William and Mary   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED TECHNIQUES; BIOLOGICAL MODELS; CARDINALITIES; COMPLEX DYNAMICS; CONTINUOUS SIMULATION; MODELING ENVIRONMENTS; MODELING FORMALISMS; SIGNAL TRANSDUCTION PATHWAYS; SIMULATION MODELING; SYSTEMS BIOLOGY; VERIFICATION AND TESTING;

DISCRETE EVENT SIMULATION;

SIGNAL TRANSDUCTION;

EID: 79951642121     PISSN: 08917736     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/WSC.2010.5679126     Document Type: Conference Paper

References (24)

1. Breitling, R., R. A. Donaldson, D. R. Gilbert, and M. Heiner. 2010. Biomodel Engineering - From Structure to Behaviour. Transactions on Computational Systems Biology XII Springer-Verlag, LNBI 5945:1-12.
2. Calder, M., S. Gilmore, and J. Hillston. 2006. Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. Transactions on Computational Systems Biology.
3. Cho, K., S.-Y. Shin, W. Kolch, and O. Wolkenhauer. 2003, December. Experimental design in systems biology, based on parameter sensitivity analysis using a Monte Carlo method: A case study for the TNF α-mediated NF- κB signal transduction pathway. Simulation 79 (12): 726-739.
4. Ciocchetta, F., A. Degasperi, J. K. Heath, and J. Hillston. 2010. Modelling and analysis of the NF- κB pathway in Bio-PEPA. In Transactions on Computational Systems Biology XII, Volume 5945, 229-262: Springer.
5. Ciocchetta, F., and J. Hillston. 2009, August. Bio-PEPA: A framework for the modelling and analysis of biological systems. Theoretical Computer Science Concurrent Systems Biology: To Nadia Busi (1968-2007), 410 (33-34): 3065-3084.
6. Ciocchetta, F., J. Hillston, M. Kos, and D. Tollervey. 2008. Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA. Theoretical Computer Science 408 (1): 41-54.
7. Duguid, A., S. Gilmore, M. Guerriero, J. Hillston, and L. Loewe. 2009. Design and development of the software tools for Bio-PEPA. In Proceedings of the Winter Simulation Conference, 956-967. Austin, Texas: IEEE Press.
8. Fages, F., and A. Rizk. 2007. On the analysis of numerical data time series in temporal logic. In Computational Methods in Systems Biology '07, Volume 4695 of Lecture Notes in Computer Science, 48-63: Springer.
9. Gibson, M. A., and J. Bruck. 2000. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A 104:1876-1889.
10. Gillespie, D. T. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (25): 2340-2361.
11. Gillespie, D. T. 2001. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115 (4): 1716-1733. (Pubitemid 32715518)
12. Gillespie, D. T. 2009. Deterministic limit of stochastic chemical kinetics. J. Phys. Chem. B 113:1640-1644.
13. Grafahrend-Belau, E., F. Schreiber, M. Heiner, A. Sackmann, B. H. Junker, S. Grunwald, A. Speer, K. Winder, and I. Koch. 2008. Modularization of biochemical networks based on classification of Petri net t-invariants. BMC Bioinformatics 9 (90).
14. Heiner, M., D. Gilbert, and R. Donaldson. 2008. Petri nets in systems and synthetic biology. In SFM'08:Bio, 215-264: Springer. LNCS 5016.
15. Hillston, J. 2006. A compositional approach to performance modelling. Cambridge University Press.
16. Hillston, J., and A. Duguid. 2009. Deriving differential equations from process algebra models in reagent-centric style. In Algorithmic Bioprocesses, 487-504: Springer.
17. Hucka, M., S. Hoops, S. Keating, N. Le Novère, S. Sahle, and D. Wilkinson. 2008. Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions. Available from Nature Precedings. 〈http://dx.doi.org/10.1038/npre.2008.2715.1〉.
18. Kemper, P., and C. Tepper. 2009. Automated trace analysis of discrete-event system models. IEEE Transactions on Software Engineering 35 (2): 195-208.
19. Kwiatkowska, M., G. Norman, and D. Parker. 2009. PRISM: Probabilistic model checking for performance and reliability analysis. ACM SIGMETRICS Performance Evaluation Review 36 (4): 40-45.
20. Liu, X., and D. Gilbert. 2010. BioNessie: A biochemical networks simulation environment. Journal of Cell Research. To appear.
21. Martinez, J., and M. Silva. 1982. A simple and fast algorithm to obtain all invariants of a generalized Petri net. In Selected Papers from the First and the Second European Workshop on Application and Theory of Petri Nets, 301-310. London, UK: Springer-Verlag.
22. Phillips, A. 2010. Symbolic systems biology: Theory and methods, Chapter A Visual Process Calculus for Biology. Jones and Bartlett. In Press.
23. Priami, C. 1995. Stochastic π-calculus. The Computer Journal 38 (6): 578-589.
24. Regev, A. 2001. Representation and simulation of molecular pathways in the stochastic π-calculus. In Proceedings of the 2nd workshop on Computation of Biochemical Pathways and Genetic Networks.