Stochastic simulations on a grid framework for parameter sweep applications in biological models

HiBi09 - 2009 International Workshop on High Performance Computational Systems Biology

Volumn , Issue , 2009, Pages 33-42

  Mosca, Ettore ^a   Merelli, Ivan ^a   Milanesi, Luciano ^a   Cazzaniga, Paolo ^b   Pescini, Dario ^b   Mauri, Giancarlo ^b  

^a CNR   (Italy)

^b UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

Bacterial chemotaxis; Grid computing; Parameter sweep applications; Stochastic simulations; Systems biology

Indexed keywords

BACTERIAL CHEMOTAXIS; BIOCHEMICAL REACTIONS; BIOLOGICAL MODELLING; BIOLOGICAL MODELS; CHEMICAL SPECIES; CRITICAL FACTORS; DISTRIBUTED COMPUTING; GRID-BASED; LARGE SPACES; MOLECULAR LEVELS; MOLECULAR SPECIES; PARAMETER SWEEP APPLICATION; PARAMETRISATION; SCIENTIFIC COMMUNITY; STOCHASTIC MODELLING; STOCHASTIC SIMULATIONS; STOCHASTIC SIMULATORS; SYSTEM DYNAMICS; SYSTEMS BIOLOGY; SYSTEMS DYNAMICS;

BACTERIA; BACTERIOLOGY; BIOCHEMISTRY; BIOLOGICAL SYSTEMS; GRID COMPUTING; PEELING; STOCHASTIC SYSTEMS; SYSTEM THEORY;

STOCHASTIC MODELS;

EID: 73449108050     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/HiBi.2009.19     Document Type: Conference Paper

References (19)

1. T. E. Turner, S. Schnell, and K. Burrage, "Stochastic approaches for modelling in vivo reactions." Comput Biol Chem, vol. 28, no. 3, pp. 165-178, Jul 2004. [Online]. Available: http://dx.doi.org/10.1016/j. compbiolchem.2004.05.001
2. P. Cazzaniga, D. Pescini, D. Besozzi, and G. Mauri, "Tau leaping stochastic simulation method in p systems membrane computing," ser. Lecture Notes in Computer Science, H. J. Hoogeboom, G. Pǎun, G. Rozenberg, and A. Salomaa, Eds., vol. 4361, 2006, pp. 298-313.
3. "Egee project." [Online]. Available: http://www.eu-egee.org/
4. E. D. Conrad and J. J. Tyson, System Modeling in Cellular Biology. From Concepts to Nuts and Bolts. The MIT Press, 2006, ch. Modeling Molecular Interaction Networks with Nonlinear Ordinary Differential Equations, pp. 97 - 124.
5. D. T. Gillespie, "Exact stochastic simulation of coupled chemical reactions," J Phys Chem, vol. 81, pp. 2340 - 2361, 1977.
6. --, "Approximate accelerated stochastic simulation of chemically reacting systems," J. Chem. Phys., vol. 1, pp. 1716 - 1733, 2001.
7. Y. Cao, D. T. Gillespie, and L. R. Petzold, "Efficient step size selection for the tau-leaping simulation method." J Chem Phys, vol. 124, no. 4, p. 044109, Jan 2006. [Online]. Available: http://dx.doi.org/10.1063/ 1.2159468
8. D. Besozzi, P. Cazzaniga, D. Pescini, and G. Mauri, Algorithmic Bioprocesses, in press, ch. A Multivolume Approach to Stochastic Modelling with Membrane Systems.
9. D. Pescini, P. Cazzaniga, C. Ferretti, and G. Mauri, "First steps toward a wet implementation for τ -dpp," in Membrane Computing, ser. Lecture Notes in Computer Science, D. Corne, P. Frisco, G. Pǎun, G. Rozenberg, and A. Salomaa, Eds., vol. 5391, 2008.
10. H. Niederreiter, Random number generation and quasi-Monte Carlo methods. Philadelphia, PA, USA: Society for Industrial and Applied Mathematics, 1992.
11. I. Foster, C. Kesselman, and S. Tuecke, "The anatomy of the grid: Enabling scalable virtual organizations," International Journal of High Performance Computing Applications, vol. 15, pp. 200 - 222, 2001.
12. E. Laure, S. Fisher, A. Frohner, C. Grandi, P. Kunszt, A. Krenek, O. Mulmo, F. Pacini, F. Prelz, J. White, M. Barroso, P. Bunic, F. Hemmer, A. D. Meglio, and A. Edlund., "Programming the grid with glite," Computational methods in Science and Technology, vol. 12(1), pp. 33 - 45, 2006.
13. S. Campana, D. Rebatto, and A. Sciab, "Experience with the glite workload management system in atlas monte carlo production on lcg," Journal of Physics: Conference Series, vol. 119, 2008.
14. R. Buyya, D. Abramson, and J. Giddy, "Nimrod/g: an architecture for a resource management and scheduling system in a global computational grid," in Proc. Fourth International Conference/Exhibition on High Performance Computing in the Asia-Pacific Region, vol. 1, 2000, pp. 283 - 289 vol.1.
15. H. Casanova, F. Berman, G. Obertelli, and R. Wolski, "The apples parameter sweep template: User-level middleware for the grid," in Proc. ACM/IEEE 2000 Conference Supercomputing, 2000, pp. 60 - 60.
16. S. Leye, J. Himmelspach, M. Jeschke, R. Ewald, and A. Uhrmacher, "A grid-inspired mechanism for coarsegrained experiment execution," in Proc. 12th IEEE/ACM International Symposium on Distributed Simulation and Real-Time Applications DS-RT 2008, 2008, pp. 7 - 16.
17. L. Milanesi, I. Merelli, G. T. P. Cozzi, and A. Orro, Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare. Medical Information Science Reference, 2009, ch. Functional genomics applications in grid.
18. D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini, and L. Vanneschi, "A comparison of genetic algorithms and particle swarm optimization for parameter estimation in stochastic biochemical systems," in Proceedings of EvoBIO, ser. Lecture Notes on Computer Science, no. 5483, 2009, pp. 116 - 127.
19. C. Germain-Renaud, R. Texier, A. Osorio, and C. Loomis, "Grid scheduling for interactive analysis." Studies in health technology and informatics, vol. 120, pp. 25 - 33, 2006.