Cyto-Sim: A formal language model and stochastic simulator of membrane-enclosed biochemical processes

Bioinformatics

Volumn 23, Issue 20, 2007, Pages 2800-2802

  Sedwards, Sean ^a   Mazza, Tommaso ^a,b  

^a UNIVERSITY OF TRENTO   (Italy)

^b UNIVERSITY MAGNA GRAECIA OF CATANZARO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOCHEMISTRY; CELL MEMBRANE; COMPUTER AIDED DESIGN; COMPUTER PROGRAM; COMPUTER SIMULATION; DYNAMICS; GENOME; LANGUAGE; MODEL; MOLECULAR INTERACTION; PRIORITY JOURNAL; SIMULATOR;

EID: 35748973241     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm416     Document Type: Article

References (9)

1. Cavaliere,M. and Sedwards,S. (2006) Modelling cellular processes using membrane systems with peripheral and integral proteins. Lecture Notes in Computer Science, 4210, 108-126.
2. Cyto-Sim web page, http://www.cosbi.eu/Rpty_Soft_CytoSim.php/
3. Gillespie,D.T. (1977) Exact stochastic simulation of coupled chemical reactions, J. Phys. Chem., 81, 2340-2361.
4. Lind,D. and Marcus,B. (2005) An Introduction to Symbolic Dynamics and Coding. Cambridge University Press, ISBN 0521559006.
5. Nutsch,T. et al. (2005) A quantitative model of the switch cycle of an archael flagella motor and its sensory control. Biophys. J., 89, 2307-2323.
6. P Systems web page, http://psystems.disco.unimib.it/
7. PRISM web page, http://www.prismmodelchecker.org/
8. Vilar,M.G. et al. (2003) Mechanisms of noise-resistance in genetic oscillators, Proc. Natl. Acad. Sci., 99, 9.
9. Yi,T-M. et al. (2003) A quantitative characterization of the yeast heterotrimeric G protein cycle, Proc. Natl. Acad. Sci., 100, 19.