Stochastic calculus of wrapped compartments

Electronic Proceedings in Theoretical Computer Science, EPTCS

Volumn 28, Issue , 2010, Pages 82-98

  Coppo, Mario ^a   Damiani, Ferruccio ^a   Drocco, Maurizio ^a   Grassi, Elena ^a   Troina, Angelo ^a  

^a UNIVERSITY OF TURIN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

SEMANTICS; STOCHASTIC SYSTEMS;

APOPTOTIC; AUTOMATIC TOOLS; CALCULUS OF LOOPING SEQUENCES; STOCHASTIC CALCULUS; STOCHASTIC SEMANTICS;

CALCULATIONS;

EID: 79955030048     PISSN: 20752180     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.4204/EPTCS.28.6     Document Type: Conference Paper

References (29)

1. M. Aldinucci, M. Coppo, F. Damiani, M. Drocco, E. Giovannetti, E. Grassi, and A. Troina. SCWC-bio-simulator. Dipartimento di Informatica, Università di Torino, 2010. http://scwc-sim.sourceforge.net/.
2. R. Alur, C. Belta, and F. Ivancic. Hybrid modeling and simulation of biomolecular networks. In HSCC, Volume 2034 of LNCS, pages 19-32. Springer, 2001.
3. JH. Baek, YJ. Kang, and SY. Lee. Transcript and protein level analyses of the interactions among phob, phor, phou and crec in response to phosphate starvation in escherichia coli. FEMS Microbiol Lett., 277:254-259, 2007.
4. R. Barbuti, A. Maggiolo-Schettini, P. Milazzo, P. Tiberi, and A. Troina. Stochastic calculus of looping sequences for the modelling and simulation of cellular pathways. Transactions on Computational Systems Biology, IX:86-113, 2008.
5. R. Barbuti, A. Maggiolo-Schettini, P. Milazzo, and A. Troina. A calculus of looping sequences for modelling microbiological systems. Fundam. Inform., 72(1-3):21-35, 2006.
6. Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, and Angelo Troina. The calculus of looping sequences for modeling biological membranes. In Workshop on Membrane Computing, Volume 4860 of Lecture Notes in Computer Science, pages 54-76. Springer, 2007.
7. T. A. Basuki, A. Cerone, and P. Milazzo. Translating stochastic cls into maude. Electr. Notes Theor. Comput. Sci., 227:37-58, 2009.
8. S. Brown, I. Heinisch, E. Ross, K. Shaw, CD. Buckley, and J. Savill. Apoptosis disables CD31-mediated cell detachment from phagocytes promoting binding and engulfment. Nature, 418:200-203, 2002.
9. L. Cardelli. Brane calculi. In CMSB, Volume 3082 of LNCS, pages 257-278. Springer, 2005.
10. DO. Carmany, K. Hollingsworth, and WR McCleary. Genetic and biochemical studies of phosphatase activity of phor. J Bacteriol., 185:1112-1115, 2003.
11. A. Coletta, R. Gori, and F. Levi. Approximating probabilistic behaviors of biological systems using abstract interpretation. Electr. Notes Theor. Comput. Sci., 229(1):165-182, 2009.
12. G. Cox, J. Crossley, and Z. Xing. Macrophage engulfment of apoptotic neutrophils contributes to the resolution of acute pulmonary inflammation in vivo. Am J Respir Cell Mol Biol., 12:232-237, 1995.
13. V. Danos and C. Laneve. Formal molecular biology. Theor. Comput. Sci., 325(1):69-110, 2004.
14. M. Dezani-Ciancaglini, P. Giannini, and A. Troina. A type system for a stochastic cls. In MeCBIC, Volume 11 of EPTCS, pages 91-106, 2009.
15. B. Fadeel and VE. Kagan. Apoptosis and macrophage clearance of neutrophils: regulation by reactive oxygen species. Redox Rep., 8:143-150, 2003.
16. GM. Ferreira and B. Spira. The pst operon of enteropathogenic escherichia coli enhances bacterial adherence to epithelial cells. Microbiology, 154:2025-2036, 2008.
17. D. Gillespie. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem., 81:2340-2361, 1977.
18. J. Krivine, R. Milner, and A. Troina. Stochastic bigraphs. Electron. Notes Theor. Comput. Sci., 218:73-96, 2008.
19. R. Lanotte, A. Maggiolo-Schettini, and A. Troina. Decidability results for parametric probabilistic transition systems with an application to security. In SEFM'04, pages 114-121. IEEE Computer Society, 2004.
20. R. Lanotte, A. Maggiolo-Schettini, and A. Troina. Parametric probabilistic transition systems for system design and analysis. Formal Asp. Comput., 19(1):93-109, 2007.
21. H. Lodish, A. Berk, L.S. Zipursky, P. Matsudaira, D. Baltimore, and J. Darnell. Many Bacterial Responses Are Controlled by Two-Component Regulatory Systems Molecular Cell Biology. W.H. Freeman, 2000.
22. H. Matsuno, A. Doi, M. Nagasaki, and S. Miyano. Hybrid petri net representation of gene regulatory network. In Prooceedings of Pacific Symposium on Biocomputing, pages 341-352. World Scientific Press, 2000.
23. C. Priami. Stochastic pi-calculus. Comput. J., 38(7):578-589, 1995.
24. C. Priami, A. Regev, E. Y. Shapiro, and W. Silverman. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf. Process. Lett., 80(1):25-31, 2001.
25. G. Påun. Membrane computing. An introduction. Springer, 2002.
26. A. Regev and E. Shapiro. Cells as computation. Nature, 419:343 2002.
27. G. Scatena. Development of a stochastic simulator for biological systems based on the calculus of looping sequences. Master's thesis, University of Pisa, 2007.
28. SJ. Singer and GL. Nicolson. The fluid mosaic model of the structure of cell membranes. Science, 175:720-731, 1972.
29. EF. Vernon-Wilson, F. Aurad, L. Tian, IC. Rowe, MJ. Shipston, J. Savill, and SB. Brown. CD31 delays phagocyte membrane repolarization to promote efficient binding of apoptotic cells. J Leukoc Biol., 82:1278-1288, 1995.