Simulation of Kohn's molecular interaction maps through translation into stochastic CLS+

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5947 LNCS, Issue , 2010, Pages 58-69

  Barbuti, Roberto ^a   Lepri, Daniela ^b   Maggiolo Schettini, Andrea ^a   Milazzo, Paolo ^a   Pardini, Giovanni ^a   Rama, Aureliano ^a  

^a UNIVERSITY OF PISA   (Italy)

^b UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

GRAPHICAL NOTATION; MATHEMATICAL SEMANTICS; MOLECULAR LEVELS; STOCHASTIC CALCULUS;

ACTIVE NETWORKS; BEAM PLASMA INTERACTIONS; MOLECULAR INTERACTIONS; MOLECULAR STRUCTURE; STOCHASTIC SYSTEMS;

SEMANTICS;

EID: 77951144368     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-11486-1_6     Document Type: Conference Paper

References (20)

1. Aladjem, M.I., Pasa, S., Parodi, S., Weinstein, J.N., Pommier, Y., Kohn, K.W.: Molecular Interaction Maps-A Diagrammatic Graphical Language for Bioregulatory Networks. Sci. STKE 2004 (222), 8 (2004)
2. Kohn, K.W.: Molecular Interaction Maps as Information Organizers and Simulation Guides. CHAOS 11(1), 84-97 (2001)
3. Kohn, K.W., Aladjem, M.I., Weinstein, J.N., Pommier, Y.: Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology. Molecular Biology of the Cell 17, 1-13 (2006)
4. Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Tiberi, P., Troina, A.: Stochastic CLS for the Modeling and Simulation of Biological Systems. Trans. on Comput. Syst. Biol. IX 5121, 86-113 (2008)
5. Milazzo, P.: Qualitative and Quantitative Formal Modeling of Biological Systems. PhD thesis, Computer Science Department - University of Pisa (2007)
6. Milazzo, P.: Formal Modeling in Systems Biology. An approach from Theoretical Computer Science. VDM - Verlag Dr. Muller, Saarbrucken (2008)
7. Ciocchetta, F., Priami, C., Quaglia, P.: Modeling Kohn Interaction Maps with Beta-Binders: An Example. Trans. on Comput. Syst. Biol. III 3737, 33-48 (2005)
8. Priami, C., Quaglia, P.: Beta Binders for Biological Interactions. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol.3082, pp. 20-33. Springer, Heidelberg (2005)
9. Bortolussi, L., Fonda, S., Policriti, A.: Constraint-Based Simulation of Biological Systems Described by Molecular Interaction Maps. In: IEEE International Conference on Bioinformatics and Biomedicine, vol.0, pp. 288-293 (2007)
10. Kitano, H.: A Graphical Notation for Biochemical Networks. BIOSILICO 1(5), 169-176 (2003)
11. Pirson, I., Fortemaison, N., Jacobs, C., Dremier, S., Dumont, J.E., Maenhaut, C.: The Visual Display of Regulatory Information and Networks. Trends in Cell Biology 10, 404-408 (2000)
12. Systems Biology Graphical Notation, http://sbgn.org
13. Kohn, K.W., Aladjem, M.I.: Circuit Diagrams for Biological Networks. Molecular Systems Biology 2 (2006)
14. Oda, K., Matsuoka, Y., Funahashi, A., Kitano, H.: A Comprensive Pathway Map of Epidermal Growth Factor Receptor Signaling. Molecular Systems Biology 1 (2005)
15. Funahashi, A., Morohashi, M., Kitano, H.: CellDesigner: a Process Diagram Editor for Gene-Regulatory and Biochemical Networks. BIOSILICO 1(5), 159-162 (2003)
16. Danos, V., Laneve, C.: Formal molecular biology. Theor. Comp. Sci. 325(1), 69-110 (2004)
17. Faeder, J.R., Blinov, M.L., Hlavacek, W.S.: Graphical rule-based representation of signal-transduction networks. In: Symposium on Applied Computing (SAC), pp. 133-140 (2005)
18. Lepri, D.: A formal semantics for Molecular Interaction Maps. Master Thesis in Computer Science, University of Pisa (2008)
19. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81(25), 2340-2361 (1977)
20. CLSm: simulation tool, http://www.di.unipi.it/milazzo/biosims