BlenX4Bio - Blenx for biologists

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

Volumn 5688 LNBI, Issue , 2009, Pages 26-51

  Priami, Corrado ^a,b   Ballarini, Paolo ^a   Quaglia, Paola ^a,b  

^a CoSBi ^*  (Italy)

^b UNIVERSITY OF TRENTO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODELS; FILLING IN; HIGH-LEVEL INTERFACES; MAIN CHARACTERISTICS; PROGRAMMING LANGUAGE; PROGRAMMING SKILLS; SIMULATION AND ANALYSIS; SOFTWARE PLATFORMS; STATIC AND DYNAMIC;

BIOLOGICAL SYSTEMS; COMPUTER SOFTWARE; HIGH LEVEL LANGUAGES;

COMPUTATIONAL METHODS;

EID: 70349326114     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-03845-7_3     Document Type: Conference Paper

References (18)

1. BioSpice home page, http://biospice.sourceforge.net/
2. Dematté, L., Priami, C., Romanel, A.: The Beta Workbench: a computational tool to study the dynamics of biological systems. Brief. Bioinform. 9(5), 437-449 (2008)
3. Dematté, L., Priami, C., Romanel, A.: The BlenX Language: A Tutorial. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp.313-365. Springer, Heidelberg (2008)
4. Guerriero, M.L., Dudka, A., Underhill-Day, N., Heath, J.K., Priami, C.: Narrativebased computational modelling of the gp130/jak/stat signalling pathway. BMC Systems Biology 3(40) (2009)
5. Guerriero, M.L., Prandi, D., Priami, C., Quaglia, P.: Process calculi abstractions for biology. In: Condon, A., Harel, D., Kok, J.N., Salomaa, A., Winfree, E. (eds.) Algorithmic Bioprocesses. Springer, Heidelberg (2009)
6. Heath, J.K., Guerriero, M.L., Priami, C.: An automated translation from a narrative language for biological modelling into process algebra. In: Calder, M., Gilmore, S. (eds.) CMSB 2007. LNCS (LNBI), vol. 4695, pp. 136-151. Springer, Heidelberg (2007)
7. Jarnac home page, http://www.sys-bio.org/software/jarnac.htm
8. Lodish, H., Berk, A., Matsudaira, P., Kaiser, C.A., Krieger, M., Scott, M.P., Zipursky, S.L., Darnell, J.: Molecular Cell Biology, 5th edn. Freeman, New York (2004)
9. Mendes, P.: Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22, 361-363 (1997)
10. Moehren, G., Markevich, N., Demin, O., Kiyatkin, A., Goryanin, I., Hoek, J., Kholodenko, B.N.: Temperature dependence of epidermal growth factor receptor signaling network can be accounted for using a kinetic model. Biochemistry 41(1),306-320 (2002)
11. Le Novere, N., Shimizu, T.S.: StochSim: modelling of stochastic biomolecular processes. Bioinformatics 17, 575-576 (2001)
12. Priami, C.: Algorithmic systems biology. CACM 52(5), 80-88 (2009)
13. Priami, C., Quaglia, P.: Modeling the dynamics of bio-systems. Briefings in Bionformatics 5(3) (2004)
14. Priami, C., Quaglia, P.: Beta Binders for Biological Interactions. In: Danos, V., Scḧachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 20-33. Springer, Heidelberg (2005)
15. Regev, A., Shapiro, E.: Cells as computations. Nature 419, 343 (2002)
16. SBML home page, http://sbml.org/
17. Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T.S., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J.C., Hutchison, C.A.3.: E-CELL: software environment for whole-cell simulation. Bioinformatics 15(1), 72-84 (1999)
18. Virtual Cell home page, http://www.ibiblio.org/virtualcell/