Abstract
This paper presents a new programming language, BlenX. BlenX is inspired to the process calculus Beta-binders and it is intended for modelling any system whose basic step of computation is an interaction between sub-components. The original development was thought for biological systems. Therefore this tutorial exemplifies BlenX features on biology-related systems.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bravetti, M., Zavattaro, G.: Service oriented computing from a process algebraic perspective. Journal of Logic and Algebraic Programming 70(1), 3–14 (2007)
Cardelli, L.: Brane Calculi - Interactions of B iological Membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)
Danos, V., Laneve, C.: Formal molecular biology. In: TCS (2004)
Danos, V., Krivine, J.: Reversible communicating systems. In: Gardner, P., Yoshida, N. (eds.) CONCUR 2004. LNCS, vol. 3170, pp. 292–307. Springer, Heidelberg (2004)
Degano, P., Prandi, D., Priami, C., Quaglia, P.: Beta-binders for Biological Quantitative Experiments. In: Proc. of the 4th International Workshop on Quantitative Aspects of Programming Languages (QAPL 2006). ENTCS, vol. 164, pp. 101–117. Elsevier, Amsterdam (2006)
Elowitz, M., Levine, A., Siggia, E., Swain, P.: Stochastic gene expression in a single cell. Science 297, 1183–1186 (2002)
Elowitz, M.B., Leibler, S.: A synthetic oscillatory network of transcriptional regulators. Nature 403(20), 335–338 (2000)
Errampalli, D., Priami, C., Quaglia, P.: A formal language for computational systems biology. OMICS: A Journal of Integrative Biology 8(4), 370–380 (2004)
Fall, C.P., Marland, E.S., Wagner, J.M., Tyson, J.J.: Computational Cell Biology. Springer, Heidelberg (2002)
Gillespie, D.T.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. The Journal of Computational Physics 22(4), 403–434 (1976)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. The Journal of Chemical Physics 81, 2340–2361 (1977)
Gillespie, D.T.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Phys. Chem. 22, 403–434 (1976)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), 2340–2361 (1977)
Gilmore, S., Hillston, J.: The PEPA Workbench: A Tool to Support a Process Algebra-based Approach to Performance Modelling. LNCS, vol. 794, pp. 353–368. Springer, Heidelberg (1994)
Hoare, C.A.R.: A calculus of total correctness for communicating processes. Science of Computer Programming 1(1-2), 49–72 (1981)
Hume, D.: Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood 96, 2323–2328 (2000)
McAdams, H.H.: It is a noisy business! genetic regulation at the nanomolar scale. Trends Genet 15, 65–69 (1999)
Milner, R.: Communication and Concurrency. Prentice-Hall, Inc., Englewood Cliffs (1989)
Phillips, A., Cardelli, L.: A correct abstract machine for the stochastic pi-calculus. In: Bioconcur 2004, ENTCS (August 2004)
Priami, C.: The stochastic π-calculus. The Computer Journal (38), 578–589 (1995)
Priami, C., Quaglia, P.: Beta binders for biological interactions. In: CMSB, pp. 20–33 (2004)
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)
Priami, C., Quaglia, P.: Modeling the dynamics of bio-systems. Briefings in Bioinformatics 5(3), 259–269 (2004)
Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: Bioambients: an abstraction for biological compartments. Theor. Comput. Sci. 325(1), 141–167 (2004)
Ross, I., Browne, C., Hume, D.: Transcription of individual genes in eukaryotic cells occurs randomly and infrequently. In: Immunol Cell Biol. (1994)
Spudich, J., Koshland, D.E.J.: Non-genetic individuality: Chance in the single cell. Nature (1976)
Stock, A.M., Robinson, V.L., Goudreau, P.N.: Two-component signal transduction. Annu. Rev. Biochem. (69), 183–215 (2000)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Dematté, L., Priami, C., Romanel, A. (2008). The BlenX Language: A Tutorial. In: Bernardo, M., Degano, P., Zavattaro, G. (eds) Formal Methods for Computational Systems Biology. SFM 2008. Lecture Notes in Computer Science, vol 5016. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68894-5_9
Download citation
DOI: https://doi.org/10.1007/978-3-540-68894-5_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-68892-1
Online ISBN: 978-3-540-68894-5
eBook Packages: Computer ScienceComputer Science (R0)