Skip to main content
SpringerLink
Log in
Book cover

International School on Formal Methods for the Design of Computer, Communication and Software Systems

SFM 2008: Formal Methods for Computational Systems Biology pp 313–365Cite as

The BlenX Language: A Tutorial

  • Conference paper

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 5016))

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.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bravetti, M., Zavattaro, G.: Service oriented computing from a process algebraic perspective. Journal of Logic and Algebraic Programming 70(1), 3–14 (2007)

    Article  MATH  MathSciNet  Google Scholar 

  2. 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)

    Google Scholar 

  3. Danos, V., Laneve, C.: Formal molecular biology. In: TCS (2004)

    Google Scholar 

  4. Danos, V., Krivine, J.: Reversible communicating systems. In: Gardner, P., Yoshida, N. (eds.) CONCUR 2004. LNCS, vol. 3170, pp. 292–307. Springer, Heidelberg (2004)

    Google Scholar 

  5. 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)

    Google Scholar 

  6. Elowitz, M., Levine, A., Siggia, E., Swain, P.: Stochastic gene expression in a single cell. Science 297, 1183–1186 (2002)

    Article  Google Scholar 

  7. Elowitz, M.B., Leibler, S.: A synthetic oscillatory network of transcriptional regulators. Nature 403(20), 335–338 (2000)

    Article  Google Scholar 

  8. Errampalli, D., Priami, C., Quaglia, P.: A formal language for computational systems biology. OMICS: A Journal of Integrative Biology 8(4), 370–380 (2004)

    Google Scholar 

  9. Fall, C.P., Marland, E.S., Wagner, J.M., Tyson, J.J.: Computational Cell Biology. Springer, Heidelberg (2002)

    MATH  Google Scholar 

  10. 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)

    Article  MathSciNet  Google Scholar 

  11. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. The Journal of Chemical Physics 81, 2340–2361 (1977)

    Article  Google Scholar 

  12. Gillespie, D.T.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Phys. Chem. 22, 403–434 (1976)

    MathSciNet  Google Scholar 

  13. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), 2340–2361 (1977)

    Article  Google Scholar 

  14. 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)

    Google Scholar 

  15. Hoare, C.A.R.: A calculus of total correctness for communicating processes. Science of Computer Programming 1(1-2), 49–72 (1981)

    Article  MATH  MathSciNet  Google Scholar 

  16. Hume, D.: Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood 96, 2323–2328 (2000)

    Google Scholar 

  17. McAdams, H.H.: It is a noisy business! genetic regulation at the nanomolar scale. Trends Genet 15, 65–69 (1999)

    Article  Google Scholar 

  18. Milner, R.: Communication and Concurrency. Prentice-Hall, Inc., Englewood Cliffs (1989)

    MATH  Google Scholar 

  19. Phillips, A., Cardelli, L.: A correct abstract machine for the stochastic pi-calculus. In: Bioconcur 2004, ENTCS (August 2004)

    Google Scholar 

  20. Priami, C.: The stochastic π-calculus. The Computer Journal (38), 578–589 (1995)

    Google Scholar 

  21. Priami, C., Quaglia, P.: Beta binders for biological interactions. In: CMSB, pp. 20–33 (2004)

    Google Scholar 

  22. 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)

    Google Scholar 

  23. Priami, C., Quaglia, P.: Modeling the dynamics of bio-systems. Briefings in Bioinformatics 5(3), 259–269 (2004)

    Article  Google Scholar 

  24. 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)

    Article  MATH  MathSciNet  Google Scholar 

  25. Ross, I., Browne, C., Hume, D.: Transcription of individual genes in eukaryotic cells occurs randomly and infrequently. In: Immunol Cell Biol. (1994)

    Google Scholar 

  26. Spudich, J., Koshland, D.E.J.: Non-genetic individuality: Chance in the single cell. Nature (1976)

    Google Scholar 

  27. Stock, A.M., Robinson, V.L., Goudreau, P.N.: Two-component signal transduction. Annu. Rev. Biochem. (69), 183–215 (2000)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CoSBi, Trento, Italy

    Lorenzo Dematté, Corrado Priami & Alessandro Romanel

  2. Dipartimento di Ingegneria e Scienza dell’Informazione, Università di Trento, Italy

    Lorenzo Dematté, Corrado Priami & Alessandro Romanel

Authors
  1. Lorenzo Dematté
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Corrado Priami
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alessandro Romanel
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Marco Bernardo Pierpaolo Degano Gianluigi Zavattaro

Rights and permissions

Reprints 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)

Publish with us

Policies and ethics

Search

Navigation