Skip to main content
SpringerLink
Log in
SpringerLink
Log in

Some Thoughts on the Semantics of Biocharts

  • Chapter
Time for Verification

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6200))

Abstract

This paper combines three topics to which Amir Pnueli contributed significantly: the semantics of languages for concurrency, the semantics of statecharts, and reactive and hybrid systems. It is also no accident that the main motivation of our paper comes from biological systems: in recent years Amir became interested in these too. In [KLH10] we introduced Biocharts, a fully executable, two-tier compound visual language for modeling complex biological systems. The high-level part of the language is a version of statecharts, which have been shown to be successful in software and systems engineering. These statecharts can then be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the biological pathways and networks. The purpose of [KLH10] was to present the main concepts through a biological example and to illustrate the feasibility and usefulness of the approach. Here we discuss some of the questions that arise when one attempts to provide a careful definition of the semantics of Biocharts. We also compare the main requirements needed in a language for modeling biology with the way statecharts are used in software and system engineering.

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

Access this chapter

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 99.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Efroni, S., Harel, D., Cohen, I.R.: Emergent Dynamics of Thymocyte Development and Lineage Determination. PLoS Computational Biology 3(1), 3–13 (2007)

    Article  Google Scholar 

  2. Endy, D.: Foundations for engineering biology. Nature 438, 449–453 (2005)

    Article  Google Scholar 

  3. Fisher, J., Piterman, N., Hubbard, E.J.A., Stern, M.J., Harel, D.: Computational Insights into C. elegans Vulval Development. Proceedings of the National Academy of Sciences 102(6), 1951–1956 (2005)

    Article  Google Scholar 

  4. Harel, D.: Statecharts: A visual formalism for complex systems. Science of Computer Programming 8, 231–274 (1987); Preliminary version: Technical Report CS84-05, The Weizmann Institute of Science, Rehovot, Israel (February 1984)

    Google Scholar 

  5. Harel, D.: A Turing-Like Test for Biological Modeling. Nature Biotechnology 23, 495–496 (2005)

    Article  Google Scholar 

  6. Harel, D., Gery, E.: Executable object modeling with statecharts. Computer 30(7), 31–42 (1997); Also in: Proc.18th Int. Conf. Soft. Eng., Berlin, pp. 246–257. IEEE Press, Los Alamitos (March 1996)

    Article  Google Scholar 

  7. Harel, D., Kugler, H.: The RHAPSODY Semantics of Statecharts (or, On the Executable Core of the UML). In: Ehrig, H., Damm, W., Desel, J., Große-Rhode, M., Reif, W., Schnieder, E., Westkämper, E. (eds.) INT 2004. LNCS, vol. 3147, pp. 325–354. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  8. Harel, D., Naamad, A.: The statemate semantics of statecharts. ACM Trans. Software Engin. Methods 5(4), 293–333 (1996)

    Article  Google Scholar 

  9. Harel, D., Pnueli, A.: On the development of reactive systems. In: Apt, K.R. (ed.) Logics and Models of Concurrent Systems, New York. NATO ASI Series, vol. F-13, pp. 477–498. Springer, Heidelberg (1985)

    Chapter  Google Scholar 

  10. Kam, N., Cohen, I.R., Harel, D.: The immune system as a reactive system: Modeling t cell activation with statecharts. In: IEEE International Symposium on Human-Centric Computing Languages and Environments (HCC 2001), pp. 15–22. IEEE Computer Society Press, Los Alamitos (2001)

    Google Scholar 

  11. Kugler, H., Larjo, A., Harel, D.: Biocharts: A Visual Formalism for Complex Biological Systems. J. R. Soc. Interface (2010)

    Google Scholar 

  12. Setty, Y., Cohen, I.R., Dor, Y., Harel, D.: Four-Dimensional Realistic Modeling of Pancreatic Organogenesis. Proceedings of the National Academy of Sciences (2008)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. The Weizmann Institute of Science, Rehovot, Israel

    David Harel

  2. Microsoft Research, Cambridge, UK

    Hillel Kugler

Authors
  1. David Harel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hillel Kugler
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Computer Science Department, Stanford University, 94305, Stanford, CA, USA

    Zohar Manna

  2. Department of Computer Science, Bar Ilan University, 52900, Ramat Gan, Israel

    Doron A. Peled

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Harel, D., Kugler, H. (2010). Some Thoughts on the Semantics of Biocharts. In: Manna, Z., Peled, D.A. (eds) Time for Verification. Lecture Notes in Computer Science, vol 6200. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13754-9_9

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-13754-9_9

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-13753-2

  • Online ISBN: 978-3-642-13754-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation