Skip to main content
SpringerLink
Log in

On Timed Models of Gene Networks

  • Conference paper
Formal Modeling and Analysis of Timed Systems (FORMATS 2007)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4763))

Abstract

We present a systematic translation from timed models of genetic regulatory networks into products of timed automata to which one can apply verification tools in order learn about the possible qualitative behaviors of the network under a whole range of uncertain delay parameters. We have developed a tool chain starting from a high-level description of the network down to an exhaustive analysis of its behavior. We have demonstrated the potential applicability of this framework on several examples.

This work was partially supported by the French-Israeli project Computational Modeling of Incomplete Biological Regulatory Networks.

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 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

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Asarin, E., Dang, T., Frehse, G., Girard, A., Le Guernic, C., Maler, O.: Recent Progress in Continuous and Hybrid Reachability Analysis. In: CACSD (2006)

    Google Scholar 

  2. Behrmann, G., David, A., Larsen, K.G., Möller, O., Pettersson, P., Yi, W.: UPPAAL - Present and future. In: CDC 2001 (2001)

    Google Scholar 

  3. Ben Salah, R., Bozga, M., Maler, O.: On Timing Analysis of Combinational. In: Larsen, K.G., Niebert, P. (eds.) FORMATS 2003. LNCS, vol. 2791, pp. 204–219. Springer, Heidelberg (2004)

    Google Scholar 

  4. Bozga, M., Graf, S., Ober, I., Ober, I., Sifakis, J.: The IF toolset. In: SFM (2004)

    Google Scholar 

  5. Bozga, M., Jianmin, H., Maler, O., Yovine, S.: Verification of Asynchronous Circuits using Timed Automata. ENTCS 65 (2002)

    Google Scholar 

  6. Bozga, M., Maler, O., Tripakis, S.: Efficient Verification of Timed Automata using Dense and Discrete Time Semantics. In: Pierre, L., Kropf, T. (eds.) CHARME 1999. LNCS, vol. 1703, pp. 125–141. Springer, Heidelberg (1999)

    Google Scholar 

  7. Daws, C., Olivero, A., Tripakis, S., Yovine, S.: The tool KRONOS. In: Alur, R., Sontag, E.D., Henzinger, T.A. (eds.) Hybrid Systems III. LNCS, vol. 1066, pp. 208–219. Springer, Heidelberg (1996)

    Chapter  Google Scholar 

  8. Frehse, G.: PHAVer: Algorithmic Verification of Hybrid Systems Past HyTech. In: Morari, M., Thiele, L. (eds.) HSCC 2005. LNCS, vol. 3414, pp. 258–273. Springer, Heidelberg (2005)

    Google Scholar 

  9. Henzinger, T.A, Ho, P.-H., Wong-Toi, H.: Algorithmic Analysis of Nonlinear Hybrid Systems. IEEE TRans. on Automatic Control 43, 540–554 (1998)

    Article  MATH  MathSciNet  Google Scholar 

  10. Hooshangi, S., Thiberge, S., Weiss, R.: Ultrasensitivity and Noise Propagation in a Synthetic Transcriptional Cascade. PNAS 102, 3581–3586 (2005)

    Article  Google Scholar 

  11. Kauffman, S.A.: Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets. J. of Theoretical Biology 22, 437–467 (1969)

    Article  MathSciNet  Google Scholar 

  12. Maler, O., Pnueli, A.: Timing Analysis of Asynchronous Circuits using Timed Automata. In: Camurati, P.E., Eveking, H. (eds.) CHARME 1995. LNCS, vol. 987, pp. 189–205. Springer, Heidelberg (1995)

    Google Scholar 

  13. Ropers, D., de Jong, H., Page, M., Schneider, D., Geiselmann, J.: Qualitative Simulation of the Carbon Starvation Response in Escherichia coli. BioSystems 84, 124–152 (2006)

    Article  Google Scholar 

  14. Siebert, H., Bockmayr, A.: Incorporating Time Delays into the Logical Analysis of Gene Regulatory Networks. In: Priami, C. (ed.) CMSB 2006. LNCS (LNBI), vol. 4210, pp. 169–183. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  15. Stursberg, O., Kowalewski, S., Engell, S.: On the Generation of Timed Discrete Approximations for Continuous Systems. Mathematical and Computer Modelling of Dynamical Systems 6, 51–70 (2000)

    Article  MATH  Google Scholar 

  16. Thieffry, D., Thomas, R.: Dynamical Behaviour of Biological Regulatory Networks: II. Immunity Control in Bacteriophage Lambda. Bulletin of Mathematical Biology 57, 277–295 (1995)

    MATH  Google Scholar 

  17. Thomas, R., D’Ari, R.: Biological Feedback. CRC Press, Boca Raton (1990)

    MATH  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. VERIMAG, 2, av. de Vignate, 38610 Gieres, France

    Grégory Batt, Ramzi Ben Salah & Oded Maler

Authors
  1. Grégory Batt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ramzi Ben Salah
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Oded Maler
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Jean-François Raskin P. S. Thiagarajan

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Batt, G., Ben Salah, R., Maler, O. (2007). On Timed Models of Gene Networks. In: Raskin, JF., Thiagarajan, P.S. (eds) Formal Modeling and Analysis of Timed Systems. FORMATS 2007. Lecture Notes in Computer Science, vol 4763. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75454-1_5

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-75454-1_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-75453-4

  • Online ISBN: 978-3-540-75454-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation