Skip to main content
SpringerLink
Log in

Multiple Representations of Biological Processes

  • Conference paper
Transactions on Computational Systems Biology VI

Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 4220))

Abstract

This paper describes representations of biological processes based on Rewriting Logic and Petri net formalisms and mappings between these representations used in the Pathway Logic Assistant. The mappings are shown to preserve properties of interest. In addition a relevant subnet transformation is defined, that specializes a Petri net model to a specific query to reduce the number of transitions that must be considered when answering the query. The transformation is shown to preserve the query in the sense that no answers are lost.

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. Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Meseguer, J., Sonmez, K.: Pathway Logic: Symbolic analysis of biological signaling. In: Proceedings of the Pacific Symposium on Biocomputing, pp. 400–412 (2002)

    Google Scholar 

  2. Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Talcott, C.: Pathway Logic: Executable models of biological networks. In: Fourth International Workshop on Rewriting Logic and Its Applications (WRLA 2002), Pisa, Italy, 2002, September 19 — 21, 2002. Electronic Notes in Theoretical Computer Science, vol. 71. Elsevier, Amsterdam (2002), http://www.elsevier.nl/locate/entcs/volume71.html

    Google Scholar 

  3. Talcott, C., Eker, S., Knapp, M., Lincoln, P., Laderoute, K.: Pathway logic modeling of protein functional domains in signal transduction. In: Proceedings of the Pacific Symposium on Biocomputing (2004)

    Google Scholar 

  4. Clavel, M., Durán, F., Eker, S., Lincoln, P., Marti-Oliet, N., Meseguer, J., Talcott, C.: Maude 2.0 Manual (2003), http://maude.cs.uiuc.edu

  5. Clavel, M., Durán, F., Eker, S., Lincoln, P., Martí-Oliet, N., Meseguer, J., Talcott, C.L.: The Maude 2.0 system. In: Nieuwenhuis, R. (ed.) RTA 2003. LNCS, vol. 2706, pp. 76–87. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  6. Mason, I.A., Talcott, C.L.: IOP: The InterOperability Platform & IMaude: An interactive extension of Maude. In: Fifth International Workshop on Rewriting Logic and Its Applications (WRLA 2004). Electronic Notes in Theoretical Computer Science. Elsevier, Amsterdam (2004)

    Google Scholar 

  7. Kohn, K.W.: Functional capabilities of molecular network components controlling the mammalian g1/s cell cycle phase transition. Oncogene 16, 1065–1075 (1998)

    Article  Google Scholar 

  8. Weng, G., Bhalla, U.S., Iyengar, R.: Complexity in biological signaling systems. Science 284, 92–96 (1999)

    Article  Google Scholar 

  9. Shvartsman, S.Y., Hagan, M.P., Yacoub, A., Dent, P., Wiley, H., Lauffenburger, D.: Autocrine loops with positive feedback enable context-dependent cell signaling. Am. J. Physiol. Cell Physiol. 282, 545–559 (2002)

    Google Scholar 

  10. Smolen, P., Baxter, D.A., Byrne, J.H.: Mathematical modeling of gene networks. Neuron 26, 567–580 (2000)

    Article  Google Scholar 

  11. Lok, L.: Software for signaling networks, electronic and cellular. Science STKE PE11 (2002)

    Google Scholar 

  12. Rao, C.V., Wolf, D.M., Arkin, A.P.: Control, exploitation and tolerance of intracellular noise. Nature 420, 231–237 (2002)

    Article  Google Scholar 

  13. Endy, D., Brent, R.: Modelling cellular behaviour. Nature 409, 391–395 (2001)

    Article  Google Scholar 

  14. Peterson, J.L.: Petri Nets: Properties, analysis, and applications. Prentice-Hall, Englewood Cliffs (1981)

    Google Scholar 

  15. Milner, R.: A Calculus of Communicating Systems. Springer, Heidelberg (1980)

    MATH  Google Scholar 

  16. Harel, D.: Statecharts: A visual formalism for complex systems. Science of Computer Programming 8, 231–274 (1987)

    Article  MATH  MathSciNet  Google Scholar 

  17. Meseguer, J.: Conditional Rewriting Logic as a unified model of concurrency. Theoretical Computer Science 96(1), 73–155 (1992)

    Article  MATH  MathSciNet  Google Scholar 

  18. Croes, D., Couche, F., van Helden, J., Wodak, S.: Path finding in metabolic networks: measuring functional distances between enzymes. In: Open Days in Biology, Computer Science and Mathematics JOBIM 2004 (2004)

    Google Scholar 

  19. Hofestädt, R.: A Petri net application to model metabolic processes. Syst. Anal. Mod. Simul. 16, 113–122 (1994)

    MATH  Google Scholar 

  20. Reddy, V.N., Liebmann, M.N., Mavrovouniotis, M.L.: Qualitative analysis of biochemical reaction systems. Comput. Biol. Med. 26, 9–24 (1996)

    Article  Google Scholar 

  21. Goss, P.J., Peccoud, J.: Quantitative modeling of stochastic systems in molecular biology using stochastic Petri nets. Proc. Natl. Acad. Sci. U S A 95, 6750–6755 (1998)

    Article  Google Scholar 

  22. Küffner, R., Zimmer, R., Lengauer, T.: Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 16, 825–836 (2000)

    Article  Google Scholar 

  23. Matsuno, H., Doi, A., Nagasaki, M., Miyano, S.: Hybrid Petri net representation of gene regulatory network. In: Pacific Symposium on Biocomputing, vol. 5, pp. 341–352 (2000)

    Google Scholar 

  24. Oliveira, J.S., Bailey, C.G., Jones-Oliveira, J.B., Dixon, D.A., Gull, D.W., Chandler, M.L.: An algebraic-combinatorial model for the identification and mapping of biochemical pathways. Bull. Math. Biol. 63, 1163–1196 (2001)

    Article  Google Scholar 

  25. Genrich, H., Küffner, R., Voss, K.: Executable Petri net models for the analysis of metabolic pathways. Int. J. STTT 3 (2001)

    Google Scholar 

  26. Oliveira, J.S., Bailey, C.G., Jones-Oliveira, J.B., Dixon, D.A., Gull, D.W., Chandler, M.L.: A computational model for the identification of biochemical pathways in the Krebs cycle. J. Computational Biology 10, 57–82 (2003)

    Article  Google Scholar 

  27. Zevedei-Oancea, I., Schuster, S.: Topological analysis of metabolic networks based on Petri net theory. Silico Biology 3 (2003)

    Google Scholar 

  28. Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the pi-calculus process algebra. In: Altman, R.B., Dunker, A.K., Hunter, L., Klein, T.E. (eds.) Pacific Symposium on Biocomputing, vol. 6, pp. 459–470. World Scientific, Singapore (2001)

    Google Scholar 

  29. Priami, C., Regev, A., Shapiro, E., Silverman, W.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters (in press), (2001)

    Google Scholar 

  30. Calder, M., Vyshemirsky, V., Gilbert, D., Orton, R.: Analysis of signalling pathways using the PRISM model checker. In: Plotkin, G. (ed.) Proceedings of the Third International Conference on Computational Methods in System Biology (CMSB 2005) (2005)

    Google Scholar 

  31. Regev, A., Panina, E., Silverman, W., Cardelli, L., Shaprio, E.: Bioambients: An abstraction for biological compartments (2003) (to appear TCS)

    Google Scholar 

  32. Nielson, F., Nielson, H.R., Priami, C., Rosa, D.: Control flow analysis for bioambients. In: BioConcur (2003)

    Google Scholar 

  33. Kam, N., Cohen, I.R., Harel, D.: The immune system as a reactive system: Modeling t cell activation with statecharts. In: Proc. Visual Languages and Formal Methods (VLFM 2001), pp. 15–22 (2001)

    Google Scholar 

  34. Efroni, S., Harel, D., Cohen, I.R.: Towards rigorous comprehension of biological complexity: Modeling, execution and visualization of thymic t-cell maturation. Genome Research (2003); Special issue on Systems Biology (in press)

    Google Scholar 

  35. Damm, W., Harel, D.: Breathing life into message sequence charts. Formal Methods in System Design 19(1) (2001)

    Google Scholar 

  36. Kam, N., Harel, D., Kugler, H.-J., Marelly, R., Pnueli, A., Hubbard, E.J.A., Stern, M.J.: Formal modeling of C. elegans development: A scenario-based approach. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 4–20. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  37. Prez-Jimnez, M., Romero-Campero, F.: Modelling EGFR signalling cascade using continuous membrane systems. In: Plotkin, G. (ed.) Proceedings of the Third International Conference on Computational Methods in System Biology (CMSB 2005) (2005)

    Google Scholar 

  38. Fages, F., Soliman, S., Chabrier-Rivier, N.: Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM. Journal of Biological Physics and Chemistry 4(2), 64–73 (2004)

    Article  Google Scholar 

  39. Chabrier-Rivier, N., Chiaverini, M., Danos, V., Fages, F., Schächter, V.: Modeling and querying biomolecular interaction networks. Theoretical Computer Science 351(1), 24–44 (2004)

    Google Scholar 

  40. Calzone, L., Chabrier-Rivier, N., Fages, F., Gentils, L., Soliman, S.: Machine learning bio-molecular interactions from temporal logic properties. In: Plotkin, G. (ed.) Proceedings of the Third International Conference on Computational Methods in System Biology (CMSB 2005) (2005)

    Google Scholar 

  41. Baral, C., Chancellor, K., Tran, N., Tran, N., Joy, A., Berens, M.: A knowledge based approach for representing and reasoning about signaling networks. Bioinformatics 20, 15–22 (2004)

    Article  Google Scholar 

  42. Shankland, C., Tran, N., Baral, C., Kolch, W.: Reasoning about the ERK signal transduction pathway using BioSigNet-RR. In: Plotkin, G. (ed.) Proceedings of the Third International Conference on Computational Methods in System Biology (CMSB 2005) (2005)

    Google Scholar 

  43. Hucka, M., Finney, A., Sauro, H., Bolouri, H., Doyle, J., Kitano, H.: The ERATO Systems Biology Workbench: Enabling Interaction and Exchange between Software Tools for Computational Biology. In: Proceedings of the Pacific Symposium on Biocomputing (2002)

    Google Scholar 

  44. BioSpice (2004), https://community.biospice.org/

  45. IBM Discoverylink (2004), http://publib-b.boulder.ibm.com/Redbooks.nsf/0/3c7a635147cf20d785256a540064e287?OpenDocument&Highlight=0,DiscoveryLink

  46. geneticXchange (2004), http://midas-10.cs.ndsu.nodak.edu/bio/ppts/chung.pdf

  47. Schmidt, A., Hall, A.: Guanine nucleotide exchange factors for rho gtpases: Turning on the switch. Genes Dev. 16, 1587–15609 (2002)

    Article  Google Scholar 

  48. Stehr, M.-O.: A rewriting semantics for algebraic nets. In: Girault, C., Valk, R. (eds.) Petri Nets for System Engineering – A Guide to Modelling, Verification, and Applications. Springer, Heidelberg (2000)

    Google Scholar 

  49. Schmidt, K.: LoLA A Low Level Analyser. In: Nielsen, M., Simpson, D. (eds.) ICATPN 2000. LNCS, vol. 1825, pp. 465–474. Springer, Heidelberg (2000)

    Chapter  Google Scholar 

  50. LoLA: Low Level Petri net Analyzer (2004), http://www.informatik.hu-berlin.de/~kschmidt/lola.html

  51. Schmidt, K.: Stubborn sets for standard properties. In: Donatelli, S., Kleijn, J. (eds.) ICATPN 1999. LNCS, vol. 1639, pp. 46–65. Springer, Heidelberg (1999)

    Chapter  Google Scholar 

  52. Porter, D.: An Interpreter for JLambda (2004), http://mcs.une.edu.au/~iop/Data/Papers/

Download references

Author information

Authors and Affiliations

  1. SRI International,  

    Carolyn Talcott

  2. Stanford University,  

    David L. Dill

Authors
  1. Carolyn Talcott
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David L. Dill
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Piazza Manci, 17, 38050, Povo, (TN), Italy

    Corrado Priami

  2. LFCS, University of Edinburgh,  

    Gordon Plotkin

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Talcott, C., Dill, D.L. (2006). Multiple Representations of Biological Processes. In: Priami, C., Plotkin, G. (eds) Transactions on Computational Systems Biology VI. Lecture Notes in Computer Science(), vol 4220. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11880646_10

Download citation

  • DOI: https://doi.org/10.1007/11880646_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-45779-4

  • Online ISBN: 978-3-540-46236-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation