Skip to main content
SpringerLink
Log in

Process Ordering in a Process Calculus for Spatially-Explicit Ecological Models

  • Conference paper
  • First Online:
Software Engineering and Formal Methods (SEFM 2013)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 8368))

Included in the following conference series:

Abstract

In this paper we extend palps, a process calculus proposed for the spatially-explicit individual-based modeling of ecological systems, with the notion of a policy. A policy is an entity for specifying orderings between the different activities within a system. It is defined externally to a palps model as a partial order which prescribes the precedence order between the activities of the individuals of which the model is comprised. The motivation for introducing policies is twofold: one the one hand, policies can help to reduce the state-space of a model; on the other hand, they are useful for exploring the behavior of an ecosystem under different assumptions on the ordering of events within the system. To take account of policies, we refine the semantics of palps via a transition relation which prunes away executions that do not respect the defined policy. Furthermore, we propose a translation of palps into the probabilistic model checker prism. We illustrate our framework by applying prism on palps models with policies for conducting simulation and reachability analysis.

This work was carried out during the tenure by the second author of an ERCIM “Alain Bensoussan” Fellowship Programme. The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no 246016.

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 EPUB and 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

References

  1. Online PRISM documentation. http://www.prismmodelchecker.org/doc/

  2. Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Pardini, G.: Spatial calculus of looping sequences. Theoret. Comput. Sci. 412(43), 5976–6001 (2011)

    Article  MATH  MathSciNet  Google Scholar 

  3. Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Troina, A.: A calculus of looping sequences for modelling microbiological systems. Fund. Inf. 72(1–3), 21–35 (2006)

    MATH  MathSciNet  Google Scholar 

  4. Berec, L.: Techniques of spatially-explicit individual-based models: construction, simulation, and mean-field analysis. Ecol. Model. 150, 55–81 (2002)

    Article  Google Scholar 

  5. Besozzi, D., Cazzaniga, P., Pescini, D., Mauri, G.: Modelling metapopulations with stochastic membrane systems. BioSystems 91(3), 499–514 (2008)

    Article  Google Scholar 

  6. Bioglio, L., Calcagno, C., Coppo, M., Damiani, F., Sciacca, E., Spinella, S., Troina, A.: A Spatial Calculus of Wrapped Compartments. CoRR, abs/1108.3426 (2011)

    Google Scholar 

  7. Cardona, M., Colomer, M.A., Margalida, A., Palau, A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Sanuy, D.: A computational modeling for real ecosystems based on P systems. Nat. Comput. 10(1), 39–53 (2011)

    Article  MATH  MathSciNet  Google Scholar 

  8. Chen, Q., Ye, F., Li, W.: Cellular-automata-based ecological and ecohydraulics modelling. J. Hydroinf. 11(3/4), 252–272 (2009)

    Article  Google Scholar 

  9. Ciocchetta, F., Hillston, J.: Bio-PEPA: a framework for the modelling and analysis of biological systems. Theoret. Comput. Sci. 410(33–34), 3065–3084 (2009)

    Article  MATH  MathSciNet  Google Scholar 

  10. Cleaveland, R., Lüttgen, G., Natarajan, V.: Priority in process algebras. Technical report, Langley Research Center, NASA, USA (1999)

    Google Scholar 

  11. Drábik, P., Maggiolo-Schettini, A., Milazzo, P.: Modular verification of interactive systems with an application to biology. Sci. Ann. Comp. Sci. 21(1), 39–72 (2011)

    Google Scholar 

  12. Gerber, L.R., VanBlaricom, G.R.: Implications of three viability models for the conservation status of the western population of Steller sea lions (Eumetopias jubatus). Biol. Conserv. 102, 261–269 (2001)

    Article  Google Scholar 

  13. Hoare, C.A.R.: Communicating Sequential Processes. Prentice-Hall, Upper Saddle River (1985)

    MATH  Google Scholar 

  14. McCaig, C., Fenton, A., Graham, A., Shankland, C., Norman, R.: Using process algebra to develop predator–prey models of within-host parasite dynamics. J. Theor. Biol. 329, 74–81 (2013)

    Article  MathSciNet  Google Scholar 

  15. McCaig, C., Norman, R., Shankland, C.: Process algebra models of population dynamics. In: Horimoto, K., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds.) AB 2008. LNCS, vol. 5147, pp. 139–155. Springer, Heidelberg (2008)

    Google Scholar 

  16. McCaig, C., Norman, R., Shankland, C.: From individuals to populations: a mean field semantics for process algebra. Theoret. Comput. Sci. 412(17), 1557–1580 (2011)

    Article  MATH  MathSciNet  Google Scholar 

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

    Book  MATH  Google Scholar 

  18. Milner, R., Parrow, J., Walker, D.: A calculus of mobile processes, parts 1 and 2. Inf. Comput. 100, 1–77 (1992)

    Article  MATH  MathSciNet  Google Scholar 

  19. Norman, G., Palamidessi, C., Parker, D., Wu, P.: Model checking probabilistic and stochastic extensions of the \(\pi \)-calculus. IEEE Trans. Softw. Eng. 35(2), 209–223 (2009)

    Article  Google Scholar 

  20. Pardini, G.: Formal modelling and simulation of biological systems with spatiality. Ph.D thesis, University of Pisa (2011)

    Google Scholar 

  21. Pearson, R.G., Dawson, T.P.: Long-distance plant dispersal and habitat fragmentation: identifying conservation targets for spatial landscape planning under climate change. Biol. Conserv. 123, 389–401 (2005)

    Article  Google Scholar 

  22. Pescini, D., Besozzi, D., Mauri, G., Zandron, C.: Dynamical probabilistic P-systems. J. Found. Comput. Sci. 17(1), 183–204 (2006)

    Article  MATH  MathSciNet  Google Scholar 

  23. Philippou, A., Toro, M.: Process ordering in a process calculus for spatially-explicit ecological models. Technical report, Department of Computer Science, University of Cyprus, 2013. http://www.cs.ucy.ac.cy/~annap/pt-tr.pdf

  24. Philippou, A., Toro, M., Antonaki, M.: Simulation and verification for a process calculus for spatially-explicit ecological models. Sci. Ann. Comput. Sci. 23(1), 119–167 (2013)

    Article  MathSciNet  Google Scholar 

  25. Păun, G.: Computing with membranes (P systems): an introduction. In: Rozenberg, G., Salomaa, A. (eds.) Current Trends in Theoretical Computer Science, pp. 845–866. World Scientific, Singapore (2001)

    Google Scholar 

  26. Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: BioAmbients: an abstraction for biological compartments. Theoret. Comput. Sci. 325(1), 141–167 (2004)

    Article  MATH  MathSciNet  Google Scholar 

  27. Ruxton, G.D., Saravia, L.A.: The need for biological realism in the updating of cellular automata models. Ecol. Model. 107, 105–112 (1998)

    Article  Google Scholar 

  28. Sumpter, D.J.T., Broomhead, D.S.: Relating individual behaviour to population dynamics. Proc. Roy. Soc. B: Biol. Sci. 268(1470), 925–932 (2001)

    Article  Google Scholar 

  29. Tofts, C.: Processes with probabilities, priority and time. Formal Aspects Comput. 6, 536–564 (1994)

    Article  MATH  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science, University of Cyprus, Nicosia, Cyprus

    Anna Philippou & Mauricio Toro

Authors
  1. Anna Philippou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mauricio Toro
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mauricio Toro .

Editor information

Editors and Affiliations

  1. Brunel University, Uxbridge, Middlesex, United Kingdom

    Steve Counsell

  2. Universidad Complutense de Madrid, Madrid, Spain

    Manuel Núñez

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this paper

Cite this paper

Philippou, A., Toro, M. (2014). Process Ordering in a Process Calculus for Spatially-Explicit Ecological Models. In: Counsell, S., Núñez, M. (eds) Software Engineering and Formal Methods. SEFM 2013. Lecture Notes in Computer Science(), vol 8368. Springer, Cham. https://doi.org/10.1007/978-3-319-05032-4_25

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-05032-4_25

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-05031-7

  • Online ISBN: 978-3-319-05032-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation