Skip to main content

Composability: Perspectives in Ecological Modeling

  • Conference paper
Algebraic and Numeric Biology

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6479))

  • 567 Accesses

Abstract

The multiplicity of ecological interactions acting in parallel calls for novel computational approaches in modeling ecosystem dynamics. Composability, a key property of process algebra-based models can help to manage complexity and offer scalable solutions in ecological modeling. We discuss and illustrate how composability of process algebra language constructs can be used as a language aid in the construction of complicated ecosystem models.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 54.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 69.99
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. Allen, T.F.H., Starr, T.B.: Hierarchy: Perspectives for Ecological Complexity. The University of Chicago Press (1982)

    Google Scholar 

  2. Bertness, M.D., Callaway, R.: Positive interaction in communities. Trends in Ecology and Evolution 9, 191–193 (1994)

    Article  Google Scholar 

  3. Billick, I., Case, T.J.: Higher order interactions in ecological communities: what are they and how can they be detected? Ecology 75, 1529–1543 (1994)

    Article  Google Scholar 

  4. DeAngelis, D.L., Gross, L.J.: Individual-based Models and Approaches in Ecology. Chapman and Hall, New York (1992)

    Book  Google Scholar 

  5. Degano, P., Prandi, D., Priami, C., Quaglia, P.: Beta binders for biological quantitative experiments. ENTCS 164(3), 101–117 (2005)

    Google Scholar 

  6. Dematté, L., Larcher, R., Palmisano, A., Priami, C., Romanel, A.: Programming biology in BlenX. Systems Biology for Signaling Networks 1, 777–821 (2010)

    Article  Google Scholar 

  7. Dematté, L., Priami, C., Romanel, A.: The beta workbench: a computational tool to study the dynamics of biological systems. Briefings in Bioinformatics 9, 437–449 (2008)

    Article  Google Scholar 

  8. Dematté, L., Priami, C., Romanel, A.: The Blenx Language: A Tutorial. In: Bernardo, M., Degano, P., Tennenholtz, M. (eds.) SFM 2008. LNCS, vol. 5016, pp. 313–365. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  9. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81, 2340–2361 (1977)

    Article  Google Scholar 

  10. Grimm, V.: Ten years of individual-based modelling in ecology: what have we learned and what could we learn in the future? Ecological Modelling 115, 129–148 (1999)

    Article  Google Scholar 

  11. Grimm, V., Berger, U., Bastiansen, F., Eliassen, S., Ginot, V., Giske, J., Goss-Custard, J., Grand, T., Heinz, S.K., Huse, G., Huth, A., Jepsen, J.U., Jørgensen, C., Mooij, W.M., Müller, B., Peer, G., Piou, C., Railsback, S.F., Robbins, A.M., Robbins, M.M., Rossmanith, E., Rüger, N., Strand, E., Souissim, S., Stillman, R.A., Vabø, R., Visser, U., DeAngelis, D.L.: A standard protocol for describing individual-based and agent-based models. Ecological Modelling 198(1-2), 115–126 (2006)

    Article  Google Scholar 

  12. Gronewold, A., Sonnenschein, M.: Event-based modelling of ecological systems with asynchronous cellular automata. Ecological Modelling 108(1-3), 37–52 (1998)

    Article  Google Scholar 

  13. Holt, R.D.: Predation, apparent competition, and the structure of prey communities. Theoretical Population Biology 12(2), 197–229 (1977)

    Article  MathSciNet  Google Scholar 

  14. Kahramanoğulları, O., Jordán, F., Lynch, J.: CoSBiLab LIME: A language interface for stochastic dynamical modelling in ecology. Environmental Modelling and Software 26, 685–687 (2011)

    Article  Google Scholar 

  15. Kitano, H.: Systems biology: A brief overview. Science 295, 1662–1664 (2002)

    Article  Google Scholar 

  16. Levin, S.A.: Ecosystems and the biosphere as complex adaptive systems. Ecosystems 1(5), 431–436 (1998)

    Article  Google Scholar 

  17. Levin, S.A., Grenfell, B., Hastings, A., Perelson, A.S.: Mathematical and computational challenges in population biology and ecosystems science. Science 275(5298), 334–343 (1997)

    Article  MATH  Google Scholar 

  18. Lotka, A.J.: Fluctuations in the abundance of a species considered mathematically. Nature 119, 12 (1927)

    Google Scholar 

  19. Olff, H., Alonso, D., Berg, M.P., Eriksson, B.K., Loreau, M., Piersma, T., Rooney, N.: Parallel ecological networks in ecosystems. Philosophical Transactions of Royal Society B 364(1524), 1755–1779 (2009)

    Article  Google Scholar 

  20. Pimm, S.L.: Food web design and the effects of species deletion. Oikos 35, 139–149 (1980)

    Article  Google Scholar 

  21. Pimm, S.L.: The Balance of Nature? Ecological Issues in the Conservation of Species and Communities. The University of Chicago Press (1991)

    Google Scholar 

  22. Platt, T., Mann, K.H., Ulanowicz, R.E.: Mathematical Models in Biological Oceanography. The UNESCO Press (1981)

    Google Scholar 

  23. Powell, C.R., Boland, R.P.: The effects of stochastic population dynamics on food web structure. Journal of Theoretical Biology 257(1), 170–180 (2009)

    Article  MathSciNet  Google Scholar 

  24. Priami, C.: Stochastic π-calculus. The Computer Journal 38(6), 578–589 (1995)

    Article  Google Scholar 

  25. Priami, C.: Algorithmic systems biology. Communications of the ACM 52(5), 80–89 (2009)

    Article  Google Scholar 

  26. Priami, C., Quaglia, P.: Modelling the dynamics of biosystems. Briefings in Bioinformatics 5(3), 259–269 (2004)

    Article  Google Scholar 

  27. Regev, A., Shapiro, E.: Cellular abstractions: Cells as computation. Nature 419, 343 (2002)

    Article  Google Scholar 

  28. Seth, A.K.: The ecology of action selection: insights from artificial life. Philosophical Transactions of Royal Society B 362(1485), 1545–1558 (2007)

    Article  Google Scholar 

  29. Ulanowicz, R.E.: Growth and Development: Ecosystems Phenomenology. Springer, Heidelberg (1986)

    Book  MATH  Google Scholar 

  30. Valentini, R., Jordán, F.: CoSBiLab Graph: the network analysis module of CoSBiLab. Environmental Modelling and Software 25, 886–888 (2010)

    Article  Google Scholar 

  31. Vasas, V., Jordán, F.: Topological keystone species in ecological interaction networks: considering link quality and non-trophic effects. Ecological Modelling 196(3-4), 365–378 (2006)

    Article  Google Scholar 

  32. Volterra, V.: Fluctuations in the abundance of species considered mathematically. Nature 118, 558–560 (1926)

    Article  MATH  Google Scholar 

  33. Wootton, J.T.: Indirect effects and habitat use in an intertidal community: interaction chains and interaction modifications. The American Naturalist 141(1), 71–89 (1993)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Kahramanoğulları, O., Jordán, F., Priami, C. (2012). Composability: Perspectives in Ecological Modeling. In: Horimoto, K., Nakatsui, M., Popov, N. (eds) Algebraic and Numeric Biology. Lecture Notes in Computer Science, vol 6479. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28067-2_8

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-28067-2_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-28066-5

  • Online ISBN: 978-3-642-28067-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics