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.
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Allen, T.F.H., Starr, T.B.: Hierarchy: Perspectives for Ecological Complexity. The University of Chicago Press (1982)
Bertness, M.D., Callaway, R.: Positive interaction in communities. Trends in Ecology and Evolution 9, 191–193 (1994)
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)
DeAngelis, D.L., Gross, L.J.: Individual-based Models and Approaches in Ecology. Chapman and Hall, New York (1992)
Degano, P., Prandi, D., Priami, C., Quaglia, P.: Beta binders for biological quantitative experiments. ENTCS 164(3), 101–117 (2005)
Dematté, L., Larcher, R., Palmisano, A., Priami, C., Romanel, A.: Programming biology in BlenX. Systems Biology for Signaling Networks 1, 777–821 (2010)
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)
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)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81, 2340–2361 (1977)
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)
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)
Gronewold, A., Sonnenschein, M.: Event-based modelling of ecological systems with asynchronous cellular automata. Ecological Modelling 108(1-3), 37–52 (1998)
Holt, R.D.: Predation, apparent competition, and the structure of prey communities. Theoretical Population Biology 12(2), 197–229 (1977)
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)
Kitano, H.: Systems biology: A brief overview. Science 295, 1662–1664 (2002)
Levin, S.A.: Ecosystems and the biosphere as complex adaptive systems. Ecosystems 1(5), 431–436 (1998)
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)
Lotka, A.J.: Fluctuations in the abundance of a species considered mathematically. Nature 119, 12 (1927)
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)
Pimm, S.L.: Food web design and the effects of species deletion. Oikos 35, 139–149 (1980)
Pimm, S.L.: The Balance of Nature? Ecological Issues in the Conservation of Species and Communities. The University of Chicago Press (1991)
Platt, T., Mann, K.H., Ulanowicz, R.E.: Mathematical Models in Biological Oceanography. The UNESCO Press (1981)
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)
Priami, C.: Stochastic π-calculus. The Computer Journal 38(6), 578–589 (1995)
Priami, C.: Algorithmic systems biology. Communications of the ACM 52(5), 80–89 (2009)
Priami, C., Quaglia, P.: Modelling the dynamics of biosystems. Briefings in Bioinformatics 5(3), 259–269 (2004)
Regev, A., Shapiro, E.: Cellular abstractions: Cells as computation. Nature 419, 343 (2002)
Seth, A.K.: The ecology of action selection: insights from artificial life. Philosophical Transactions of Royal Society B 362(1485), 1545–1558 (2007)
Ulanowicz, R.E.: Growth and Development: Ecosystems Phenomenology. Springer, Heidelberg (1986)
Valentini, R., Jordán, F.: CoSBiLab Graph: the network analysis module of CoSBiLab. Environmental Modelling and Software 25, 886–888 (2010)
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)
Volterra, V.: Fluctuations in the abundance of species considered mathematically. Nature 118, 558–560 (1926)
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)
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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
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DOI: https://doi.org/10.1007/978-3-642-28067-2_8
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