Tytuł artykułu
Wybrane pełne teksty z tego czasopisma
Identyfikatory
Warianty tytułu
Języki publikacji
Abstrakty
We consider trophic networks, a kind of networks used in ecology to represent feeding interactions (what-eats-what) in an ecosystem. Starting from the observation that trophic networks can be naturally modelled as Petri nets, we explore the possibility of using Petri nets for the analysis and simulation of trophic networks. We define and discuss different continuous Petri net models, whose level of accuracy depends on the information available for the modelled trophic network. The simplest Petri net model we construct just relies on the topology of the network. We also propose a technique for deriving a more refined model that embeds into the Petri net the known constraints on the transition rates that represent the knowledge on metabolism and diet of the species in the network. Finally, if the information of the biomass amounts for each species at steady state is available, we discuss a way of further refining the Petri net model in order to represent dynamic behaviour. We apply our Petri net technology to a case study of the Venice lagoon and analyse the results.
Słowa kluczowe
Wydawca
Czasopismo
Rocznik
Tom
Strony
27--52
Opis fizyczny
Bibliogr. 40 poz., rys., tab., wykr.
Twórcy
autor
- Dipartimento di Matematica, Università di Padova, Italy
autor
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari di Venezia, Italy
autor
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari di Venezia, Italy
autor
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari di Venezia, Italy
autor
- Computer Science Institute, Brandenburg University of Technology, Cottbus, Germany
autor
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari di Venezia, Italy
Bibliografia
- [1] Jordán F, Scotti M, Priami C. Process algebra-based computational tools in ecological modelling. Ecological Complexity, 2011;8(4):357-363. URL https://doi.org/10.1016/j.ecocom.2011.07.006.
- [2] Murata T. Petri Nets: Properties, Analysis, and Applications. Proceedings of IEEE, 1989;77(4):541-580.
- [3] Esparza J, Nielsen M. Decidability issues for Petri Nets - a survey. Journal Inform. Process. Cybernet. EIK, 1994;30(3):143-160.
- [4] Petri Nets Tools. URL http://www.informatik.uni-hamburg.de/TGI/PetriNets/tools.
- [5] Ulanowicz RE. Quantitative Methods for Ecological Network Analysis. Computational Biology and Chemistry, 2004;28(5-6):321-339. doi:10.1016/j.compbiolchem.2004.09.001.
- [6] Ulanowicz RE. Quantitative Methods for Ecological Network Analysis and Its Application to Coastal Ecosystems. Treatise on Estuarine and Coastal Science, 2011;9:35-57. URL https://doi.org/10.1016/B978-0-12-374711-2.00904-9.
- [7] Popova-Zeugmann L, Heiner M, Koch I. Timed Petri Nets for modelling and analysis of biochemical networks. Fundamenta Informaticae, 2005;67:149-162. URL http://dl.acm.org/citation.cfm?id=2370176.2370188.
- [8] Lotka AJ. Elements of Physical Biology. Williams and Wilkins, 1925.
- [9] Volterra V. Variazioni e fluttuazioni del numero d’individui in specie animali conviventi. Memorie Accademia dei Lincei, 1926;2:31-113. URL https://books.google.pl/books?id=1ai9PgAACAAJ.
- [10] Brigolin D, Pastres R. Influence of Intra-Seasonal Variability of Metabolic Rates on the Output of a Steady-State Food Web Model. In: F J, SE J (eds.), Models of the Ecological Hierarchy: From Molecules to the Ecosphere, Developments in Environmental Modelling, Elsevier, 2012 pp. 165-179. doi:10.1016/B978-0-444-59396-2.00011-0.
- [11] Baldan P, Bocci M, Brigolin D, Cocco N, Simeoni M. Petri nets for modelling and analyzing trophic networks. In: Wagler A, Heiner M (eds.), BioPPN 2015, Biological Processes & Petri Nets, volume 1373 of CEUR Workshop Proceedings. ceur-ws.org, 2015. URL http://ceur-ws.org/Vol-1373/paper2.pdf.
- [12] Vézina A, Platt T. Food web dynamics in the ocean. I. Best-estimates of flow networks using inverse methods. Marine Ecology - Progress Series, 1988;42:269-287. doi:10.3354/meps042269.
- [13] van Oevelen D, van den Meersche K, Meysman FR, Soetaert K, Middelburg J, Vézina A. Quantifying Food Web Flows Using Linear Inverse Models. Ecosystems, 2010;13(1):32-45. doi:10.1007/s10021-009-9297-6.
- [14] Christensen V. ECOPATH a software balancing steady-state models and calculating network characteristics. Ecological modelling, 1992;61(3-4):169-185. URL https://doi.org/10.1016/0304-3800(92)90016-8.
- [15] Christensen V, Walters CJ. Ecopath with Ecosim: methods, capabilities and limitations. Ecological modelling, 2004;172(2-4):109-139. URL https://doi.org/10.1016/j.ecolmodel.2003.09.003.
- [16] Christensen V, Walters CJ, Pauly D. Ecopath with Ecosim: a users guide. Fisheries Centre, University of British Columbia, Vancouver, 2005.
- [17] Heymans JJ, Ulanowicz RE, Bondavalli C. Network analysis of the South Florida Everglades graminoid marshes and comparison with nearby cypress ecosystems. Ecological Modelling, 2002;149(1-2):5-23. URL https://doi.org/10.1016/S0304-3800(01)00511-7.
- [18] Vasconcellos M, Mackinson S, Sloman K, Pauly D. The stability of trophic mass-balance models of marine ecosystems: a comparative analysis. Ecological Modelling, 1997;100(1-3):125-134. URLhttps://doi.org/10.1016/S0304-3800(97)00150-6.
- [19] Allesina S, Ulanowicz RE. Cycling in ecological networks: Finn’s index revisited. Computational Biology and Chemistry, 2004;28(3):227-233. URL https://doi.org/10.1016/j.compbiolchem.2004.04.002.
- [20] Odum E. The strategy of Ecosystem development. Science, 1969;164(3877):262-270. doi:10.1126/science.164.3877.262.
- [21] Finn J. Measures of ecosystem structure and function derived from the analysis of flows. Journal of Theoretical Biology, 1976;56(2):363-380.
- [22] Han B. On several measures concerning flow variables in ecosystems. Ecological Modelling, 1997;104(2-3):289-302. URL https://doi.org/10.1016/S0304-3800(97)00137-3.
- [23] Heiner M, Gilbert D, Donaldson R. Petri Nets for Systems and Synthetic Biology, volume 5016 of LNCS, Springer, 2008 pp. 215-264. doi:10.1007/978-3-540-68894-5_7.
- [24] Schrijver A. Theory of linear and integer programming. Interscience series in discrete mathematics and optimization. Wiley, 1999. ISBN:978-0-471-98232-6.
- [25] Desel J, Esparza J. Free Choice Petri Nets. Cambridge University Press, 2005. ISBN:0521019451, 9780521019453.
- [26] Desel J, Esparza J. Free Choice Petri Nets. Cambridge Tracts in Theoretical Computer Science. Cambridge University Press, 2005. ISBN-10:0521019451.
- [27] Heiner M, Herajy M, Liu F, Rohr C, Schwarick M. Snoopy a unifying Petri net tool. In: Proc. of Petri Nets 2012, volume 7347 of LNCS. Springer, 2012 pp. 398-407. doi:10.1007/978-3-642-31131-4_22.
- [28] Heiner M, Schwarick M, Wegener J. Charlie - an extensible Petri net analysis tool. In: Proc. of Petri Nets 2015, volume 9115 of LNCS. Springer, 2015 pp. 200-211. doi:10.1007/978-3-319-19488-2_10.
- [29] 4ti2 team. 4ti2-A software package for algebraic, geometric and combinatorial problems on linear spaces. URL http://www.4ti2.de.
- [30] GNU Project. GLPK (GNU Linear Programming Kit). URL https://www.gnu.org/software/glpk.
- [31] Sorokin I, Giovanardi O. Trophic characteristics of the Manila clam. ICES Journal of Marine Science, 1995;52(5):853-862. doi:10.1006/jmsc.1995.0082.
- [32] Vézina A, Pace M. An Inverse Model Analysis of Planktonic Food Webs in Experimental Lakes. Canadian Journal of Fisheries and Aquatic Sciences, 1994;51(9):2034-2044.
- [33] Parsons TR, Takahashi M, Hargrave B. Biological Oceanographic Processes. Pergamon Press, 1984. ISBN-10:0080307655.
- [34] Conover R. Factors affecting the assimilation of organic matter by zooplankton and the question of superfluous feeding. Limnology and Oceanography, 2003;11(3):346-354. doi:10.4319/lo.1966.11.3.0346.
- [35] Reinthaler T, Winter C, Herndl GJ. Relationship between bacterioplankton richness, respiration, and production in the southern North Sea. Applied and Environmental Microbiology, 2005;71(5):2260-2266. URL http://hdl.handle.net/(...)2c-8461-6af760fc26a3.
- [36] Carlson C, Del Giorgio P, Herndl G. Microbes and the dissipation of energy and respiration: from cells to ecosystems. Oceanography, 2007;20(2):89-100. URL http://dx.doi.org/10.5670/oceanog.2007.52#sthash.1zvIlgor.dpuf.
- [37] Wetzel RG. Limnology. Lake and River Ecosystems. Elsevier, 2001. ISBN:978-0-12-744760-5.
- [38] Barnes R, Hughes R. An introduction to Marine Ecology. Wiley, 1999. ISBN:978-0-86542-834-8.
- [39] Brigolin D, Savenkoff C, Zucchetta M, Pranovi F, Franzoi P, Torricelli P, R P. An inverse model for the analysis of the Venice lagoon food web. Ecological Modelling, 2011;222:2404-2413. doi:10.1016/j.ecolmodel.2011.04.002.
- [40] Brigolin D, Facca C, Franco A, Franzoi P, Pastres R, Sfriso A, Sigovini M, Soldatini C, Tagliapietra D, Torricelli P, Zucchetta M, Pranovi F. Linking food web functioning and habitat diversity for an ecosystem based management: A Mediterranean lagoon case-study. Marine Environmental Research, 2014;97:58-66. doi:10.1016/j.marenvres.2014.02.006.
Uwagi
Opracowanie rekordu w ramach umowy 509/P-DUN/2018 ze środków MNiSW przeznaczonych na działalność upowszechniającą naukę (2018).
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-27c5f33b-f0e0-4e92-b27e-05196d41ae88