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Minimal probabilistic P systems for modelling ecological systems. (English) Zbl 1333.92068

Summary: In this paper we propose MPP systems as modelling notation for ecological systems, and we show how they can be used together with simulation and statistical model checking tools to study properties of such kind of systems. As a case study we consider the ecological problem of stability of European water frog populations. The paper shows that MPP systems allow easy and concise modelling of real ecological problems. Moreover, MPP systems models can be easily simulated and translated into the PRISM input language to enable statistical model checking of properties.

MSC:

92D40 Ecology
68Q05 Models of computation (Turing machines, etc.) (MSC2010)
68Q60 Specification and verification (program logics, model checking, etc.)
68U20 Simulation (MSC2010)

Software:

PRISM
PDFBibTeX XMLCite
Full Text: DOI

References:

[1] Abt, G.; Reyer, H. U., Mate choice and fitness in a hybrid frog: Rana esculenta females prefer Rana lessonae males over their own, Behav. Ecol. Sociobiol., 32, 4, 221-228 (1993)
[2] Andrei, O.; Ciobanu, G.; Lucanu, D., Structural Operational Semantics of P Systems (2006), Springer · Zbl 1135.68400
[3] Andrei, O.; Ciobanu, G.; Lucanu, D., A rewriting logic framework for operational semantics of membrane systems, Theoret. Comput. Sci., 373, 3, 163-181 (2007) · Zbl 1111.68064
[4] Anholt, B. R.; Hotz, H.; Guex, G. D.; Semlitsch, R. D., Overwinter survival of Rana lessonae and its hemiclonal associate Rana esculenta, Ecology, 84, 2, 391-397 (2003)
[5] Barbuti, R.; Levi, F.; Milazzo, P.; Scatena, G., Maximally parallel probabilistic semantics for multiset rewriting, Fund. Inform., 112, 1, 1-17 (2011) · Zbl 1232.68077
[6] Barbuti, R.; Bove, P.; Schettini, A. M.; Milazzo, P.; Pardini, G., A computational formal model of the invasiveness of eastern species in European water frog populations, (Counsell, S.; Núñez, M., Software Engineering and Formal Methods. Software Engineering and Formal Methods, Lecture Notes in Computer Science, vol. 8368 (2014), Springer International Publishing), 329-344
[7] Barbuti, R.; Caravagna, G.; Maggiolo-Schettini, A.; Milazzo, P.; Pardini, G., The calculus of looping sequences, (Formal Methods for Computational Systems Biology. Formal Methods for Computational Systems Biology, Lecture Notes in Computer Science, vol. 5016 (2008), Springer: Springer Berlin, Heidelberg), 387-423
[8] Barbuti, R.; Cataudella, S.; Maggiolo-Schettini, A.; Milazzo, P.; Troina, A., A probabilistic model for molecular systems, Fund. Inform., 67, 1, 13-27 (2005) · Zbl 1096.68101
[9] Barbuti, R.; Maggiolo-Schettini, A.; Milazzo, P.; Pardini, G., Spatial calculus of looping sequences, Theoret. Comput. Sci., 412, 43, 5976-6001 (2011) · Zbl 1230.92002
[10] Barbuti, R.; Maggiolo-Schettini, A.; Milazzo, P.; Pardini, G., Simulation of spatial P system models, Theoret. Comput. Sci., 529, 11-45 (2014) · Zbl 1358.68098
[11] Barbuti, R.; Maggiolo-Schettini, A.; Milazzo, P.; Pardini, G.; Tesei, L., Spatial P systems, Nat. Comput., 10, 1, 3-16 (2011) · Zbl 1213.68256
[12] Barbuti, R.; Maggiolo-Schettini, A.; Milazzo, P.; Tini, S., Compositional semantics and behavioral equivalences for P systems, Theoret. Comput. Sci., 395, 1, 77-100 (2008) · Zbl 1145.68033
[13] Barbuti, R.; Maggiolo-Schettini, A.; Milazzo, P.; Tini, S., A P systems flat form preserving step-by-step behaviour, Fund. Inform., 87, 1, 1-34 (2008) · Zbl 1154.68048
[14] Barbuti, R.; Maggiolo-Schettini, A.; Milazzo, P.; Tini, S., Compositional semantics of spiking neural P systems, J. Log. Algebr. Program., 79, 6, 304-316 (2010) · Zbl 1208.68123
[15] Barbuti, R.; Maggiolo-Schettini, A.; Milazzo, P.; Tini, S., An overview on operational semantics in membrane computing, Internat. J. Found. Comput. Sci., 22, 01, 119-131 (2011) · Zbl 1213.68357
[16] Bergen, K.; Semlitsch, R. D.; Reyer, H. U., Hybrid female matings are directly related to the availability of Rana lessonae and Rana esculenta males in experimental populations, Copeia, 1997, 2, 275-283 (1997)
[17] Berger, L., Systematics and hybridization in European green frogs of Rana esculenta complex, J. Herpetol., 7, 1, 1-10 (1973)
[18] Besozzi, D.; Cazzaniga, P.; Pescini, D.; Mauri, G., Modelling metapopulations with stochastic membrane systems, Biosystems, 91, 3, 499-514 (2008)
[19] Bottoni, P.; Martín-Vide, C.; Păun, G.; Rozenberg, G., Membrane systems with promoters/inhibitors, Acta Inform., 38, 10, 695-720 (2002) · Zbl 1034.68038
[20] Bove, P.; Milazzo, P.; Barbuti, R., The role of deleterious mutations in the stability of hybridogenetic water frog complexes, BMC Evol. Biol., 14, 1, 107 (2014)
[21] Busi, N., Using well-structured transition systems to decide divergence for catalytic P systems, Theoret. Comput. Sci., 372, 2, 125-135 (2007) · Zbl 1111.68037
[22] 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) · Zbl 1213.68258
[23] Ciobanu, G.; Cornacel, L., Probabilistic transitions for P systems, Prog. Nat. Sci., 17, 4, 432-441 (2007) · Zbl 1160.68380
[24] Clarke, E. M.; Emerson, E. A.; Sistla, A. P., Automatic verification of finite-state concurrent systems using temporal logic specifications, ACM Trans. Program. Lang. Syst., 8, 2, 244-263 (1986) · Zbl 0591.68027
[25] Clarke, E. M.; Grumberg, O.; Peled, D., Model Checking (1999), MIT Press
[26] Engeler, B.; Reyer, H. U., Choosy females and indiscriminate males: mate choice in mixed populations of sexual and hybridogenetic water frogs (Rana lessonae, Rana esculenta), Behav. Ecol., 12, 5, 600-606 (2001)
[27] Guex, G. D.; Hotz, H.; Semlitsch, R. D., Deleterious alleles and differential viability in progeny of natural hemiclonal frogs, Evolution, 56, 5, 1036-1044 (2002)
[28] Hansson, H.; Jonsson, B., A logic for reasoning about time and reliability, Form. Asp. Comput., 6, 5, 512-535 (1994) · Zbl 0820.68113
[29] Hastings, A., Population Biology: Concepts and Models (1997), Springer Science & Business Media
[30] Hellriegel, B.; Reyer, H. U., Factors influencing the composition of mixed populations of a hemiclonal hybrid and its sexual host, J. Evol. Biol., 13, 6, 906-918 (2000)
[31] Hotz, H.; Semlitsch, R. D.; Gutmann, E.; Guex, G. D.; Beerli, P., Spontaneous heterosis in larval life-history traits of hemiclonal frog hybrids, Proc. Natl. Acad. Sci., 96, 5, 2171-2176 (1999)
[32] Kwiatkowska, M.; Norman, G.; Parker, D., Prism 4.0: verification of probabilistic real-time systems, (Computer Aided Verification (2011), Springer), 585-591
[33] Madhu, M., Probabilistic rewriting P systems, Internat. J. Found. Comput. Sci., 14, 1, 157-166 (2003) · Zbl 1099.68047
[34] Manca, V.; Bianco, L., Biological networks in metabolic P systems, Biosystems, 91, 3, 489-498 (2008)
[35] Mee, J. A.; Otto, S. P., Variation in the strength of male mate choice allows long-term coexistence of sperm-dependent asexuals and their sexual hosts, Evolution, 64, 10, 2808-2819 (2010)
[36] Păun, G., Membrane Computing: An Introduction, Natural Computing Series (2002), Springer-Verlag GmbH · Zbl 1034.68037
[37] Păun, G., Computing with membranes, J. Comput. System Sci., 61, 1, 108-143 (2000) · Zbl 0956.68055
[38] Păun, G.; Rozenberg, G.; Salomaa, A., The Oxford Handbook of Membrane Computing (2010), Oxford University Press, Inc. · Zbl 1237.68001
[39] Pérez-Jiménez, M. J.; Romero-Campero, F. J., P systems, a new computational modelling tool for systems biology, (Transactions on Computational Systems Biology VI (2006), Springer), 176-197
[40] Pescini, D.; Besozzi, D.; Mauri, G.; Zandron, C., Dynamical probabilistic P systems, Internat. J. Found. Comput. Sci., 17, 1, 183-204 (2006) · Zbl 1088.68062
[41] Renshaw, E., Modelling Biological Populations in Space and Time, vol. 11 (1993), Cambridge University Press · Zbl 0779.92016
[42] Reyer, H.; Frei, G.; Som, C., Cryptic female choice: frogs reduce clutch size when amplexed by undesired males, Proc. R. Soc. Lond., B Biol. Sci., 266, 1433, 2101-2107 (1999)
[43] Roesli, M.; Reyer, H. U., Male vocalization and female choice in the hybridogenetic Rana lessonae/Rana esculenta complex, Anim. Behav., 60, 6, 745-755 (2000)
[44] Semlitsch, R. D.; Schmiedehausen, S.; Hotz, H.; Beerli, P., Genetic compatibility between sexual and clonal genomes in local populations of the hybridogenetic Rana esculenta complex, Evol. Ecol., 10, 5, 531-543 (1996)
[45] Sen, K.; Viswanathan, M.; Agha, G., Statistical model checking of black-box probabilistic systems, (Computer Aided Verification (2004), Springer), 202-215 · Zbl 1103.68639
[46] Som, C.; Anholt, B. R.; Reyer, H. U., The effect of assortative mating on the coexistence of a hybridogenetic waterfrog and its sexual host, Amer. Nat., 156, 1, 34-46 (2000)
[47] Spicher, A.; Michel, O.; Cieslak, M.; Giavitto, J. L.; Prusinkiewicz, P., Stochastic P systems and the simulation of biochemical processes with dynamic compartments, Biosystems, 91, 3, 458-472 (2008)
[48] Tejedo, M.; Semlitsch, R. D.; Hotz, H., Differential morphology and jumping performance of newly metamorphosed frogs of the hybridogenetic Rana esculenta complex, J. Herpetol., 34, 2, 201-210 (2000)
[49] Vorburger, C., Fixation of deleterious mutations in clonal lineages: evidence from hybridogenetic frogs, Evolution, 55, 11, 2319-2332 (2001)
[50] Vorburger, C.; Reyer, H. U., A genetic mechanism of species replacement in European waterfrogs?, Conserv. Genet., 4, 2, 141-155 (2003)
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