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2017 | OriginalPaper | Buchkapitel

Applications of P Systems in Population Biology and Ecology: The Cases of MPP and APP Systems

verfasst von : Roberto Barbuti, Pasquale Bove, Paolo Milazzo, Giovanni Pardini

Erschienen in: Membrane Computing

Verlag: Springer International Publishing

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Abstract

We describe two extensions of P systems for the modelling of populations and ecosystems. They are the Minimal Probabilistic P systems (MPP systems) and the Attributed Probabilistic P systems (APP systems). We describe also two case studies in which the two formalisms have been applied to the study of real ecological systems. The first case study deals with the causes of the stability of European hybrid populations of water frogs. The second case study deals with social interactions and the establishment of dominance hierarchies in primates.

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Literatur
1.
Zurück zum Zitat Albers, P.C., de Vries, H.: Elo-rating as a tool in the sequential estimation of dominance strengths. Anim. Behav. 61(2), 489–495 (2001)CrossRef Albers, P.C., de Vries, H.: Elo-rating as a tool in the sequential estimation of dominance strengths. Anim. Behav. 61(2), 489–495 (2001)CrossRef
2.
Zurück zum Zitat Martínez-del-Amor, M.A., et al.: DCBA: simulating population dynamics P systems with proportional object distribution. In: Csuhaj-Varjú, E., Gheorghe, M., Rozenberg, G., Salomaa, A., Vaszil, G. (eds.) CMC 2012. LNCS, vol. 7762, pp. 257–276. Springer, Heidelberg (2013). doi:10.1007/978-3-642-36751-9_18 CrossRef Martínez-del-Amor, M.A., et al.: DCBA: simulating population dynamics P systems with proportional object distribution. In: Csuhaj-Varjú, E., Gheorghe, M., Rozenberg, G., Salomaa, A., Vaszil, G. (eds.) CMC 2012. LNCS, vol. 7762, pp. 257–276. Springer, Heidelberg (2013). doi:10.​1007/​978-3-642-36751-9_​18 CrossRef
3.
Zurück zum Zitat Barbuti, R., Levi, F., Milazzo, P., Scatena, G.: Maximally parallel probabilistic semantics for multiset rewriting. Fundamenta Informaticae 112(1), 1–17 (2011)MathSciNetMATH Barbuti, R., Levi, F., Milazzo, P., Scatena, G.: Maximally parallel probabilistic semantics for multiset rewriting. Fundamenta Informaticae 112(1), 1–17 (2011)MathSciNetMATH
4.
Zurück zum Zitat Barbuti, R., Bompadre, A., Bove, P., Milazzo, P., Pardini, G.: Attributed probabilistic P systems and their application to the modelling of social interactions in primates. In: Bianculli, D., Calinescu, R., Rumpe, B. (eds.) SEFM 2015. LNCS, vol. 9509, pp. 176–191. Springer, Heidelberg (2015). doi:10.1007/978-3-662-49224-6_15 CrossRef Barbuti, R., Bompadre, A., Bove, P., Milazzo, P., Pardini, G.: Attributed probabilistic P systems and their application to the modelling of social interactions in primates. In: Bianculli, D., Calinescu, R., Rumpe, B. (eds.) SEFM 2015. LNCS, vol. 9509, pp. 176–191. Springer, Heidelberg (2015). doi:10.​1007/​978-3-662-49224-6_​15 CrossRef
5.
Zurück zum Zitat 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. In: Counsell, S., Núñez, M. (eds.) SEFM 2013. LNCS, vol. 8368, pp. 329–344. Springer, Cham (2014). doi:10.1007/978-3-319-05032-4_24 CrossRef 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. In: Counsell, S., Núñez, M. (eds.) SEFM 2013. LNCS, vol. 8368, pp. 329–344. Springer, Cham (2014). doi:10.​1007/​978-3-319-05032-4_​24 CrossRef
6.
Zurück zum Zitat Barbuti, R., Bove, P., Milazzo, P., Pardini, G.: Minimal probabilistic P systems for modelling ecological systems. Theor. Comput. Sci. 608, 36–56 (2015)MathSciNetCrossRefMATH Barbuti, R., Bove, P., Milazzo, P., Pardini, G.: Minimal probabilistic P systems for modelling ecological systems. Theor. Comput. Sci. 608, 36–56 (2015)MathSciNetCrossRefMATH
7.
Zurück zum Zitat Barbuti, R., Caravagna, G., Maggiolo–Schettini, A., Milazzo, P., Pardini, G.: The calculus of looping sequences. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 387–423. Springer, Heidelberg (2008). doi:10.1007/978-3-540-68894-5_11 CrossRef Barbuti, R., Caravagna, G., Maggiolo–Schettini, A., Milazzo, P., Pardini, G.: The calculus of looping sequences. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 387–423. Springer, Heidelberg (2008). doi:10.​1007/​978-3-540-68894-5_​11 CrossRef
8.
Zurück zum Zitat Barbuti, R., Cataudella, S., Maggiolo-Schettini, A., Milazzo, P., Troina, A.: A probabilistic model for molecular systems. Fundamenta Informaticae 67(1), 13–27 (2005)MathSciNetMATH Barbuti, R., Cataudella, S., Maggiolo-Schettini, A., Milazzo, P., Troina, A.: A probabilistic model for molecular systems. Fundamenta Informaticae 67(1), 13–27 (2005)MathSciNetMATH
9.
Zurück zum Zitat Barbuti, R., Cerone, A., Maggiolo-Schettini, A., Milazzo, P., Setiawan, S.: Modelling population dynamics using grid systems. In: Cerone, A., Persico, D., Fernandes, S., Garcia-Perez, A., Katsaros, P., Shaikh, S.A., Stamelos, I. (eds.) SEFM 2012. LNCS, vol. 7991, pp. 172–189. Springer, Heidelberg (2014). doi:10.1007/978-3-642-54338-8_14 Barbuti, R., Cerone, A., Maggiolo-Schettini, A., Milazzo, P., Setiawan, S.: Modelling population dynamics using grid systems. In: Cerone, A., Persico, D., Fernandes, S., Garcia-Perez, A., Katsaros, P., Shaikh, S.A., Stamelos, I. (eds.) SEFM 2012. LNCS, vol. 7991, pp. 172–189. Springer, Heidelberg (2014). doi:10.​1007/​978-3-642-54338-8_​14
10.
Zurück zum Zitat Barbuti, R., Gori, R., Levi, F., Milazzo, P.: Investigating dynamic causalities in reaction systems. Theor. Comput. Sci. 623, 114–145 (2016)MathSciNetCrossRefMATH Barbuti, R., Gori, R., Levi, F., Milazzo, P.: Investigating dynamic causalities in reaction systems. Theor. Comput. Sci. 623, 114–145 (2016)MathSciNetCrossRefMATH
11.
Zurück zum Zitat Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Tini, S.: A P systems flat form preserving step-by-step behaviour. Fundamenta Informaticae 87(1), 1–34 (2008)MathSciNetMATH Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Tini, S.: A P systems flat form preserving step-by-step behaviour. Fundamenta Informaticae 87(1), 1–34 (2008)MathSciNetMATH
12.
Zurück zum Zitat Besozzi, D., Cazzaniga, P., Pescini, D., Mauri, G.: Modelling metapopulations with stochastic membrane systems. Biosystems 91(3), 499–514 (2008)CrossRef Besozzi, D., Cazzaniga, P., Pescini, D., Mauri, G.: Modelling metapopulations with stochastic membrane systems. Biosystems 91(3), 499–514 (2008)CrossRef
13.
14.
Zurück zum Zitat Bove, P.: Development of extensions of P systems for modelling and simulation of population dynamics. Ph.D. thesis, University of Pisa, October 2016 Bove, P.: Development of extensions of P systems for modelling and simulation of population dynamics. Ph.D. thesis, University of Pisa, October 2016
15.
Zurück zum Zitat Bove, P., Milazzo, P., Barbuti, R.: The role of deleterious mutations in the stability of hybridogenetic water frog complexes. BMC Evol. Biol. 14(1), 1 (2014)CrossRef Bove, P., Milazzo, P., Barbuti, R.: The role of deleterious mutations in the stability of hybridogenetic water frog complexes. BMC Evol. Biol. 14(1), 1 (2014)CrossRef
16.
Zurück zum Zitat Cardona, M., Colomer, M.A., Margalida, A., Palau, A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Sanuy, D.: A computational modelingfor real ecosystems based on P systems. Nat. Comput. 10(1), 39–53 (2011)MathSciNetCrossRefMATH Cardona, M., Colomer, M.A., Margalida, A., Palau, A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Sanuy, D.: A computational modelingfor real ecosystems based on P systems. Nat. Comput. 10(1), 39–53 (2011)MathSciNetCrossRefMATH
17.
Zurück zum Zitat Cavigelli, S.A., Pereira, M.E.: Mating season aggression and fecal testosterone levels in male ring-tailed lemurs (Lemur catta). Horm. Behav. 37(3), 246–255 (2000)CrossRef Cavigelli, S.A., Pereira, M.E.: Mating season aggression and fecal testosterone levels in male ring-tailed lemurs (Lemur catta). Horm. Behav. 37(3), 246–255 (2000)CrossRef
18.
Zurück zum Zitat Cerone, A., Scotti, M.: Research challenges in modelling ecosystems. In: Canal, C., Idani, A. (eds.) SEFM 2014. LNCS, vol. 8938, pp. 276–293. Springer, Cham (2015). doi:10.1007/978-3-319-15201-1_18 Cerone, A., Scotti, M.: Research challenges in modelling ecosystems. In: Canal, C., Idani, A. (eds.) SEFM 2014. LNCS, vol. 8938, pp. 276–293. Springer, Cham (2015). doi:10.​1007/​978-3-319-15201-1_​18
20.
Zurück zum Zitat Nieto Coria, C.A., Tesei, L., Scarcella, G., Russo, T., Merelli, E.: Sea-scale agent-based simulator of Solea solea in the adriatic sea. In: Canal, C., Idani, A. (eds.) SEFM 2014. LNCS, vol. 8938, pp. 259–275. Springer, Cham (2015). doi:10.1007/978-3-319-15201-1_17 Nieto Coria, C.A., Tesei, L., Scarcella, G., Russo, T., Merelli, E.: Sea-scale agent-based simulator of Solea solea in the adriatic sea. In: Canal, C., Idani, A. (eds.) SEFM 2014. LNCS, vol. 8938, pp. 259–275. Springer, Cham (2015). doi:10.​1007/​978-3-319-15201-1_​17
21.
Zurück zum Zitat Gori, R., Levi, F.: Abstract interpretation based verification of temporal properties for bioambients. Inform. Comput. 208(8), 869–921 (2010)MathSciNetCrossRefMATH Gori, R., Levi, F.: Abstract interpretation based verification of temporal properties for bioambients. Inform. Comput. 208(8), 869–921 (2010)MathSciNetCrossRefMATH
22.
Zurück zum Zitat Grimm, V.: Ten years of individual-based modelling in ecology: what have we learned and what could we learn in the future? Ecol. Model. 115(2), 129–148 (1999)CrossRef Grimm, V.: Ten years of individual-based modelling in ecology: what have we learned and what could we learn in the future? Ecol. Model. 115(2), 129–148 (1999)CrossRef
23.
Zurück zum Zitat Grimm, V., Berger, U., Bastiansen, F., Eliassen, S., Ginot, V., Giske, J., Goss-Custard, J., Grand, T., Heinz, S.K., Huse, G., et al.: A standard protocol for describing individual-based and agent-based models. Ecol. Model. 198(1), 115–126 (2006)CrossRef Grimm, V., Berger, U., Bastiansen, F., Eliassen, S., Ginot, V., Giske, J., Goss-Custard, J., Grand, T., Heinz, S.K., Huse, G., et al.: A standard protocol for describing individual-based and agent-based models. Ecol. Model. 198(1), 115–126 (2006)CrossRef
24.
Zurück zum Zitat 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)CrossRef 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)CrossRef
25.
Zurück zum Zitat Kahramanoğulları, O., Lynch, J.F., Priami, C.: Algorithmic systems ecology: experiments on multiple interaction types and patches. In: Cerone, A., Persico, D., Fernandes, S., Garcia-Perez, A., Katsaros, P., Shaikh, S.A., Stamelos, I. (eds.) SEFM 2012. LNCS, vol. 7991, pp. 154–171. Springer, Heidelberg (2014). doi:10.1007/978-3-642-54338-8_13 Kahramanoğulları, O., Lynch, J.F., Priami, C.: Algorithmic systems ecology: experiments on multiple interaction types and patches. In: Cerone, A., Persico, D., Fernandes, S., Garcia-Perez, A., Katsaros, P., Shaikh, S.A., Stamelos, I. (eds.) SEFM 2012. LNCS, vol. 7991, pp. 154–171. Springer, Heidelberg (2014). doi:10.​1007/​978-3-642-54338-8_​13
26.
Zurück zum Zitat Kwiatkowska, M., Norman, G., Parker, D.: PRISM 4.0: verification of probabilistic real-time systems. In: Gopalakrishnan, G., Qadeer, S. (eds.) CAV 2011. LNCS, vol. 6806, pp. 585–591. Springer, Heidelberg (2011). doi:10.1007/978-3-642-22110-1_47 CrossRef Kwiatkowska, M., Norman, G., Parker, D.: PRISM 4.0: verification of probabilistic real-time systems. In: Gopalakrishnan, G., Qadeer, S. (eds.) CAV 2011. LNCS, vol. 6806, pp. 585–591. Springer, Heidelberg (2011). doi:10.​1007/​978-3-642-22110-1_​47 CrossRef
27.
Zurück zum Zitat Legay, A., Delahaye, B., Bensalem, S.: Statistical model checking: an overview. In: Barringer, H., Falcone, Y., Finkbeiner, B., Havelund, K., Lee, I., Pace, G., Roşu, G., Sokolsky, O., Tillmann, N. (eds.) RV 2010. LNCS, vol. 6418, pp. 122–135. Springer, Heidelberg (2010). doi:10.1007/978-3-642-16612-9_11 CrossRef Legay, A., Delahaye, B., Bensalem, S.: Statistical model checking: an overview. In: Barringer, H., Falcone, Y., Finkbeiner, B., Havelund, K., Lee, I., Pace, G., Roşu, G., Sokolsky, O., Tillmann, N. (eds.) RV 2010. LNCS, vol. 6418, pp. 122–135. Springer, Heidelberg (2010). doi:10.​1007/​978-3-642-16612-9_​11 CrossRef
28.
Zurück zum Zitat Murray, J.D.: Mathematical Biology I: An Introduction. Interdisciplinary Applied Mathematics, vol. 17. Springer, New York (2002)MATH Murray, J.D.: Mathematical Biology I: An Introduction. Interdisciplinary Applied Mathematics, vol. 17. Springer, New York (2002)MATH
29.
Zurück zum Zitat Nakamichi, M., Koyama, N.: Social relationships among ring-tailed lemurs (Lemur catta) in two free-ranging troops at berenty reserve, madagascar. Int. J. Primatol. 18(1), 73–93 (1997)CrossRef Nakamichi, M., Koyama, N.: Social relationships among ring-tailed lemurs (Lemur catta) in two free-ranging troops at berenty reserve, madagascar. Int. J. Primatol. 18(1), 73–93 (1997)CrossRef
30.
Zurück zum Zitat Palagi, E., Paoli, T., Tarli, S.B.: Aggression and reconciliation in two captive groups of Lemur catta. Int. J. Primatol. 26(2), 279–294 (2005)CrossRef Palagi, E., Paoli, T., Tarli, S.B.: Aggression and reconciliation in two captive groups of Lemur catta. Int. J. Primatol. 26(2), 279–294 (2005)CrossRef
31.
Zurück zum Zitat Penna, P., Paoletti, N., Scarcella, G., Tesei, L., Marini, M., Merelli, E.: DISPAS: an agent-based tool for the management of fishing effort. In: Counsell, S., Núñez, M. (eds.) SEFM 2013. LNCS, vol. 8368, pp. 362–367. Springer, Cham (2014). doi:10.1007/978-3-319-05032-4_26 CrossRef Penna, P., Paoletti, N., Scarcella, G., Tesei, L., Marini, M., Merelli, E.: DISPAS: an agent-based tool for the management of fishing effort. In: Counsell, S., Núñez, M. (eds.) SEFM 2013. LNCS, vol. 8368, pp. 362–367. Springer, Cham (2014). doi:10.​1007/​978-3-319-05032-4_​26 CrossRef
32.
Zurück zum Zitat Pescini, D., Besozzi, D., Mauri, G., Zandron, C.: Dynamical probabilistic P systems. Int. J. Found. Comput. Sci. 17(1), 183–204 (2006)MathSciNetCrossRefMATH Pescini, D., Besozzi, D., Mauri, G., Zandron, C.: Dynamical probabilistic P systems. Int. J. Found. Comput. Sci. 17(1), 183–204 (2006)MathSciNetCrossRefMATH
33.
Zurück zum Zitat Philippou, A., Toro, M., Antonaki, M.: Simulation and verification in a process calculus for spatially-explicit ecological models. Sci. Ann. Comput. Sci. 23(1), 119–167 (2013)MathSciNet Philippou, A., Toro, M., Antonaki, M.: Simulation and verification in a process calculus for spatially-explicit ecological models. Sci. Ann. Comput. Sci. 23(1), 119–167 (2013)MathSciNet
34.
Zurück zum Zitat Setiawan, S., Cerone, A.: Stochastic modelling of seasonal migration using rewriting systems with spatiality. In: Counsell, S., Núñez, M. (eds.) SEFM 2013. LNCS, vol. 8368, pp. 313–328. Springer, Cham (2014). doi:10.1007/978-3-319-05032-4_23 CrossRef Setiawan, S., Cerone, A.: Stochastic modelling of seasonal migration using rewriting systems with spatiality. In: Counsell, S., Núñez, M. (eds.) SEFM 2013. LNCS, vol. 8368, pp. 313–328. Springer, Cham (2014). doi:10.​1007/​978-3-319-05032-4_​23 CrossRef
35.
Zurück zum Zitat Som, C., Anholt, B.R., Reyer, H.U.: The effect of assortative mating on the coexistence of a hybridogenetic waterfrog and its sexual host. Am. Nat. 156(1), 34–46 (2000)CrossRef Som, C., Anholt, B.R., Reyer, H.U.: The effect of assortative mating on the coexistence of a hybridogenetic waterfrog and its sexual host. Am. Nat. 156(1), 34–46 (2000)CrossRef
Metadaten
Titel
Applications of P Systems in Population Biology and Ecology: The Cases of MPP and APP Systems
verfasst von
Roberto Barbuti
Pasquale Bove
Paolo Milazzo
Giovanni Pardini
Copyright-Jahr
2017
DOI
https://doi.org/10.1007/978-3-319-54072-6_3

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