Population Dynamics P System (PDP) Models: A Standardized Protocol for Describing and Applying Novel Bio-Inspired Computing Tools

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Colomer, Maria Àngels ^a   Margalida, Antoni ^b   Pérez Jiménez, Mario J ^c  

^a UNIVERSITY OF LLEIDA   (Spain)

^b UNIVERSITY OF BERN   (Switzerland)

^c UNIVERSITY OF SEVILLE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CELL COMPONENT; CELL MEMBRANE POTENTIAL; COMPUTER AIDED DESIGN; COMPUTER SIMULATION; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; ENVIRONMENT; HUMAN; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MORTALITY; NONHUMAN; POPULATION DYNAMICS; POPULATION DYNAMICS P SYSTEM MODEL; POPULATION GROWTH; POPULATION SIZE; PRACTICE GUIDELINE; PREDATION; REPRODUCTION; TREND STUDY;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; ECOSYSTEM; MODELS, BIOLOGICAL; MODELS, THEORETICAL; POPULATION DYNAMICS;

EID: 84876043901     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060698     Document Type: Article

References (32)

1. Sinclair ARE, Mduma S, Brashares JS, (2003) Patterns of predation in a diverse predator-prey system. Nature 425: 288-290.
2. Bascompte J, Melia C, Sala E, (2005) Interaction strength combinations and the overfishing of a marine food web. Proc Natl Acad Sci USA 102: 5443-5447.
3. Ives AR, Cardinale BJ, Snyder WE, (2005) A synthesis of subdisciplines: predator-prey interactions, and biodiversity and ecosystem functioning. Ecol Lett 8: 102-116.
4. Paine RT, (1980) Food webs: linkage, interaction strength and community infrastructure. J Anim Ecol 49: 667-685.
5. Bascompte J, (2009) Disentangling the web of life. Science 325: 416-419.
6. Kendall BE, Bjornstad O, Bascompte J, Keitt THD, Fagan WF, (2000) Dispersal, environmental correlation, and spatial synchrony in population dynamics. Am Nat 155: 628-636.
7. Ostfeld RS, Keesing F, (2000) Pulsed resources and community dynamics of consumers in terrestrial ecosystems. Trends Ecol Evol 6: 232-237.
8. Ings TC, Montoya JM, Bascompte J, Blütgen N, Brown L, et al. (2009) Review: Ecological networks-beyond food webs. J Anim Ecol 78: 253-269.
9. Bastolla U, Fortuna MA, Pascual-García A, Ferrera A, Luque B, et al. (2009) The architecture of mutualistic networks minimizes competition and increases biodiversity. Nature 458: 1018-1020.
10. Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, et al. (2011) Detecting novel associations in large data sets. Science 334: 1518-1524.
11. Brook B, Cannon R, Lacy R, Mirande C, Frankham R, (1999) Comparison of the population analysis packages GAPPS, INMAT, RAMAS and VORTEX for the whooping crane (Grus americana). Anim Conserv 2: 23-31.
12. Mullon C, Cury P, Shannon L, (2004) Viability model of trophic interactions in marine ecosystems. Nat Res Model 17: 71-102.
13. Bousquet FC, Le Page C, (2004) Multi-agent simulations and ecosystem management: a review. Ecol Model 176: 313-332.
14. Grimm V, Revilla E, Berger U, Jetsch F, Mooij W, et al. (2005) Pattern-oriented modeling of agent-based complex systems: lessons from ecology. Science 310: 987-991.
15. McGowan CP, Runge MC, Larson MA, (2011) Incorporating parametric uncertainty into population viability analysis models. Biol Conserv 144: 1400-1408.
16. Colomer MA, Margalida A, Sanuy D, Pérez-Jiménez MJ, (2011) A bio-inspired computing model as a new tool for modeling ecosystems: the avian scavengers as a case study. Ecol Model 222: 33-47.
17. Pǎun G, (1998) Computing with membranes. J Comput Syst Sci 61: 108-143.
18. Pǎun G, Rozenberg G, Salomaa A (2010) The Oxford Handbook of Membrane Computing. Oxford: Oxford University Press.
19. Cardona M, Colomer MA, Pérez Hurtado I, Pérez Jiménez MJ, Sanuy D, et al. (2009) Modelling ecosystems using P Systems: the Bearded Vulture, a case study. LNCS 5391: 137-156.
20. Margalida A, Colomer MA, Sanuy D, (2011) Can wild ungulate carcasses provide enough biomass to maintain avian scavenger populations? An empirical assessment using a bio-inspired computational model. PLoS One 6: e20248.
21. Grimm V, Berger U, Bastiansen F, Eliassen S, Ginot V, et al. (2006) A standard protocol for describing individual-based and agent-based models. Ecol Model 198: 115-126.
22. Pérez-Hurtado I, Valencia L, Pérez-Jiménez MJ, Colomer MA, Riscos A (2010) MeCoSim: A general purpose software tool for simulating biological phenomena by means of P Systems. In: K Li, Z Tang, R Li, AK Nagar, R Thamburaj (eds.) Proceedings 2010 IEEE Fifth International Conference on Bio-inspired Computing: Theories and Applications: 637-643. Vol 1. Changsha: IEEE Press.
23. Díaz D, Pérez-Hurtado I, Pérez-Jiménez MJ, Riscos A, (2009) A P-lingua programming environment for Membrane Computing. LNCS 5391: 187-203.
24. Martínez-del-Amor M A., Pérez-Hurtado I, García-Quismondo M, Macías-Ramos L F., Valencia-Cabrera L et al. (2012) DCBA: Simulating population dynamics P systems with proportional object distribution. 13th International Conference on Membrane Computing (CMC13), Budapest, Hungary, p.291-310.
25. Russell JC, Lecomte V, Dumont Y, Le Correa M, (2009) Intraguild predation and mesopredator release effect on long-lived prey. Ecol Model 220: 1098-1104.
26. Margalida A, Colomer MA, (2012) Modelling the effects of sanitary policies on European vulture conservation. Sci Rep 2: 753.
27. Donázar JA, Margalida A, Carrete M, Sánchez-Zapata JA, (2009) Too sanitary for vultures. Science 326: 664.
28. Margalida A, Donázar JA, Carrete M, Sánchez-Zapata JA, (2010) Sanitary versus environmental policies: fitting together two pieces of the puzzle of European vulture conservation. J Appl Ecol 47: 931-935.
29. Margalida A, Carrete M, Sánchez-Zapata JA, Donázar JA, (2012) Good news for European vultures. Science 335: 284.
30. Colomer MA, Pérez-Hurtado I, Pérez-Jiménez MJ, Riscos A, (2011) Comparing simulation algorithms for multienvironment probabilistic P system over a standard virtual ecosystem. Nat Comp 11: 369-379.
31. Cardona M, Colomer MA, Margalida A, Pérez-Hurtado I, Pérez-Jiménez MJ, et al. (2010) A P-System based model of an ecosystem of some scavenger birds. LNCS 5957: 182-195.
32. Fisher J, Henzinger TA, (2007) Executable cell biology. Nature Biotech 25: 1279-1249.