13th International Conference on Membrane Computing - MTA Sztaki

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P. Ramón, A. Troina hand, the Calculus of Looping Sequences allows to define ordered sequences in a more succinct way (for examples when describing sequences of genes in DNA or sequences of amino acids in proteins). 14 On the other hand, CWC reflects in a more realistic way the fluid mosaic model of the lipid bilayer (for example in the case of cellular membrane description, where proteins are free to float), and, the addition of compartment labels allows to characterise the properties peculiar to given classes of compartments. Ultimately, focusing on multisets and avoiding to deal explicitly with ordered sequences (and, thus, variables for sequences) strongly simplifies the pattern matching procedure in the development of a simulation tool. The Calculus of Looping Sequences has been extended with type systems in [6,28,29,8,16]. As an application to ecology, stochastic CLS (see [7]) is used in [12] to model population dynamics. P-Systems have been proposed as a computational model inspired by biological structures. They are defined as a nesting of membranes in which multisets of objects can react according to pre defined rewrite rules. Maximal-parallelism is the key feature of P-Systems: at each evolution step all rewrite rules, in all membranes, are applied as many times as possible. Such a feature makes P-Systems a very powerful computational model and a versatile instrument to evaluate expressiveness of languages. However, it is not practical to describe stochastic systems with a maximally-parallel evolution: exact stochastic simulations based on race conditions model systems evolutions as a sequence of successive steps, each of which with a particular duration modelled by an exponential probability distribution. There is a large body of literature about applications of P-Systems to ecological modelling. In [20,21,22], P-Systems are enriched with a probabilistic semantics to model different ecological systems in the Catalan Pyrenees. Rules could still be applied in a parallel fashion since reduction durations are not explicitly taken into account. In [13,14,15], P-Systems are enriched with a stochastic semantics and used to model metapopulation dynamics. The addition of mute rules allows to keep a form of parallelism reducing the maximal consumption of objects. While all these calculi allow to manage systems topology through nesting and compartmentalisation, explicit spatial models are able to depict more precise localities and ecological niches, describing how organisms or populations respond to the distribution of resources and competitors [35]. The spatial extensions of CWC [17], CLS [9] and P-Systems [10] could be used to express this kind of analysis allowing to deal with spatial coordinates. References 1. Aguirre, Z., Kvist, P., Sánchez, O.: Floristic composition and conservation status of the dry forests in ecuador. Lyonia 8(2) (2005) 14 An ordered sequence can be expressed in CWC as a series of nested compartments, ordered from the outermost compartment to the innermost one. 402
Modelling ecological systems with the calculus of wrapped compartments 2. Aldinucci, M., Coppo, M., Damiani, F., Drocco, M., Giovannetti, E., Grassi, E., Sciacca, E., Spinella, S., Troina, A.: CWC Simulator. Dipartimento di Informatica, Università di Torino (2010), http://cwcsimulator.sourceforge.net/ 3. Aldinucci, M., Coppo, M., Damiani, F., Drocco, M., Sciacca, E., Spinella, S., Torquati, M., Troina, A.: On parallelizing on-line statistics for stochastic biological simulations. In: HiBB’11. Lecture Notes in Computer Science, vol. 7156, pp. 3–12. Springer (2011) 4. Aldinucci, M., Coppo, M., Damiani, F., Drocco, M., Torquati, M., Troina, A.: On designing multicore-aware simulators for biological systems. In: Proc. of Intl. Euromicro PDP 2011: Parallel Distributed and network-based Processing. pp. 318– 325. IEEE Computer Society (2011) 5. Aldinucci, M., Torquati, M.: FastFlow website. FastFlow (Oct 2009), http:// mc-fastflow.sourceforge.net/ 6. Aman, B., Dezani-Ciancaglini, M., Troina, A.: Type disciplines for analysing biologically relevant properties. Electr. Notes Theor. Comput. Sci. 227, 97–111 (2009) 7. Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Tiberi, P., Troina, A.: Stochastic calculus of looping sequences for the modelling and simulation of cellular pathways. Transactions on Computational Systems Biology IX, 86–113 (2008) 8. Barbuti, R., Dezani-Ciancaglini, M., Maggiolo-Schettini, A., Milazzo, P., Troina, A.: A formalism for the description of protein interaction. Fundam. Inform. 103(1- 4), 1–29 (2010) 9. Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Pardini, G.: Spatial calculus of looping sequences. Theoretical Computer Science 412(43), 5976 – 6001 (2011) 10. Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Pardini, G., Tesei, L.: Spatial p systems. Natural Computing 10(1), 3–16 (2011) 11. Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Troina, A.: The calculus of looping sequences for modeling biological membranes. In: Workshop on Membrane Computing. Lecture Notes in Computer Science, vol. 4860, pp. 54–76. Springer (2007) 12. Basuki, T.A., Cerone, A., Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Rossi, E.: Modelling the dynamics of an aedes albopictus population. In: AMCA-POP. vol. 33, pp. 18–36. EPTCS (2010) 13. Besozzi, D., Cazzaniga, P., Pescini, D., Mauri, G.: Seasonal variance in p system models for metapopulations. Progress in Natural Science 17(4), 392–400 (2007) 14. Besozzi, D., Cazzaniga, P., Pescini, D., Mauri, G.: Modelling metapopulations with stochastic membrane systems. Biosystems 91(3), 499–514 (2008) 15. Besozzi, D., Cazzaniga, P., Pescini, D., Mauri, G.: An analysis on the influence of network topologies on local and global dynamics of metapopulation systems. In: AMCA-POP. vol. 33, pp. 1–17. EPTCS (2010) 16. Bioglio, L., Dezani-Ciancaglini, M., Giannini, P., Troina, A.: Typed stochastic semantics for the calculus of looping sequences. Theor. Comp. Sci. 431, 165–180 (2012) 17. Bioglio, L., Calcagno, C., Coppo, M., Damiani, F., Sciacca, E., Spinella, S., Troina, A.: A spatial calculus of wrapped compartments. In: MeCBIC. vol. abs/1108.3426. CoRR (2011) 18. Bolker, B.: Ecological models and data in R. Princeton University Press (2008) 19. Calcagno, C., Coppo, M., Damiani, F., Drocco, M., Sciacca, E., Spinella, S., Troina, A.: Modelling spatial interactions in the arbuscular mycorrhizal symbiosis using the calculus of wrapped compartments. In: CompMod 2011. vol. 67, pp. 3–18. EPTCS (2011) 403
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Erzsébet Csuhaj-Varjú Marian Gheo
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Editors Erzsébet Csuhaj-Varjú Dep
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Preface In addition to the texts or
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Contents M.A. Martínez-del-Amor, I
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(Tissue) P systems with decaying ob
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Sorin Istrail, Solomon Marcus of pr
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Sorin Istrail, Solomon Marcus proba
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Sorin Istrail, Solomon Marcus stati
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Sorin Istrail, Solomon Marcus his f
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Turing’s three pioneering initiat
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Turing’s three pioneering initiat
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MP systems for systems biology tere
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Yu. Rogozhin this obstacle and to g
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Yu. Rogozhin 10. J. Cocke, M. Minsk
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M. Stannett The question arises, wh
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Regular Contributions
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T. Ahmed, G. DeLancy, A. Paun almos
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T. Ahmed, G. DeLancy, A. Paun purpo
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T. Ahmed, G. DeLancy, A. Paun Fig.
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T. Ahmed, G. DeLancy, A. Paun gener
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T. Ahmed, G. DeLancy, A. Paun
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T. Ahmed, G. DeLancy, A. Paun Table
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Asynchronuous and maximally paralle
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A. Alhazov, R. Freund, H. Heikenwä
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A. Alhazov, Yu. Rogozhin With coope
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A. Alhazov, Yu. Rogozhin 2.3 P Syst
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A. Alhazov, Yu. Rogozhin Such a sys
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A. Alhazov, Yu. Rogozhin applied, f
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A. Alhazov, Yu. Rogozhin - one extr
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B. Aman, G. Ciobanu formalisms is e
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B. Aman, G. Ciobanu membranes appea
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B. Aman, G. Ciobanu • [ ] recep r
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B. Aman, G. Ciobanu Definition 3. A
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B. Aman, G. Ciobanu { w i , for all
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B. Aman, G. Ciobanu The four transi
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B. Aman, G. Ciobanu A state space i
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B. Aman, G. Ciobanu to reiterate th
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On structures and behaviors of spik
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L. Cienciala, L. Ciencialová, M. P
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H. ElGindy, R. Nicolescu, H. Wu pat
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H. ElGindy, R. Nicolescu, H. Wu pro
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H. ElGindy, R. Nicolescu, H. Wu (b)
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H. ElGindy, R. Nicolescu, H. Wu 8 r
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H. ElGindy, R. Nicolescu, H. Wu Pse
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H. ElGindy, R. Nicolescu, H. Wu to
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H. ElGindy, R. Nicolescu, H. Wu ter
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H. ElGindy, R. Nicolescu, H. Wu 4.
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H. ElGindy, R. Nicolescu, H. Wu Tab
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H. ElGindy, R. Nicolescu, H. Wu 6 R
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H. ElGindy, R. Nicolescu, H. Wu (wh
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A formal framework for P systems wi
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A new approach for solving SAT by P
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Maintenance of chronobiological inf
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4 3.5 3 2.5 2 1.5 1 0.5 0 0 50 100
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Using a kernel P system to solve th
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Spiking neural P systems with funct
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L.F. Macías-Ramos, M.J. Pérez-Jim
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Membranes with local environments A
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Membranes with local environments T
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Membranes with local environments -
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Membranes with local environments -
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Membranes with local environments I
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On efficient algorithms for SAT dis
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On efficient algorithms for SAT 2 S
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On efficient algorithms for SAT 2.4
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On efficient algorithms for SAT inc
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On efficient algorithms for SAT •
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On efficient algorithms for SAT Not
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On efficient algorithms for SAT the
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On efficient algorithms for SAT 32.
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A. Obtu̷lowicz - its underlying tr
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A. Obtu̷lowicz 2−ramification
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A. Obtu̷lowicz The correctness of
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A. Obtu̷lowicz The arcs (links) fr
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Page 444 and 445: S. Verlan, J. Quiros We consider a
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S. Verlan, J. Quiros 5. M. Maliţa,
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Simplifying Event-B models of P sys
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Author Index Adorna H., 143 Agrigor
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13th International Conference on Membrane Computing - MTA Sztaki

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