Advertisement

An Overview of P-Lingua 2.0

  • Manuel García-Quismondo
  • Rosa Gutiérrez-Escudero
  • Ignacio Pérez-Hurtado
  • Mario J. Pérez-Jiménez
  • Agustín Riscos-Núñez
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5957)

Abstract

P–Lingua is a programming language for membrane computing which aims to be a standard to define P systems. In order to implement this idea, a Java library called pLinguaCore has been developed as a software framework for cell–like P systems. It is able to handle input files (either in XML or in P–Lingua format) defining P systems from a number of different cell–like P system models. Moreover, the library includes several built–in simulators for each supported model. For the sake of software portability, pLinguaCore can export a P system definition to any convenient output format (currently XML and binary formats are available). This software is not a closed product, but it can be extended to accept new input or output formats and also new models or simulators.

The term P–Lingua 2.0 refers to the software package consisting of the above mentioned library together with a user interface called pLinguaPlugin (more details can be found at http://www.p-lingua.org).

Finally, in order to illustrate the software, this paper includes an application using pLinguaCore for describing and simulating ecosystems by means of P systems.

Keywords

Dependency Graph Active Membrane Input Format Evolution Rule Elementary Membrane 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Cardona, M., Colomer, M.A., Pérez–Jiménez, M.J., Sanuy, D., Margalida, A.: Modeling ecosystems using P systems: The Bearded Vulture, a case study. In: Corne, D.W., Frisco, P., Paun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2008. LNCS, vol. 5391, pp. 137–156. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  2. 2.
    Cardona, M., Colomer, M.A., Margalida, A., Pérez–Hurtado, I., Pérez–Jiménez, M.J., Sanuy, D.: P System based model of an ecosystem of the scavenger birds. In: Păun, G., et al. (eds.) WMC 2009. LNCS, vol. 5957. Springer, Heidelberg (2010)Google Scholar
  3. 3.
    Díaz–Pernil, D., Pérez–Hurtado, I., Pérez–Jiménez, M.J., Riscos–Núñez, A.: A P-lingua programming environment for membrane computing. In: Proce. 9th Workshop on Membrane Computing, pp. 155–172 (2008)Google Scholar
  4. 4.
    Fontana, F., Bianco, L., Manca, V.: P systems and the modelling of biochemical oscillations. In: Freund, R., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2005. LNCS, vol. 3850, pp. 199–208. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  5. 5.
    Freund, R., Verlan, S.: A formal framework for static (tissue) P systems. In: Eleftherakis, G., Kefalas, P., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2007. LNCS, vol. 4860, pp. 271–284. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  6. 6.
    Gibson, M.A., Bruck, J.: Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. 104, 1876–1889 (2000)Google Scholar
  7. 7.
    Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340–2361 (1977)CrossRefGoogle Scholar
  8. 8.
    Gutiérrez–Naranjo, M.A., Pérez–Jiménez, M.J., Riscos–Núñez, A.: Towards a programming language in cellular computing. Electronic Notes in Theoretical Computer Science 123, 93–110 (2005)CrossRefGoogle Scholar
  9. 9.
    Ito, M., Martín–Vide, C., Păun, G.: A characterization of Parikh sets of ET0L languages in terms of P systems. In: Ito, M., Păun, G., Yu, S. (eds.) Words, semigroups and transducers, pp. 239–254. Word Scientific, Singapore (2001)Google Scholar
  10. 10.
    Madhu, M., Krithivasan, K.: P systems with membrane creation: Universality and efficiency. In: Margenstern, M., Rogozhin, Y. (eds.) MCU 2001. LNCS, vol. 2055, pp. 276–287. Springer, Heidelberg (2001)Google Scholar
  11. 11.
    Martínez–del–Amor, M.A., Pérez–Hurtado, I., Pérez–Jiménez, M.J., Cecilia, J.M., Guerrero, G.D., García, J.M.: Simulation of recognizer P systems by using manycore GPUs. In: Păun, G., et al. (eds.) WMC 2009. LNCS, vol. 5957. Springer, Heidelberg (2010)Google Scholar
  12. 12.
    Obtulowicz, A.: Probabilistic P systems. In: Păun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.) WMC 2002. LNCS, vol. 2597, pp. 377–387. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  13. 13.
    Păun, A., Păun, G.: The power of communication: P systems with symport/antiport. New Generation Computing 20(3), 295–305 (2002)zbMATHCrossRefGoogle Scholar
  14. 14.
    Păun, G.: Computing with membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000)zbMATHCrossRefMathSciNetGoogle Scholar
  15. 15.
    Păun, G.: P systems with active membranes. Journal of Automata, Languages and Combinatorics 1, 75–90 (2001)Google Scholar
  16. 16.
    Pérez–Jiménez, M.J., Romero–Campero, F.J.: Modelling gene expression control using P systems: The Lac operon, a case study. BioSystems 91, 438–457 (2008)CrossRefGoogle Scholar
  17. 17.
    Pérez–Jiménez, M.J., Romero–Campero, F.J.: A model of the quorum sensing system in Vibrio Fischeri using P systems. Artificial Life 14, 95–109 (2008)CrossRefGoogle Scholar
  18. 18.
    Pérez–Jiménez, M.J., Romero–Campero, F.J.: P Systems, a new computational modelling tool for systems biology. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 176–197. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  19. 19.
    Pescini, D., Besozzi, D., Mauri, G., Zandron, C.: Dynamical probabilistic P systems. International Journal of Foundations of Computer Science 17(1), 183–195 (2006)zbMATHCrossRefMathSciNetGoogle Scholar
  20. 20.
    Romero–Campero, F.J.: P Systems, a Computational Modelling Framework for Systems Biology. Doctoral Thesis, University of Seville, Department of Computer Science and Artificial Intelligence (2008)Google Scholar
  21. 21.
    The GNU General Public License, http://www.gnu.org/copyleft/gpl.html
  22. 22.
    Java web page, http://www.java.com/
  23. 23.
    The Eclipse Project, http://www.eclipse.org
  24. 24.
    The P-Lingua website, http://www.p-lingua.org

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Manuel García-Quismondo
    • 1
  • Rosa Gutiérrez-Escudero
    • 1
  • Ignacio Pérez-Hurtado
    • 1
  • Mario J. Pérez-Jiménez
    • 1
  • Agustín Riscos-Núñez
    • 1
  1. 1.Research Group on Natural Computing, Department of Computer Science and Artificial IntelligenceUniversity of SevillaSevillaSpain

Personalised recommendations