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Available Membrane Computing Software

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Applications of Membrane Computing

Part of the book series: Natural Computing Series ((NCS))

Abstract

The simulation of a P system with current computers is a quite complex task. P systems are intrinsically nondeterministic computational devices and therefore their computation trees are difficult to store and handle with computers with one processor (or a bounded number of processors). Nevertheless, there exists a first generation of simulators which can be successfully used for pedagogical purposes and as assistant tools for researchers. This chapter summarizes some of these simulators, presenting the state of the art of the available software for simulating (different variants of) cell-like membrane systems.

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References

  1. A. Alhazov: Maximally Parallel Multiset-Rewriting Systems: Browsing the Configurations. Proc. Third Brainstorming Week on Membrane Computing, Sevilla, 2005, RGNC Report 01/2005, 1–10.

    Google Scholar 

  2. A. Alhazov, M. Margenstern, V. Rogozhin, Yu. Rogozhin, S. Verlan: Communicative P systems with Minimal Cooperation. In Gh. Păun, M.J. Pérez-Jiménez, G. Rozenberg, A. Salomaa, eds.: Membrane Computing. International Workshop WMC5, Milano, Italy, 2004. Revised Papers. LNCS 3365, Springer, Berlin, 2005 [35].

    Google Scholar 

  3. A. Alhazov, C. Martín-Vide, Gh. Păun, eds.: Pre-Proceedings of the Workshop on Membrane Computing, Tarragona, Spain, 2003, Report RGML 28/03.

    Google Scholar 

  4. I.I. Ardelean, M. Cavaliere: Modelling Biological Processes by Using a Probabilistic P System Software. Natural Computing, 2,2 (2003), 173–197.

    Article  MATH  Google Scholar 

  5. F. Arroyo, A.V. Baranda, J. Castellanos, C. Luengo, L.F. de Mingo: A Recursive Algorithm for Describing Evolution in Transition P Systems. In Gh. Păun, eds.: Pre-Proceedings of Workshop on Membrane Computing, Curtea de Argeş, Romania, August 2001. Technical Report GRLMC 17/01, Rovira i Virgili University, Tarragona, Spain, 2001 [33], 19–30.

    Google Scholar 

  6. F. Arroyo, A.V. Baranda, J. Castellanos, C. Luengo, L.F. de Mingo: Structures and Bio-Language to Simulate Transition P Systems on Digital Computers. In Gh. Păun, G. Rozenberg, A. Salomaa, eds.: Multiset Processing. Mathematical, Computer Science and Molecular Computing Points of View, LNCS 2235, Springer, Berlin, 2001 [17], 1–16.

    Google Scholar 

  7. F. Arroyo, C. Luengo, A.V. Baranda, L.F. de Mingo: A Software Simulation of Transition P Systems in Haskell. In G. Rozenberg, A. Salomaa, C. Zandron, eds.: Membrane Computing, International Workshop WMC-CdeA 2002, Curtea de Argeş, Romania. Revised Papers. LNCS 2597, Springer, Berlin, 2003 [43], 19–32.

    Chapter  Google Scholar 

  8. H. Attiya, J. Welch: Distributed Computing: Fundamentals, Simulations and Advanced Topics. McGraw-Hill, 2000.

    Google Scholar 

  9. A.V. Baranda, J. Castellanos, F. Arroyo, R. Gonzalo: Data Structures for Implementing P Systems in Silico. In M.J. Dinneen, Gh. Păun, eds.: Pre-Proceedings of Workshop on Multiset Processing, Curtea de Argeş, Romania, CDMTCS TR 140, Univ. of Auckland, 2000 [16], 21–34.

    Google Scholar 

  10. A.V. Baranda, J. Castellanos, F. Arroyo, R. Gonzalo: Towards an Electronic Implementation of Membrane Computing: A Formal Description of Nondeterministic Evolution in Transition P Systems. In Proceedings of DNA-Based Computers, Tampa, Florida, 2002 (N. Jonoska, N.C. Seeman, eds.), LNCS 2340, Springer, Berlin, 2002, 350–359.

    Google Scholar 

  11. A.V. Baranda, J. Castellanos, R. Gonzalo, F. Arroyo, L.F. de Mingo: Data Structures for Implementing Transition P Systems in Silico. Romanian Journal of Information Science and Technology, 4,1–2, (2001), 21–32.

    Google Scholar 

  12. D. Balbontín-Noval, M.J. Pérez-Jiménez, F. Sancho-Caparrini: A MzScheme Implementation of Transition P Systems. In G. Rozenberg, A. Salomaa, C. Zandron, eds.: Membrane Computing, International Workshop WMC-CdeA 2002, Curtea de Argeş, Romania. Revised Papers. LNCS 2597, Springer, Berlin, 2003 [43], 58–73.

    Chapter  Google Scholar 

  13. L. Bianco: A P System Simulator: Introduction to Psim. Unpublished manuscript, 2004.

    Google Scholar 

  14. L. Bianco, F. Fontana, G. Franco, V. Manca: P Systems for Biological Dynamics. In this volume.

    Google Scholar 

  15. A. Binder, R. Freund, G. Lojka, M. Oswald: Implementation of Catalytic P Systems. Proceedings of CIAA 2004, Ninth International Conference on Implementation and Application of Automata, Kingston, Canada, 2004, 24–33.

    Google Scholar 

  16. C.S. Calude, M.J. Dinneen, Gh. Păun, eds.: Pre-Proceedings of Workshop on Multiset Processing, Curtea de Argeş, Romania, CDMTCS TR 140, Univ. of Auckland, 2000.

    Google Scholar 

  17. C.S. Calude, Gh. Păun, G. Rozenberg, A. Salomaa, eds.: Multiset Processing. Mathematical, Computer Science and Molecular Computing Points of View, LNCS 2235, Springer, Berlin, 2001.

    MATH  Google Scholar 

  18. M. Cavaliere: Evolution-Communication P Systems. In G. Rozenberg, A. Salomaa, C. Zandron, eds.: Membrane Computing, International Workshop WMC-CdeA 2002, Curtea de Argeş, Romania. Revised Papers. LNCS 2597, Springer, Berlin, 2003 [43], 134–145.

    Chapter  Google Scholar 

  19. M. Cavaliere, I.I. Ardelean: Modelling Respiration in Bacteria and Respiration/Photosynthesis Interaction in Cyanobacteria by Using a P System Simulator. In this volume.

    Google Scholar 

  20. M. Cavaliere, C. Martín-Vide, Gh. Păun, eds.: Proceedings of the Brainstorming Week on Membrane Computing, Tarragona, Spain, 2003, Report RGML 26/03.

    Google Scholar 

  21. G. Ciobanu, D. Paraschiv: P System Software Simulator. Fundamenta Informaticae, 49,1–3 (2002), 61–66.

    MATH  Google Scholar 

  22. G. Ciobanu, Gh. Păun, Gh. Ştefănescu: Sevilla Carpets Associated with P Systems. In C. Martín-Vide, Gh. Păun, eds.: Proceedings of the Brainstorming Week on Membrane Computing, Tarragona, Spain, 2003, Report RGML 26/03 [20], 135–140.

    Google Scholar 

  23. G. Ciobanu, G. Wenyuan: A Parallel Implementation of Transition P Systems. In C. Martín-Vide, Gh. Păun, eds.: Pre-Proceedings of the Workshop on Membrane Computing, Tarragona, Spain, 2003, Report RGML 28/03 [3], 169–184.

    Google Scholar 

  24. G. Ciobanu, G. Wenyuan: P Systems Running on a Cluster of Computers. In Gh. Păun, G. Rozenberg, A. Salomaa, eds.: Membrane Computing. International Workshop WMC2003, Tarragona, Spain, 2003. Revised Papers. LNCS 2933, Springer, Berlin, 2004 [34], 123–139.

    Google Scholar 

  25. A. Cordón-Franco, M.A. Gutiérrez-Naranjo. M.J. Pérez-Jiménez, A. Riscos-Núñez, F. Sancho-Caparrini: Implementing in Prolog an Effective Cellular So-lution to the Knapsack Problem. In Gh. Păun, G. Rozenberg, A. Salomaa, eds.: Membrane Computing. International Workshop WMC2003, Tarragona, Spain, 2003. Revised Papers. LNCS 2933, Springer, Berlin, 2004 [34], 140–152.

    Google Scholar 

  26. A. Cordón-Franco, M.A. Gutiérrez-Naranjo, M.J. Pérez-Jiménez, A. Riscos-Núñez, F. Sancho-Caparrini: Cellular Solutions of Some Numerical NP-Complete Problems: A Prolog Implementation. In Molecular Computational Models: Unconventional Approaches (M. Gheorghe, ed.), Idea Group, Inc., 2005, 115–149.

    Google Scholar 

  27. A. Cordón-Franco, M.A. Gutiérrez-Naranjo, M.J. Pérez-Jiménez, F. Sancho-Caparrini: A Prolog Simulator for Deterministic P Systems with Active Membranes. New Generation Computing, 22,4 (2004), 349–364.

    Article  MATH  Google Scholar 

  28. M.A. Gutiérrez-Naranjo, M.J. Pérez-Jiménez, A. Riscos-Núñez: A Fast P System for Finding Balanced 2-Partition. Soft Computing, 9 (2005).

    Google Scholar 

  29. M.A. Gutiérrez-Naranjo, M.J. Pérez-Jiménez, A. Riscos-Núñez: On Descriptive Complexity of P Systems. In Gh. Păun, C. Zandron, eds.: Pre-Proceedings of the Workshop on Membrane Computing WMC5, Universitá di Milano-Bicocca, Italy, 2004 [36], 245–255.

    Google Scholar 

  30. M. Maliţa: Membrane Computing in Prolog. In M.J. Dinneen, Gh. Păun, eds.: Pre-Proceedings of Workshop on Multiset Processing, Curtea de Argeş, Romania, CDMTCS TR 140, Univ. of Auckland, 2000 [16], 159–175.

    Google Scholar 

  31. V. Manca: On the Dynamics of P Systems. In Gh. Păun, C. Zandron, eds.: Pre-Proceedings of the Workshop on Membrane Computing WMC5, Universitá di Milano-Bicocca, Italy, 2004 [36], 29–43.

    Google Scholar 

  32. M. Margenstern, V. Rogozhin, Yu. Rogozhin, S. Verlan: About P Systems with Minimal Symport/Antiport Rules and Four Membranes. In Gh. Păun, C. Zandron, eds.: Pre-Proceedings of the Workshop on Membrane Computing WMC5, Universitá di Milano-Bicocca, Italy, 2004 [36], 283–294.

    Google Scholar 

  33. C. Martín-Vide, Gh. Păun, eds.: Pre-Proceedings of Workshop on Membrane Computing, Curtea de Argeş, Romania, August 2001. Technical Report GRLMC 17/01, Rovira i Virgili University, Tarragona, Spain, 2001.

    Google Scholar 

  34. C. Martín-Vide, Gh. Păun, G. Rozenberg, A. Salomaa, eds.: Membrane Computing. International Workshop WMC2003, Tarragona, Spain, 2003. Revised Papers. LNCS 2933, Springer, Berlin, 2004.

    MATH  Google Scholar 

  35. G. Mauri, Gh. Păun, M.J. Pérez-Jiménez, G. Rozenberg, A. Salomaa, eds.: Membrane Computing. International Workshop WMC5, Milano, Italy, 2004. Revised Papers. LNCS 3365, Springer, Berlin, 2005.

    MATH  Google Scholar 

  36. G. Mauri, Gh. Păun, C. Zandron, eds.: Pre-Proceedings of the Workshop on Membrane Computing WMC5, Universitá di Milano-Bicocca, Italy, 2004.

    Google Scholar 

  37. I.A. Nepomuceno-Chamorro: A Java Simulator for Basic Transition P Systems. In A. Riscos-Núñez, A. Romero-Jiménez, F. Sancho-Caparrini, eds.: Proceedings of the Second Brainstorming Week on Membrane Computing, Sevilla, Spain, Report RGNC 01/04, 2004 [42], 309–315.

    Google Scholar 

  38. D.V. Nicolau Jr., G. Solana, F. Fulga, D.V. Nicolau: A C Library for Simulating P Systems. Fundamenta Informaticae, 49,1–3 (2002), 241–248.

    MATH  Google Scholar 

  39. Gh. Păun: Computing with Membranes. Turku Centre for Computer Science, TUCS Technical Report, Nr.208, 1998.

    Google Scholar 

  40. Gh. Păun: Computing with Membranes. Journal of Computer and System Sciences, 61,1 (2000), 108–143.

    Article  MATH  MathSciNet  Google Scholar 

  41. Gh. Păun: P Systems with Active Membranes: Attacking NP-Complete Problems. Journal of Automata, Languages and Combinatorics, 6,1 (2001), 75–90.

    MATH  MathSciNet  Google Scholar 

  42. Gh. Păun, A. Riscos-Núñez, A. Romero-Jiménez, F. Sancho-Caparrini, eds.: Proceedings of the Second Brainstorming Week on Membrane Computing, Sevilla, Spain, Report RGNC 01/04, 2004.

    Google Scholar 

  43. Gh. Păun, G. Rozenberg, A. Salomaa, C. Zandron, eds.: Membrane Computing, International Workshop WMC-CdeA 2002, Curtea de Argeş, Romania. Revised Papers. LNCS 2597, Springer, Berlin, 2003.

    MATH  Google Scholar 

  44. Gh. Păun: Membrane Computing. An Introduction. Springer, Berlin, 2002.

    MATH  Google Scholar 

  45. M.J. Pérez-Jiménez, F. Romero-Campero: A CLIPS Simulator for Recognizer P Systems with Active Membranes. In A. Riscos-Núñez, A. Romero-Jiménez, F. Sancho-Caparrini, eds.: Proceedings of the Second Brainstorming Week on Membrane Computing, Sevilla, Spain, Report RGNC 01/04, 2004 [42], 387–413.

    Google Scholar 

  46. M.J. Pérez-Jiménez, A. Romero-Jiménez, F. Sancho-Caparrini: Solving VALIDITY Problem by Active Membranes with Input. In C. Martín-Vide, Gh. Păun, eds.: Proceedings of the Brainstorming Week on Membrane Computing, Tarragona, Spain, 2003, Report RGML 26/03 [20], 279–290.

    Google Scholar 

  47. M.J. Pérez-Jiménez, F. Sancho-Caparrini: A Formalization of Transition P Systems. Fundamenta Informaticae, 49,1–3 (2002), 261–272.

    MATH  MathSciNet  Google Scholar 

  48. B. Petreska, C. Teuscher: A Reconfigurable Hardware Membrane System. In Gh. Păun, G. Rozenberg, A. Salomaa, eds.: Membrane Computing. International Workshop WMC2003, Tarragona, Spain, 2003. Revised Papers. LNCS 2933, Springer, Berlin, 2004 [34], 269–285.

    Google Scholar 

  49. A. Riscos-Núñez: Cellular Programming: Efficient Resolution of Numerical NP-Complete Problems. Ph.D. Thesis, University of Seville, 2004.

    Google Scholar 

  50. Y. Suzuki, H. Tanaka: On a LISP Implementation of a Class of P Systems. Romanian Journal of Information Science and Technology, 3,2 (2000), 173–186.

    Google Scholar 

  51. Y. Suzuki, Y. Fujiwara, H. Tanaka, J. Takabayashi: Artificial Life Applications of a Class of P Systems: Abstract Rewriting Systems on Multisets. In Gh. Păun, G. Rozenberg, A. Salomaa, eds.: Multiset Processing. Mathematical, Computer Science and Molecular Computing Points of View, LNCS 2235, Springer, Berlin, 2001 [17], 299–346.

    Google Scholar 

  52. A. Syropoulos, E.G. Mamatas, P.C. Allilomes, K.T. Sotiriades: A Distributed Simulation of Transition P Systems. In Gh. Păun, G. Rozenberg, A. Salomaa, eds.: Membrane Computing. International Workshop WMC2003, Tarragona, Spain, 2003. Revised Papers. LNCS 2933, Springer, Berlin, 2004 [34], 357–368.

    Google Scholar 

  53. http://research.araneous.com

    Google Scholar 

  54. http://www.lpsi.eui.upm.es/nncg/

    Google Scholar 

  55. http://psystems.disco.unimib.it/

    Google Scholar 

  56. http://www.di.univr.it

    Google Scholar 

  57. http://www.gcn.us.es

    Google Scholar 

  58. http://www.teuscher.ch/psystems

    Google Scholar 

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Author information

Authors and Affiliations

  1. Research Group on Natural Computing Department of Computer Science and Artificial Intelligence, University of Sevilla, Avda. Reina Mercedes s/n, 41012, Sevilla, Spain

    Miguel Angel Gutiérrez-Naranjo, Mario J. Pérez-Jiménez & Agustín Riscos-Núñez

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  1. Miguel Angel Gutiérrez-Naranjo
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  2. Mario J. Pérez-Jiménez
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  3. Agustín Riscos-Núñez
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Editor information

Editors and Affiliations

  1. Institute of Computer Science of the Romanian Academy, Blvd. Copou 8, 700506, Iaşi, Romania

    Gabriel Ciobanu

  2. Research Group on Natural Computing Department of Computer Science and Artificial Intelligence, University of Seville, Avda. Reina Mercedes s/n, 41012, Seville, Spain

    Gheorghe Păun  & Mario J. Pérez-Jiménez  & 

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Gutiérrez-Naranjo, M.A., Pérez-Jiménez, M.J., Riscos-Núñez, A. (2006). Available Membrane Computing Software. In: Ciobanu, G., Păun, G., Pérez-Jiménez, M.J. (eds) Applications of Membrane Computing. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-29937-8_15

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  • DOI: https://doi.org/10.1007/3-540-29937-8_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25017-3

  • Online ISBN: 978-3-540-29937-0

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