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Tools and Simulators for Membrane Computing-A Literature Review

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Bio-inspired Computing – Theories and Applications (BIC-TA 2016)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 681))

Abstract

Membrane Computing comes under the field of Natural Computing. This was introduced by Gheorghe Paun. This field has been there from a decade. To realize Membrane Computing it is important to have tools that can be used either to process or simulate membrane computing. There have been several attempts in this area. This paper is an attempt to provide the details of the tools that are available for membrane computing. Primarily the tools are classified into two components. On one hand we have tools that are being used for specific type of P Systems or the tools which have a specific application. On the other hand there are tools which are comparatively generic in nature. Further this paper lists the tools that have been designed and developed to be used for the biological applications of P Systems. After classification, a brief description of the tools is given in this paper. Finally a brief quantitative analysis of the tools is done. Though there have been few surveys of P System tools, this is a slightly different paper which tries to classify and tries to a give review of the tools.

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References

  1. CLIPS. www.ghg.net/clips/CLIPS.html

  2. MeCoGUI. https://www.p-lingua.org/wiki/index.php/MeCoGUI

  3. Multi-Compartmental Stoachastic Simulation. http://www.infobiotics.org/completeDocumentation/modelSimulation/modelSimulation.html

  4. Parallel Programming and Computing Platform — CUDA. http://www.nvidia.com/object/cuda_home_new.html

  5. PMCGPU. http://www.p-lingua.org/wiki/index.php/PMCGPU

  6. PRISM Model Checker. http://www.prismmodelchecker.org/

  7. What is ANTLR? http://www.antlr.org/

  8. Software - The P Systems Page (2016). http://ppage.psystems.eu/index.php/Software

  9. Ardelean, I.I., Cavaliere, M.: Modelling biological processes by using a probabilistic P system software. Nat. Comput. 2(2), 173–197 (2003)

    Article  MATH  Google Scholar 

  10. Arroyo, F., Luengo, C., Baranda, A.V., Mingo, L.: A software simulation of transition P systems in Haskell. In: PĂun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.) WMC 2002. LNCS, vol. 2597, pp. 19–32. Springer, Heidelberg (2003). doi:10.1007/3-540-36490-0_2

    Chapter  Google Scholar 

  11. Bangalan, Z.F., Soriano, K.A.N., Juayong, R.A.B., Cabarle, F.G.C., Adorna, H.N., del Amor, M.A.M., et al.: A GPU Simulation for Evolution-Communication P Systems with Energy Having no Antiport Rules (2013)

    Google Scholar 

  12. Bianco, L., Manca, V., Marchetti, L., Petterlini, M.: Psim: a simulator for biomolecular dynamics based on P systems. In: 2007 IEEE Congress on Evolutionary Computation, pp. 883–887. IEEE (2007)

    Google Scholar 

  13. Blakes, J., Twycross, J., Romero, F.J., Krasnogor, N., et al.: The infobiotics workbench: an integrated in silico modelling platform for systems and synthetic biology. Bioinformatics 27(23), 3323–3324 (2011)

    Article  Google Scholar 

  14. Bonchiş, C., Ciobanu, G., Izbaşa, C., Petcu, D.: A web-based P systems simulator and its parallelization. In: Calude, C.S., Dinneen, M.J., Păun, G., Pérez-Jímenez, M.J., Rozenberg, G. (eds.) UC 2005. LNCS, vol. 3699, pp. 58–69. Springer, Heidelberg (2005). doi:10.1007/11560319_7

    Chapter  Google Scholar 

  15. Borrego-Ropero, R., Dıaz-Pernil, D., Pérez-Jiménez, M.J.: Tissue simulator: a graphical tool for tissue P systems. In: Proceedings of the International Workshop Automata for Cellular and Molecular Computing. Satellite of the 16th International Symposium on Fundamentals of Computational Theory. MTA SZTAKI, Budapest, Hungary, pp. 23–34 (2007)

    Google Scholar 

  16. Buiu, C., Arsene, O., Cipu, C., Patrascu, M.: A software tool for modeling and simulation of numerical P systems. BioSystems 103(3), 442–447 (2011)

    Article  Google Scholar 

  17. Cabarle, F., Adorna, H., Martinez-del Amor, M.A.: Simulating Spiking Neural P systems without delays using GPUs (2014)

    Google Scholar 

  18. Cabarle, F.G.C., Adorna, H., Martínez, M.A.: A spiking neural P system simulator based on CUDA. In: Gheorghe, M., Păun, G., Rozenberg, G., Salomaa, A., Verlan, S. (eds.) CMC 2011. LNCS, vol. 7184, pp. 87–103. Springer, Heidelberg (2012). doi:10.1007/978-3-642-28024-5_8

    Chapter  Google Scholar 

  19. Cabarle, F.G.C., Adorna, H., Martinez-del Amor, M.A.: An improved GPU simulator for spiking neural P systems. In: 2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA), pp. 262–267. IEEE (2011)

    Google Scholar 

  20. Campos, M., Llorens, C., Sempere, J.M., Futami, R., Rodriguez, I., Carrasco, P., Capilla, R., Latorre, A., Coque, T.M., Moya, A., et al.: A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES). Biol. Direct 10(1), 1 (2015)

    Article  Google Scholar 

  21. Castellini, A., Manca, V.: MetaPlab: a computational framework for metabolic P systems. In: Corne, D.W., Frisco, P., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2008. LNCS, vol. 5391, pp. 157–168. Springer, Heidelberg (2009). doi:10.1007/978-3-540-95885-7_12

    Chapter  Google Scholar 

  22. Cecilia, J.M., García, J.M., Guerrero, G.D., Martínez-del Amor, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J.: Simulating a P system based efficient solution to SAT by using GPUs. J. Logic Algebraic Program. 79(6), 317–325 (2010)

    Article  MATH  MathSciNet  Google Scholar 

  23. Cecilia, J.M., García, J.M., Guerrero, G.D., Martínez-del Amor, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J.: Simulation of P systems with active membranes on CUDA. Brief. Bioinform. 11(3), 313–322 (2010)

    Article  Google Scholar 

  24. Ciobanu, G., Paraschiv, D.: P system software simulator. Fundamenta Informaticae 49(1–3), 61–66 (2002)

    MATH  Google Scholar 

  25. Ciobanu, G., Păun, G., Pérez-Jiménez, M.J.: Applications of Membrane Computing, vol. 17. Springer, Heidelberg (2006)

    Google Scholar 

  26. Ciobanu, G., Paun, G., Stefanescu, G.: Sevilla carpets associated with P systems. In: Proceedings of the Brainstorming Week on Membrane Computing, Tarragona, Spain, pp. 135–140 (2003)

    Google Scholar 

  27. Ciobanu, G., Wenyuan, G.: P systems running on a cluster of computers. In: Martín-Vide, C., Mauri, G., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2003. LNCS, vol. 2933, pp. 123–139. Springer, Heidelberg (2004). doi:10.1007/978-3-540-24619-0_9

    Chapter  Google Scholar 

  28. Cordón-Franco, A., Gutiérrez-Naranjo, M.A., Pérez-Jiménez, M.J., Sancho-Caparrini, F.: A prolog simulator for deterministic P systems with active membranes. New Gen. Comput. 22(4), 349–363 (2004)

    Article  MATH  Google Scholar 

  29. Das, D.K., Renz, T.: A simulation model for P systems with active membranes. In: 2006 IEEE Conference on Emerging Technologies-Nanoelectronics, pp. 338–340. IEEE (2006)

    Google Scholar 

  30. Díaz Pernil, D., de Mendoza, I.P.H., de Jesús Pérez Jiménez, M., Núñez, A.R., et al.: P-Lingua: A Programming Language for Membrane Computing (2008)

    Google Scholar 

  31. Manuel Garca-Quismondo Fernndez. A Java-Based P-Lingua Simulator for Enzymatic Numerical P Systems Available. http://www.cs.us.es/blogs/mgarcia/research/software_tools/java_simulator_enps/

  32. Florea, A.G., Buiu, C.: Lulu-a software simulator for P colonies. Use case scenarios and demonstration videos (2015)

    Google Scholar 

  33. Florea, A.G., Buiu, C.: Development of a software simulator for P colonies-applications in robotics. Int. J. Unconv. Comput. 12, 189–205 (2016)

    Google Scholar 

  34. Frisco, P., Gibson, R.T.: A simulator and an evolution program for conformon-P systems. In: SYNASC, vol. 7, pp. 26–27 (2005)

    Google Scholar 

  35. Ciobanu, G., Paraschiv, D.: Membrane software. A P system simulator. Technical report, Pre-Proceedings of Workshop on Membrane Computing, Curtea de Arges, Romania, August 2001, Technical report 17/01 of Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain (2001)

    Google Scholar 

  36. Quismondo, M.G., Pavel, A.B., de Jesús Pérez Jiménez, M. et al.: Simulating Large-Scale ENPS Models by Means of GPU (2012)

    Google Scholar 

  37. García-Quismondo, M., Martínez-del-Amor, M.A., Pérez-Jiménez, M.J.: Probabilistic guarded P systems, a new formal modelling framework. In: Gheorghe, M., Rozenberg, G., Salomaa, A., Sosík, P., Zandron, C. (eds.) CMC 2014. LNCS, vol. 8961, pp. 194–214. Springer, Heidelberg (2014). doi:10.1007/978-3-319-14370-5_12

    Google Scholar 

  38. Gheorghe, M.: System Modeling Framework (2016). http://staffwww.dcs.shef.ac.uk/people/M.Gheorghe/PSimulatorWeb/Tools.htm

  39. Paun, G., Rozenberg, G.: A guide to membrane computing. Theor. Comput. Sci. 287(1), 73–100 (2002)

    Article  MATH  MathSciNet  Google Scholar 

  40. Grosu, R., Smolka, S.A.: Monte carlo model checking. In: Halbwachs, N., Zuck, L.D. (eds.) TACAS 2005. LNCS, vol. 3440, pp. 271–286. Springer, Heidelberg (2005). doi:10.1007/978-3-540-31980-1_18

    Chapter  Google Scholar 

  41. Naranjo, M.A.G., de Jesús Pérez Jiménez, M., Núñez, A.R., et al.: A Simulator for Confluent P Systems (2005)

    Google Scholar 

  42. Hucka, M., Finney, A., Sauro, H.M., Bolouri, H., Doyle, J.C., Kitano, H., Arkin, A.P., Bornstein, B.J., Bray, D., Cornish-Bowden, A., et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4), 524–531 (2003)

    Article  Google Scholar 

  43. Ionescu, M., Păun, A., Păun, G., Pérez-Jiménez, M.J.: Computing with spiking neural P systems: traces and small universal systems. In: Mao, C., Yokomori, T. (eds.) DNA 2006. LNCS, vol. 4287, pp. 1–16. Springer, Heidelberg (2006). doi:10.1007/11925903_1

    Chapter  Google Scholar 

  44. Ionescu, M., Păun, G., Yokomori, T.: Spiking neural P systems. Fundamenta Informaticae 71(2, 3), 279–308 (2006)

    MATH  MathSciNet  Google Scholar 

  45. Macías–Ramos, L.F., Pérez–Hurtado, I., García–Quismondo, M., Valencia–Cabrera, L., Pérez–Jiménez, M.J., Riscos–Núñez, A.: A P–lingua based simulator for spiking neural P systems. In: Gheorghe, M., Păun, G., Rozenberg, G., Salomaa, A., Verlan, S. (eds.) CMC 2011. LNCS, vol. 7184, pp. 257–281. Springer, Heidelberg (2012). doi:10.1007/978-3-642-28024-5_18

    Chapter  Google Scholar 

  46. Macías-Ramos, L.F., Valencia-Cabrera, L., Song, B., Song, T., Pan, L., Pérez-Jiménez, M.J.: A P_lingua based simulator for P systems with symport/antiport rules. Fundamenta Informaticae 139(2), 211–227 (2015)

    Article  MATH  MathSciNet  Google Scholar 

  47. Malita, M.: Membrane computing in prolog. In: Pre-Proceedings of The Workshop on Multiset Processing (WMP-CdeA 2000), p. 8 (2000)

    Google Scholar 

  48. Maroosi, A., Muniyandi, R.C.: Accelerated simulation of membrane computing to solve the N-queens problem on multi-core. In: Panigrahi, B.K., Suganthan, P.N., Das, S., Dash, S.S. (eds.) SEMCCO 2013. LNCS, vol. 8298, pp. 257–267. Springer, Heidelberg (2013). doi:10.1007/978-3-319-03756-1_23

    Chapter  Google Scholar 

  49. Maroosi, A., Muniyandi, R.C., Sundararajan, E.A., Zin, A.M.: Improved implementation of simulation for membrane computing on the graphic processing unit. Procedia Technol. 11, 184–190 (2013)

    Article  Google Scholar 

  50. Martínez-del-Amor, M.A., Macías-Ramos, L.F., Valencia-Cabrera, L., Riscos-Núñez, A., Pérez-Jiménez, M.J.: Accelerated simulation of P systems on the GPU: a survey. In: Pan, L., Păun, G., Pérez-Jiménez, M.J., Song, T. (eds.) BIC-TA 2014. CCIS, vol. 472, pp. 308–312. Springer, Heidelberg (2014). doi:10.1007/978-3-662-45049-9_50

    Google Scholar 

  51. 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

    Chapter  Google Scholar 

  52. Martínez-del Amor, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Riscos-Núñez, A.: A P-lingua based simulator for tissue P systems. J. Logic Algebraic Program. 79(6), 374–382 (2010)

    Article  MATH  MathSciNet  Google Scholar 

  53. Martínez del Amor, M.A., Karlin, I., Jensen, R.E., de Jesús Pérez Jiménez, M., Elster, A.C., et al.: Parallel simulation of probabilistic P systems on multicore platforms. In: Proceedings of the Tenth Brainstorming Week on Membrane Computing, vol. 2, pp. 17–26. Sevilla, ETS de Ingeniería Informática, 30 de Enero-3 de Febrero (2012)

    Google Scholar 

  54. del Amor, M.A.M., Carrasco, J.P., de Jesús Pérez Jiménez, M., et al.: Simulating a Family of Tissue P Systems Solving SAT on the GPU (2013)

    Google Scholar 

  55. de los Ángeles Nepomuceno Chamorro, I., et al.: A Java Simulator for Basic Transition P Systems (2004)

    Google Scholar 

  56. de los Ángeles Nepomuceno Chamorro, I., Chamorro, J.A.N., Campero, F.J.R., et al.: A tool for using the SBML format to represent P systems which model biological reaction networks (2005)

    Google Scholar 

  57. Nishida, T.Y.: Membrane algorithms: approximate algorithms for NP-complete optimization problems. In: Ciobanu, G., Paun, G., Pérez-Jiménez, M.J. (eds.) Applications of Membrane Computing, pp. 303–314. Springer, Heidelberg (2006)

    Google Scholar 

  58. Balbontín Noval, D., Pérez Jiménez, M.J., Sancho Caparrini, F.: A MzScheme implementation of transition P systems. In: PĂun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.) WMC 2002. LNCS, vol. 2597, pp. 58–73. Springer, Heidelberg (2003). doi:10.1007/3-540-36490-0_5

    Chapter  Google Scholar 

  59. Pieris Oleracea. PGSP Systems. http://www.p-lingua.org/wiki/index.php/PGSP_systems:_Pieris_oleracea

  60. Martín, D.O., Díaz, C.G., del Amor, M.Á.M., Núñez, A.R., Cabrera, L.V., et al.: Revisiting sevilla carpets: a new tool for the P-lingua era. In: Proceedings of the Twelfth Brainstorming Week on Membrane Computing, pp. 281–292. Sevilla, ETS de Ingeniería Informática, 3–7 de Febrero (2014)

    Google Scholar 

  61. Paun, G.: Membrane Computing: An Introduction. Springer Science & Business Media, Heidelberg (2012)

    MATH  Google Scholar 

  62. Paun, G., Rozenberg, G., Salomaa, A.: The Oxford Handbook of Membrane Computing. Oxford University Press Inc., Oxford (2010)

    Book  MATH  Google Scholar 

  63. Perez-Hurtado, I., Valencia-Cabrera, L., Chacon, J.M., Riscos-Nunez, A., Perez-Jimenez, M.J.: A P-lingua based simulator for tissue P systems with cell separation. Sce. Technol. 17(1), 89–102 (2014)

    Google Scholar 

  64. Pérez-Hurtado, I., Valencia-Cabrera, L., Pérez-Jiménez, M.J., Colomer, M.A., Riscos-Núñez, A.: MeCoSim: a general purpose software tool for simulating biological phenomena by means of P systems. In: 2010 IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA), pp. 637–643. IEEE (2010)

    Google Scholar 

  65. de Jesús Pérez Jiménez, M., Campero, F.J.R., et al.: A CLIPS Simulator for Recognizer P Systems with Active Membranes (2004)

    Google Scholar 

  66. Pescini, D., Besozzi, D., Mauri, G., Zandron, C.: Dynamical probabilistic P systems. Int. J. Found. Comput. Sci. 17(01), 183–204 (2006)

    Article  MATH  MathSciNet  Google Scholar 

  67. Martínez, D.R., Naranjo, M.A.G., et al.: A Software Tool for Dealing with Spiking Neural P Systems (2007)

    Google Scholar 

  68. Ravie, C., Ali, M.: Enhancing the simulation of membrane system on the GPU for the N-queens problem. Chin. J. Electron. 24(4), 740–743 (2015)

    Article  Google Scholar 

  69. Rivero-Gil, E., Gutiérrez-Naranjo, M.A., Romero-Jiménez, A., Riscos-Núñez, A.: A software tool for generating graphics by means of P systems. Nat. Comput. 10(2), 879–890 (2011)

    Article  MATH  MathSciNet  Google Scholar 

  70. Sedwards, S., Mazza, T.: Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes. Bioinformatics 23(20), 2800–2802 (2007)

    Article  Google Scholar 

  71. Suzuki, Y., Tanaka, H.: On a LISP implementation of a class of P systems. Rom. J. Inf. Sci. Technol. 3(2), 173–186 (2000)

    Google Scholar 

  72. Syropoulos, A., Mamatas, E.G., Allilomes, P.C., Sotiriades, K.T.: A distributed simulation of transition P systems. In: Martín-Vide, C., Mauri, G., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2003. LNCS, vol. 2933, pp. 357–368. Springer, Heidelberg (2004). doi:10.1007/978-3-540-24619-0_25

    Chapter  Google Scholar 

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  1. National Institute of Technology Karnataka Surathkal, Mangalore, India

    S. Raghavan & K. Chandrasekaran

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  1. S. Raghavan
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  1. Xidian University, Xi’an, China

    Maoguo Gong

  2. Huazhong University of Science and Technology, Wuhan, China

    Linqiang Pan

  3. China University of Petroleum, Qingdao, China

    Tao Song

  4. Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Kuching, China

    Gexiang Zhang

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Raghavan, S., Chandrasekaran, K. (2016). Tools and Simulators for Membrane Computing-A Literature Review. In: Gong, M., Pan, L., Song, T., Zhang, G. (eds) Bio-inspired Computing – Theories and Applications. BIC-TA 2016. Communications in Computer and Information Science, vol 681. Springer, Singapore. https://doi.org/10.1007/978-981-10-3611-8_23

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