Skip to main content

A Bioinspired Computing Approach to Model Complex Systems

  • Conference paper
  • First Online:
Membrane Computing (CMC 2014)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8961))

Included in the following conference series:

Abstract

The use of models is intrinsic to any scientific activity. In particular, formal/mathematical models provide a relevant tool for scientific investigation. This paper presents a new Membrane Computing based computational paradigm as a framework for modelling processes and real-life phenomena. P systems, devices in Membrane Computing, are not used as a computing paradigm, but rather as a formalism for describing the behaviour of the system to be modelled. They offer an approach to the development of models for biological systems that meets the requirements of a good modelling framework: relevance, understandability, extensibility and computability.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Cardona, M., Colomer, M.A., Margalida, A., Palau, A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Sanuy, D.: A computational modeling for real ecosystems based on P systems. Natural Computing 10(1), 39–53 (2011)

    Article  MATH  MathSciNet  Google Scholar 

  2. Cheruku, S., Păun, A., Romero, F.J., Pérez-Jiménez, M.J., Ibarra, O.H.: Simulating FAS-induced apoptosis by using P systems. Progress in Natural Science 17(4), 424–431 (2007)

    Article  MATH  MathSciNet  Google Scholar 

  3. Colomer, M.A., Margalida, A., Sanuy, D., Pérez-Jiménez, M.J.: A bio-inspired computing model as a new tool for modeling ecosystems: The avian scavengers as a case study. Ecological modelling 222(1), 33–47 (2011)

    Article  Google Scholar 

  4. Colomer, M.A., Margalida, A., Valencia, L., Palau, A.: Application of a computational model for complex fluvial ecosystems: The population dynamics of zebra mussel Dreissena polymorpha as a case study. Ecological Complexity 20, 116–126 (2014)

    Article  Google Scholar 

  5. Colomer, M.A., Margalida, A., Pérez-Jiménez, M.J.: Population Dynamics P System (PDP) Models: A Standardized Protocol for Describing and Applying Novel Bio-Inspired Computing Tools. PLOS ONE 8(4), e60698 (2013). doi:10.1371/journal.pone.0060698

    Article  Google Scholar 

  6. Colomer, M.A., Lavín, S., Marco, I., Margalida, A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Sanuy, D., Serrano, E., Valencia-Cabrera, L.: Modeling population growth of Pyrenean chamois (Rupicapra p. pyrenaica) by using P-systems. In: Gheorghe, M., Hinze, T., Păun, Gh., Rozenberg, G., Salomaa, A. (eds.) CMC 2010. LNCS, vol. 6501, pp. 144–159. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  7. Colomer, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Riscos, A.: Comparing simulation algorithms for multienvironment probabilistic P system over a standard virtual ecosystem. Natural Computing 11, 369–379 (2012)

    Article  MATH  MathSciNet  Google Scholar 

  8. Crampe, J.P., Gaillard, J.M., Loison, A.: L’enneigement hivernal: un facteur de variation du recrutement chez l’isard (Rupicapra pyrenaica pyrenaica). Canadian Journal of Zoology 80, 306–1312 (2002)

    Article  Google Scholar 

  9. Funahashi, A., Morohashi, M., Kitano, H.: Cell Designer: a Process Diagram Editor for Gene-regulatory and Biochemical Networks. Biosilico 1, 159–162 (2003)

    Article  Google Scholar 

  10. Gillespie, D.T.: A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. Journal of Computational Physics 22, 403–434 (1976)

    Article  MathSciNet  Google Scholar 

  11. Gillespie, D.T.: Exact Stochastic Simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry 81(25), 2340–2361 (1977)

    Article  Google Scholar 

  12. Gillespie, D.T.: Approximate Accelerated Stochastic Simulation of Chemically Reacting Systems. Journal of Chemical Physics 115(4), 1716–1733 (2001)

    Article  Google Scholar 

  13. Gillespie, D.T.: Improved Leap-size Selection for Accelerated Stochastic Simulation. Journal of Chemical Physics 119(16), 8229–8234 (2003)

    Article  Google Scholar 

  14. Hua, F., Cornejo, M., Cardone, M., Stokes, C., Lauffenburger, D.: Effects of Bcl-2 Levels on FAS Signaling-Induced Caspase-3 Activation: Molecular Genetic Tests of Computational Model Predictions. The Journal of Immunology 175(2), 985–995 (2005). (and correction 175(9), 6235–6237 (2005))

    Article  Google Scholar 

  15. Jørgensen, S.E.: Ecological Modelling. An introduction. WIT Press, Southampton (2009)

    Google Scholar 

  16. 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, Gy. (eds.) CMC 2012. LNCS, vol. 7762, pp. 257–276. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  17. Nunes de Castro, L., Silveira, R., Pasti, R., Dourado, R., Szabo, A., Gomes, D.: The Grand Challenges in Natural Computing Research: The Quest for a New Science. International Journal of Natural Computing Research 2(4), 17–30 (2011)

    Article  Google Scholar 

  18. Pérez-Jímenez, 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)

    Chapter  Google Scholar 

  19. Regev, A., Shapiro, E.: The \(\pi \)-calculus as an abstraction for biomolecular systems. In: Ciobanu, G., Rozenberg, G. (eds.) Modelling in Molecular Biology. Springer, Berlin (2004)

    Google Scholar 

  20. Romero, F.J., Pérez-Jiménez, M.J.: Modelling gene expression control using P systems: The Lac Operon, a case study. BioSystems 91(3), 438–457 (2008)

    Article  Google Scholar 

  21. Romero, F.J., Pérez-Jiménez, M.J.: A model of the Quorum Sensing System in Vibrio Fischeri using P systems. Artificial Life 14(1), 95–109 (2008)

    Article  Google Scholar 

  22. Ruíz Altaba, C., Jiménez, P.J., López, M.A.: El temido mejillón cebra empieza a invadir los ríos españoles desde el curso bajo del río Ebro. Quercus 188, 50–51 (2001)

    Google Scholar 

  23. Scaffidi, C., Fulda, S., Srinivasan, A., Friesen, C., Li, F., Tomaselli, K.J., Debatin, K.M., Krammer, P.H., Peter, M.E.: Two CD95 (APO-1/Fas) signaling pathways. The Embo Journal 17, 1675–1687 (1998)

    Article  Google Scholar 

  24. ISI web page. http://esi-topics.com/erf/october2003.html

  25. SciLab Web Site. http://scilabsoft.inria.fr/

  26. P Systems Modelling Framework Web Site. http://www.dcs.shef.ac.uk/~marian/PSystemMF.htm

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Mario J. Pérez-Jiménez .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this paper

Cite this paper

Pérez-Jiménez, M.J. (2014). A Bioinspired Computing Approach to Model Complex Systems. In: Gheorghe, M., Rozenberg, G., Salomaa, A., Sosík, P., Zandron, C. (eds) Membrane Computing. CMC 2014. Lecture Notes in Computer Science(), vol 8961. Springer, Cham. https://doi.org/10.1007/978-3-319-14370-5_2

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-14370-5_2

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-14369-9

  • Online ISBN: 978-3-319-14370-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics