P Systems, a New Computational Modelling Tool for Systems Biology

  • Mario Jesús Pérez-Jiménez
  • Francisco José Romero-Campero
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4220)


In this paper we present P systems as a reliable computational modelling tool for Systems Biology that takes into account the discrete character of the quantity of components of biological systems, the inherently randomness in biological phenomena and the key role played by membranes in the functioning of living cells. We will introduce two different strategies for the evolution of P systems, namely, Multi-compartmental Gillespie’s Algorithm based on the well known Gillespie’s Algorithm but running on more than one compartment; and Deterministic Waiting Times Algorithm, an exact deterministic method. In order to illustrate these two strategies we have modelled two biological systems: the EGFR Signalling Cascade and the Quorum Sensing System in the bacterium Vibrio Fischeri. Our simulations results show that for the former system a deterministic approach is valid whereas for the latter a stochastic approach like Multi-compartmental Gillespie’s Algorithm is necessary.


Epidermal Growth Factor System Biology Membrane Structure Quorum Sensing Venn Diagram 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Mario Jesús Pérez-Jiménez
    • 1
  • Francisco José Romero-Campero
    • 1
  1. 1.Research Group on Natural Computing, Department of Computer Science and Artificial IntelligenceUniversity of SevillaSevillaSpain

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