In this work we present Bio-PEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performanceanalysis of computer systems, in order to handle some features of biological models, suchas stoichiometry and the use of general kinetic laws. Bio-PEPA may be seen as an intermediate, formal, compositional representation of biological systems, on which different kindsof analysis can be carried out. Bio-PEPA is enriched with some notions of equivalence.Specifically, the isomorphism and strong bisimulation for PEPA have been considered andextended to our language. Finally, we show the translation of a biological model into thenew language and we report some analysis results.

References in zbMATH (referenced in 105 articles , 1 standard article )

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  1. Akman, Ozgur E.; Ciocchetta, Federica; Degasperi, Andrea; Guerriero, Maria Luisa: Modelling biological clocks with Bio-PEPA: Stochasticity and robustness for the neurospora crassa circadian network (2009) ioport
  2. Ballarini, Paolo; Mardare, Radu; Mura, Ivan: Analysing biochemical oscillation through probabilistic model checking (2009)
  3. Bortolussi, Luca; Policriti, Alberto: Dynamical systems and stochastic programming: to ordinary differential equations and back (2009)
  4. Brown, Daniel; Pucella, Riccardo: Categories of timed stochastic relations (2009)
  5. Calder, Muffy; Hillston, Jane: Process algebra modelling styles for biomolecular processes (2009)
  6. Ciocchetta, Federica: Bio-PEPA with events (2009)
  7. Ciocchetta, Federica; Degasperi, Andrea; Hillston, Jane; Calder, Muffy: Some investigations concerning the CTMC and the ODE model derived from bio-PEPA (2009)
  8. Ciocchetta, Federica; Duguid, Adam; Guerriero, Maria Luisa: A compartmental model of the camp/PKA/MAPK pathway in bio-PEPA (2009) ioport
  9. Ciocchetta, Federica; Guerriero, Maria Luisa: Modelling biological compartments in bio-PEPA (2009)
  10. Ciocchetta, Federica; Hillston, Jane: Bio-PEPA: A framework for the modelling and analysis of biological systems (2009)
  11. Del Tedesco, Filippo; Piazza, Carla: External control in process algebra for systems biology (2009)
  12. Galpin, Vashti; Hillston, Jane: Equivalence and discretisation in Bio-PEPA (2009) ioport
  13. Guerriero, Maria Luisa: Qualitative and quantitative analysis of a Bio-PEPA model of the gp130/JAK/STAT signalling pathway (2009) ioport
  14. Henzinger, Thomas A.; Jobstmann, Barbara; Wolf, Verena: Formalisms for specifying Markovian population models (2009)
  15. Loewe, Laurence; Moodie, Stuart; Hillston, Jane: Quantifying the implicit process flow abstraction in SBGN-PD diagrams with bio-PEPA (2009) ioport
  16. Priami, Corrado (ed.); Back, Ralph-Johan (ed.); Petre, Ion (ed.): Transactions on Computational Systems Biology XI (2009)
  17. Versari, Cristian; Busi, Nadia: Stochastic biological modelling in the presence of multiple compartments (2009)
  18. Barbuti, Roberto; Maggiolo-Schettini, Andrea; Milazzo, Paolo; Tiberi, Paolo; Troina, Angelo: Stochastic calculus of looping sequences for the modelling and simulation of cellular pathways (2008)
  19. Cannata, Nicola (ed.); Merelli, Emanuela (ed.): Proceedings of the first workshop “From biology to concurrency and back (FBTC 2007)”, Lisbon, Portugal, September 8, 2007 (2008)
  20. Ciobanu, Gabriel (ed.): MeCBIC 2008. 2nd international meeting on membrane computing and biologically inspired process calculi. Papers based on the presentations at the meeting, Iaşi, Romania, September 3--4, 2008. (2008)

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