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. Tschaikowski, Max; Tribastone, Mirco: Exact fluid lumpability in Markovian process algebra (2014)
  2. Brim, Luboš; Češka, Milan; Šafránek, David: Model checking of biological systems (2013)
  3. Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Guzman, Michell; Olarte, Carlos: Simulating signalling pathways with bioways (2013) ioport
  4. Ciobanu, Gabriel: General patterns of interaction in stochastic fusion (2013)
  5. Compagnoni, Adriana; Sharma, Vishakha; Bao, Yifei; Libera, Matthew; Sukhishvili, Svetlana; Bidinger, Philippe; Bioglio, Livio; Bonelli, Eduardo: BioScape: a modeling and simulation language for bacteria-materials interactions (2013) ioport
  6. Degasperi, A.; Calder, M.: A process algebra framework for multi-scale modelling of biological systems (2013)
  7. Ding, Jie; Gu, Hong; Lin, Zhigui: Fundamental results on the reactionâdiffusion equations associated with a PEPA model (2013)
  8. Georgoulas, Anastasis; Guerriero, Maria Luisa: A software interface between the narrative language and Bio-PEPA (2013) ioport
  9. Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea: An algorithm for the identification of components in biochemical pathways (2013)
  10. Versari, Cristian; Zavattaro, Gianluigi: Complex functional rates in the modeling of nano devices (extended abstract) (2013) ioport
  11. Barbuti, Roberto; Caravagna, Giulio; Maggiolo-Schettini, Andrea; Milazzo, Paolo; Tini, Simone: Foundational aspects of multiscale modeling of biological systems with process algebras (2012)
  12. Bartocci, Ezio; Liò, Pietro; Merelli, Emanuela; Paoletti, Nicola: Multiple verification in complex biological systems: the bone remodelling case study (2012)
  13. Benkirane, Soufiene; Norman, Rachel; Scott, Erin; Shankland, Carron: Measles epidemics and PEPA: an exploration of historic disease dynamics using process algebra (2012)
  14. Caravagna, Giulio; Hillston, Jane: Bio-PEPAd: a non-Markovian extension of Bio-PEPA (2012)
  15. Coppo, Mario; Damiani, Ferruccio; Drocco, Maurizio; Grassi, Elena; Sciacca, Eva; Spinella, Salvatore; Troina, Angelo: Simulation techniques for the calculus of wrapped compartments (2012)
  16. Donaldson, Robin; Calder, Muffy: Modular modelling of signalling pathways and their cross-talk (2012)
  17. Galpin, Vashti: Modelling trafficking of proteins within the mammalian cell using bio-PEPA (2012) ioport
  18. Massink, M.; Latella, D.; Bracciali, A.; Harrison, M. D.; Hillston, J.: Scalable context-dependent analysis of emergency egress models (2012) ioport
  19. Angius, Alessio; Horváth, András: Product form approximation of transient probabilities in stochastic reaction networks (2011)
  20. Ding, Jie; Lin, Zhigui; Yu, Ting: On reaction-diffusion equations derived from a PEPA model (2011)

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