Bio-PEPA

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 77 articles , 1 standard article )

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  1. Bortolussi, Luca: Hybrid behaviour of Markov population models (2016)
  2. Bortolussi, Luca; Milios, Dimitrios; Sanguinetti, Guido: Smoothed model checking for uncertain continuous-time Markov chains (2016)
  3. Cardelli, Luca; Tribastone, Mirco; Tschaikowski, Max; Vandin, Andrea: Symbolic computation of differential equivalences (2016)
  4. Colvin, Robert J.: Modelling and analysing neural networks using a hybrid process algebra (2016)
  5. Olarte, C.; Chiarugi, D.; Falaschi, M.; Hermith, D.: A proof theoretic view of spatial and temporal dependencies in biochemical systems (2016)
  6. Aman, Bogdan; Ciobanu, Gabriel: Verification of membrane systems with delays via Petri nets with delays (2015)
  7. Angius, Alessio; Balbo, Gianfranco; Beccuti, Marco; Bibbona, Enrico; Horvath, Andras; Sirovich, Roberta: Approximate analysis of biological systems by hybrid switching jump diffusion (2015)
  8. Barbot, Beno^ıt; Kwiatkowska, Marta: On quantitative modelling and verification of DNA walker circuits using stochastic Petri nets (2015)
  9. Casagrande, Alberto; Piazza, Carla: Unwinding biological systems (2015)
  10. Iacobelli, Giulio; Tribastone, Mirco; Vandin, Andrea: Differential bisimulation for a Markovian process algebra (2015)
  11. Ito, Sohei; Ichinose, Takuma; Shimakawa, Masaya; Izumi, Naoko; Hagihara, Shigeki; Yonezaki, Naoki: Qualitative analysis of gene regulatory networks by temporal logic (2015)
  12. Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea: Component identification in biochemical pathways (2015)
  13. Tschaikowski, Max; Tribastone, Mirco: A unified framework for differential aggregations in Markovian process algebra (2015)
  14. Caravagna, Giulio; d’Onofrio, Alberto; Antoniotti, Marco; Mauri, Giancarlo: Stochastic hybrid automata with delayed transitions to model biochemical systems with delays (2014)
  15. Galpin, Vashti: Hybrid semantics for Bio-PEPA (2014)
  16. Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea: Identification of components in biochemical pathways: extensive aqpplication to SBML models (2014)
  17. Tschaikowski, Max; Tribastone, Mirco: Exact fluid lumpability in Markovian process algebra (2014)
  18. Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Guzman, Michell; Olarte, Carlos: Simulating signalling pathways with bioways (2013)
  19. Ciobanu, Gabriel: General patterns of interaction in stochastic fusion (2013)
  20. 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)

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Further publications can be found at: http://homepages.inf.ed.ac.uk/jeh/Bio-PEPA/References.html