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 92 articles , 1 standard article )

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  1. Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco: Approximate Bayesian inference in semi-mechanistic models (2017)
  2. Boreale, Michele: Algebra, coalgebra, and minimization in polynomial differential equations (2017)
  3. Grzegorczyk, Marco; Aderhold, Andrej; Husmeier, Dirk: Targeting Bayes factors with direct-path non-equilibrium thermodynamic integration (2017)
  4. Bortolussi, Luca: Hybrid behaviour of Markov population models (2016)
  5. Bortolussi, Luca; Gast, Nicolas: Mean-field limits beyond ordinary differential equations (2016)
  6. Bortolussi, Luca; Milios, Dimitrios; Sanguinetti, Guido: Smoothed model checking for uncertain continuous-time Markov chains (2016)
  7. Cardelli, Luca; Tribastone, Mirco; Tschaikowski, Max; Vandin, Andrea: Symbolic computation of differential equivalences (2016)
  8. Colvin, Robert J.: Modelling and analysing neural networks using a hybrid process algebra (2016)
  9. Děd, T.; Šafránek, D.; Troják, M.; Klement, M.; Šalagovič, J.; Brim, L.: Formal biochemical space with semantics in kappa and BNGL (2016)
  10. Hillston, Jane: Quantitative analysis of collective adaptive systems (2016)
  11. Olarte, C.; Chiarugi, D.; Falaschi, M.; Hermith, D.: A proof theoretic view of spatial and temporal dependencies in biochemical systems (2016)
  12. Vandin, Andrea; Tribastone, Mirco: Quantitative abstractions for collective adaptive systems (2016)
  13. Aman, Bogdan; Ciobanu, Gabriel: Verification of membrane systems with delays via Petri nets with delays (2015)
  14. Angius, Alessio; Balbo, Gianfranco; Beccuti, Marco; Bibbona, Enrico; Horvath, Andras; Sirovich, Roberta: Approximate analysis of biological systems by hybrid switching jump diffusion (2015)
  15. Barbot, Beno^ıt; Kwiatkowska, Marta: On quantitative modelling and verification of DNA walker circuits using stochastic Petri nets (2015)
  16. Casagrande, Alberto; Piazza, Carla: Unwinding biological systems (2015)
  17. Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos: Verification of spatial and temporal modalities in biochemical systems (2015)
  18. Chiarugi, Davide; Falaschi, Moreno; Olarte, Carlos; Palamidessi, Catuscia: A declarative view of signaling pathways (2015)
  19. Grzegorczyk, Marco; Aderhold, Andrej; Husmeier, Dirk: Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles (2015)
  20. Iacobelli, Giulio; Tribastone, Mirco; Vandin, Andrea: Differential bisimulation for a Markovian process algebra (2015)

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