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. Děd, T.; Šafránek, D.; Troják, M.; Klement, M.; Šalagovič, J.; Brim, L.: Formal biochemical space with semantics in Kappa and BNGL (2016)
  2. Olarte, C.; Chiarugi, D.; Falaschi, M.; Hermith, D.: A proof theoretic view of spatial and temporal dependencies in biochemical systems (2016)
  3. Vandin, Andrea; Tribastone, Mirco: Quantitative abstractions for collective adaptive systems (2016)
  4. Aman, Bogdan; Ciobanu, Gabriel: Verification of membrane systems with delays via Petri nets with delays (2015)
  5. Angius, Alessio; Balbo, Gianfranco; Beccuti, Marco; Bibbona, Enrico; Horvath, Andras; Sirovich, Roberta: Approximate analysis of biological systems by hybrid switching jump diffusion (2015)
  6. Barbot, Benoît; Kwiatkowska, Marta: On quantitative modelling and verification of DNA walker circuits using stochastic Petri nets (2015)
  7. Casagrande, Alberto; Piazza, Carla: Unwinding biological systems (2015)
  8. Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos: Verification of spatial and temporal modalities in biochemical systems (2015)
  9. Chiarugi, Davide; Falaschi, Moreno; Olarte, Carlos; Palamidessi, Catuscia: A declarative view of signaling pathways (2015)
  10. Grzegorczyk, Marco; Aderhold, Andrej; Husmeier, Dirk: Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles (2015)
  11. Iacobelli, Giulio; Tribastone, Mirco; Vandin, Andrea: Differential bisimulation for a Markovian process algebra (2015)
  12. Ito, Sohei; Ichinose, Takuma; Shimakawa, Masaya; Izumi, Naoko; Hagihara, Shigeki; Yonezaki, Naoki: Qualitative analysis of gene regulatory networks by temporal logic (2015)
  13. Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea: Component identification in biochemical pathways (2015)
  14. Tschaikowski, Max; Tribastone, Mirco: A unified framework for differential aggregations in Markovian process algebra (2015)
  15. Zunino, Roberto; Nikolić, Đurica; Priami, Corrado; Kahramanoğulları, Ozan; Schiavinotto, Tommaso: (\ell): an imperative DSL to stochastically simulate biological systems (2015) ioport
  16. Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco: Statistical inference of regulatory networks for circadian regulation (2014)
  17. Caravagna, Giulio; d’Onofrio, Alberto; Antoniotti, Marco; Mauri, Giancarlo: Stochastic hybrid automata with delayed transitions to model biochemical systems with delays (2014)
  18. Galpin, Vashti: Hybrid semantics for Bio-PEPA (2014)
  19. Kolesnichenko, Anna; Senni, Valerio; Pourranjabar, Alireza; Remke, Anne: Applying mean-field approximation to continuous time Markov chains (2014)
  20. Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea: Identification of components in biochemical pathways: extensive aqpplication to SBML models (2014)

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