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 105 articles , 1 standard article )

Showing results 61 to 80 of 105.
Sorted by year (citations)
  1. Galpin, Vashti: Equivalences for a biological process algebra (2011)
  2. Galpin, Vashti; Hillston, Jane: A semantic equivalence for Bio-PEPA based on discretisation of continuous values (2011)
  3. Liu, Bing; Hsu, David; Thiagarajan, P. S.: Probabilistic approximations of ODEs based bio-pathway dynamics (2011)
  4. Loewe, Laurence; Guerriero, Maria Luisa; Watterson, Steven; Moodie, Stuart; Ghazal, Peter; Hillston, Jane: Translation from the quantified implicit process flow abstraction in SBGN-PD diagrams to bio-PEPA illustrated on the cholesterol pathway (2011) ioport
  5. Massink, Mieke; Latella, Diego; Bracciali, Andrea; Hillston, Jane: Modelling non-linear crowd dynamics in bio-PEPA (2011) ioport
  6. Paulevé, Loïc; Magnin, Morgan; Roux, Olivier: Refining dynamics of gene regulatory networks in a stochastic (\pi)-calculus framework (2011)
  7. Priami, Corrado (ed.); Back, Ralph-Johan (ed.); Petre, Ion (ed.); de Vink, Erik (ed.): Transactions on Computational Systems Biology XIII (2011)
  8. Sciacca, Eva; Spinella, Salvatore; Genre, Andrea; Calcagno, Cristina: Analysis of calcium spiking in plant root epidermis through CWC modeling (2011) ioport
  9. Silva, Manuel; Júlvez, Jorge; Mahulea, Cristian; Vázquez, C. Renato: On fluidization of discrete event models: Observation and control of continuous Petri nets (2011)
  10. Andrei, Oana; Calder, Muffy: A model and analysis of the AKAP scaffold (2010)
  11. Buti, F.; Cacciagrano, D.; Corradini, F.; Merelli, E.; Tesei, L.; Pani, M.: Bone remodelling in \textscBioShape (2010)
  12. Ciocchetta, Federica; Degasperi, Andrea; Heath, John K.; Hillston, Jane: Modelling and analysis of the NF-(\kappa)B pathway in Bio-PEPA (2010) ioport
  13. Degasperi, Andrea; Calder, Muffy: Relating PDEs in cylindrical coordinates and CTMCs with levels of concentration (2010)
  14. Degasperi, Andrea; Calder, Muffy: Process algebra with hooks for models of pattern formation (2010)
  15. Drábik, Peter; Maggiolo-Schettini, Andrea; Milazzo, Paolo: Modular verification of interactive systems with an application to biology (2010)
  16. John, Mathias; Lhoussaine, Cédric; Niehren, Joachim; Uhrmacher, Adelinde M.: The attributed pi-calculus with priorities (2010)
  17. Kuttler, Céline; Lhoussaine, Cédric; Nebut, Mirabelle: Rule-based modeling of transcriptional attenuation at the tryptophan operon (2010)
  18. Montagna, Sara; Viroli, Mirko: A framework for modelling and simulating networks of cells (2010)
  19. Pedersen, Michael; Plotkin, Gordon D.: A language for biochemical systems: design and formal specification (2010)
  20. Priami, Corrado (ed.); Breitling, Rainer (ed.); Gilbert, David (ed.); Heiner, Monika (ed.); Uhrmacher, Adelinde M. (ed.): Transactions on Computational Systems Biology XII. Special issue on modeling methodologies (2010)

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