References

The main reference for Bio-PEPA is:


Bio-PEPA: a Framework for the Modelling and Analysis of Biochemical Networks.
F. Ciocchetta and J. Hillston.
To appear in Theoretical Computer Science.
Preprint version.


Other references are:

  • Bio-PEPA: a Framework for the Modelling and Analysis of Biochemical Networks.
    F. Ciocchetta and J. Hillston.
    School of Informatics University of Edinburgh Technical Report EDI-INF-RR-1231, 2008. Download the TR here.
    This technical report contains the definition of the language as reported in the first submission of the reference paper, with the addition of further definitions and examples. Note that the final version of Bio-PEPA has small differences with respect to the one presented in this techincal report, but the main concepts are the same.

  • Calculi for Biological Systems.
    F. Ciocchetta and J. Hillston.
    Chapter for the tutorial of SFM-08:Bio, LNCS, volume 5016, pages 265-312, 2008.
    [doi:10.1007/978-3-540-68894-5_8]. Paper.

  • Modelling Biological Compartments in Bio-PEPA.
    F. Ciocchetta and M.L. Guerriero.
    Proc. of MeCBIC 2008. To appear in ENTCS. Preprint version.
    This paper contains the extension of Bio-PEPA with locations.

  • Integrated Simulation and Model-Checking for the Analysis of Biochemical Systems.
    F. Ciocchetta, S. Gilmore, M.L. Guerriero and J. Hillston.
    Proc. of PASM'08. To appear in ENTCS. Preprint version.
    In this paper we discuss how to integrate simulation and model checking for the anlysis of biochemical networks.

  • Some Investigations Concerning the CTMC and the ODE Model Derived from Bio-PEPA.
    F.Ciocchetta, A. Degasperi, J. Hillston and M. Calder.
    Proc. of FBTC 2008. To appear in ENTCS. Preliminary version.
    This is the reference for the CTMC with levels. By using Kurtz's theorem, we show the convergence of the CTMC with levels and ODE derived from the same Bio-PEPA system, when the step size tends to zero.

  • Bio-PEPA with SBML-like Events.
    F.Ciocchetta.
    Proc. of Computational Models for Cell Processes, 2008. Extended version.
    This is the reference for the extension of Bio-PEPA with events.

  • Bio-PEPA: an Extension of the Process Algebra PEPA for Biochemical Networks.
    F. Ciocchetta and J. Hillston.
    Proc. of FBTC 2007 and ENTCS, volume 194, iussue 3, pages 103-117, 2008. Download the paper here.
    This paper presents the first version of Bio-PEPA.

  • From PEPA Reagent-Centric View to Bio-PEPA.
    F. Ciocchetta and J. Hillston.
    Proc. of Pasta 2007, London. Download the paper here.

  • An Automatic Mapping from the Systems Biology Markup Language to the Bio-PEPA Process Algebra
    Kanimozhi Ellavarason.
    MSc Thesis within European Master in Informatics. Download the thesis here.

Some presentations about Bio-PEPA are reported below.