References

Bio-PEPA: a Framework for the Modelling and Analysis of Biochemical Networks.
F. Ciocchetta and J. Hillston.
Theoretical Computer Science 410 (33-34), pp.\ 3065-3084, 2009.
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. In ENTCS Vol. 227, pp. 77-95, 2009. 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. In ENTCS Vol. 232, pp 17-38, 2009. 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. In ENTCS Vol 229(1), pp. 145-163, 2009. Preprint 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 Events.
  F.Ciocchetta.
  T. Comp. Sys. Biology 11, pages 45-68, 2009. Preprint version.
  This is the reference for the extension of Bio-PEPA with events. Preliminary version appeared in CompMod'08.

• Modelling and analysis of the NF-kappa B pathway in Bio-PEPA.
  F. Ciocchetta, A. Degasperi, J. Heath and J. Hillston.
  To appear in Transactions on Computational Systems Biology. Preprint version.
  This paper presents a detailed study of the NF kappa B pathway. The model construction takes advantage of both locations and events and a variety of different analysis techniques are applied.

• Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network.
  O.E. Akman, F. Ciocchetta, A. Degasperi and M.L. Guerriero.
  Proc. of CMSB'09, LNCS, Vol. 5688, pp. 52-67, 2009. Preprint version.
  This paper presents a Bio-PEPA model of the circadian clock of Neurospora crassa, and studies its robustness, particularly taking advantage of the stochastic analysis.

• Equivalence and discretisation in Bio-PEPA.
  V. Galpin and J. Hillston
  Proc. of CMSB'09, LNCS, Vol. 5688, pp. 189-204, 2009.
  This paper presents the definition of equivalence relations for Bio-PEPA.

• Qualitative and Quantitative Analysis of a Bio-PEPA Model of the Gp130/JAK/STAT Signalling Pathway
  M.L. Guerriero.
  Trans. of Computational Systems Biology XI, Vol. 5750, pp. 90-115, 2009. Preprint version.
  A case study of the gp130 JAK STAT pathway, particularly investigating the role that model checking can play in validating and interrogating pathway models.

• A compartmental model of the cAMP/PKA/MAPK pathway in Bio-PEPA
  F. Ciocchetta, A. Duguid and M.L. Guerriero.
  Proc. of MeCBIC'09, EPTCS, Vol. 11, pp. 71-90, 2009. Preprint version.
  In this paper we describe a signalling pathway model as case study for multi-compartment modelling in Bio-PEPA.

• An Automatic Mapping from the Systems Biology Markup Language to the Bio-PEPA Process Algebra
  Kanimozhi Ellavarason.
  MSc Thesis within European Master in Informatics 2008. Download the thesis here.

• Bio-PEPA for epidemiological models
  F. Ciocchetta and J. Hillston.
  Proc. of PASM'09, ENTCS, Vol. 261, pp. 43-69, 2010. Preprint version.
  In this work Bio-PEPA was applied to the study of epidemiological models of avian influenza, based on different assumptions about the spatial structure and the possible kind of treatment.

• Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA
  L. Loewe, S. Moodie and J. Hillston.
  Proc. of CompMod'09, EPTCS, Vol 6, pp. 93-107. Available here.
  This work builds a compiler that maps biochemical models from SBGN-PD to Bio-PEPA to build a bridge from visual model construction to automated simulations.

• Complementary approaches to understanding the plant circadian clock
  O.E. Akman, M.L. Guerriero, L. Loewe and C. Troein.
  Proc. of FBTC'10, EPTCS, Vol. 19, pp. 1-19, 2010. Preprint version.
  In this paper we model the circadian clock of Ostreococcus tauri in Bio-PEPA and present several analysis results based on stochastic simulation, model-checking and differential equations.

• Investigating modularity in the analysis of process algebra models of biochemical systems
  F. Ciocchetta, M.L. Guerriero and J. Hillston.
  Proc. of FBTC'10, EPTCS, Vol. 19, pp. 55-69, 2010. Preprint version.
  This paper concerns the application of decomposition and modular analysis of Bio-PEPA models. The pheromone pathway is used as a case study to illustrate the approach.

• Reconciling Population and Agent Models for Crowd Dynamics
  A. Bracciali, J. Hillston, D. Latella and M. Massink.
  Proc. of LAM'10, 2010, to appear.
  This paper shows the appication of the Bio-PEPA language to the modelling of crowd dynamics.

Some presentations about Bio-PEPA are reported below.

• Presentation made at SFM-08:Bio, Bertinoro, June 2008.

• Presentation made at CMSB 2008, Rostock, October 2008.