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Updated 18 May 2012 17:41
System Dynamics Project Models Home Page

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Funded by
EPSRC

PEPA and WSCCS models associated with the project

We have constructed many models as part of this project, but there is usually not enough space to include the full model in publications. We are making the full models available here. Download files are simply text files.

Measles Models in Bio-PEPA

DEB Models of Pacific Oyster in Bio-PEPA

Immunological Models in Bio-PEPA

Immunological Models in PEPA

Models in PEPA used in the EPA project

  • InternetWorm.pepa (transmission of malware, taken from J. T. Bradley, S. T. Gilmore, and J. Hillston, Analysing distributed Internet worm attacks using continuous state-space approximation of process algebra models, Journal of Computer and System Sciences, vol. 74, no. 6, pp. 1013-1032, 2008.)
  • HIV.pepa (HIV spread within a fluctuating population, taken from C. McCaig, R. Norman, and C. Shankland, From individuals to populations: A symbolic process algebra approach to epidemiology, Mathematics in Computer Science, vol. 2, no. 3, pp. 139-155, 2009).
  • dining1.pepa (The original problem is due to C. Hoare, Communicating sequential processes, Communications of the ACM, vol. 21, pp. 666-677, 1978. This version is taken from S. Benkirane, Process algebra and epidemiology: evaluating the ability of PEPA to describe biological systems, Ph.D. dissertation, University of Stirling, 2011, draft, to be submitted in 2011.)
  • dining2.pepa (adaptation of above, to monitor starvation of processes).
  • crowd.pepa (crowd movement between town squares, original idea from M. Massink, D. Latella, A. Bracciali, and J. Hillston, Modelling Crowd Dynamics in Bio-PEPA, in 9th Workshop on Process Algebra and Stochastically Timed Activities, 2010, pp. 1-11. This model from E. Scott, PEPA & Bio-PEPA: A Comparison, 2011, final year honours project, Institute of Computing Science and Mathematics, University of Stirling.).
  • gprotein.pepa Activation cycle of G-proteins. Model adapted from Y. Bao, A. Compagnoni, J. Glavy, and T. White. Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors. In Proceedings of 4th Workshop on Membrane Computing and Biologically Inspired Process Calculi, volume 40 of Electronic Proceedings in Theoretical Computer Science, pages 39-53, 2010.
  • repressilator.pepaThe cyclic gene activation repressilator model. Adapted from R. Blossey, L. Cardelli, and A. Phillips. Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation. HFSP, 2:17-28, 2008.

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Project Pages maintained by Carron Shankland
Email carron at cs.stir.ac.uk - Web www.cs.stir.ac.uk/~ces - Tel 01786 467444 - Fax 01786 464551
Mail Computing Science and Mathematics, University of Stirling, Stirling, Scotland, FK9 4LA
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