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
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 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,
- 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
- 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
- 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,