Some case studies for Bio-PEPA are listed below. Other models will be added soon.
Goldbeter's model describing the oscillation of cyclin in the cell cycle. For the translation of this model into Bio-PEPA and some examples of analysis applied to the model see for instance the technical report for Bio-PEPA and the tutorial for SFM-08:Bio.
Edelstein's model for the acethylcholine receptor (with events). For details see the paper presented at the Workshop "Computational Models for Cell Processes."
Model for complex intracellular calcium oscillations (by Goldbeter and co-authors). In this model we consider the Bio-PEPA with locations defined in the paper presented at the workshop MeCBIC 2008.
The MAPK model, for details see here.
The gp130/JAK/STAT pathway. The Bio-PEPA source code of the model can be found here and is suitable for loading into the Bio-PEPA Eclipse Plug-in. Instead, this file together with these parameters settings can be loaded into the tool. An automatically generated report on the model is also available.
The Circadian Clock in Neurospora. The ACDG_CMSB09_Supplement.zip file contains the Bio-PEPA source files, the generated Dizzy files and information on the scaling used. For full details see the paper.
The NFkB pathway. Based on the earlier model by Lipniacki et al., this model uses both events and locations in Bio-PEPA to express the behaviour of NFkB in the cell under external stimulus by TNF, taking into account the NFkB shuttling between cytosol and nucleus. The zip file contains the Bio-PEPA, Dizzy and Matlab source models.
The Yeast Pheromone pathway. This model was used to explore issues arising in quantitative modular analysis. The modularisation was based on a previous paper by Kofahl and Klipp. The zip file contains a Bio-PEPA model of the pathway, modularised as described in the paper, and the derived PRISM models corresponding to the two modules presented there.
Emergency egress models analysed in the paper for SEFM2010 and the paper for LAM2010 and Formal Aspects of Computing (to appear). The PEPA and Bio-PEPA source files and additional information can be found here.