Tools

Bio-PEPA is going to be supported by two analysis tools.

A first tool is the Bio-PEPA workbench, implemented by Stephen Gilmore. In this tool, modellers to write models in the Bio-PEPA language and analyse them by using different techniques, such as stochastic simulation and model checking in PRISM. You can read more about the Bio-PEPA workbench and download it here.

Another analysis framework for Bio-PEPA is based on the Eclipse plug-in. Details can be found here.

More information on these tools can be found in

• The Bio-PEPA Tool Suite
  F. Ciocchetta, A. Duguid, S. Gilmore, M.L. Guerriero and J. Hillston.
  Proc. of QEST'09, pp. 309-310, 2009. Preprint version.
  A short paper presenting the tool available for Bio-PEPA.

• Design and development of software tools for Bio-PEPA
  A. Duguid, S. Gilmore, M.L. Guerriero, J. Hillston, and L. Loewe.
  Proc. of WSC'09, pp. 956-967, 2009. Preprint version.
  Detailed description of the software tool support for modelling and analysis in Bio-PEPA.

Laurence Loewe has recently developed a mapping from the graphical notation SBGN-PD, to Bio-PEPA.
From here a prototype of the tool can downloaded. Further details on how SBGN-PD models can be mapped to Bio-PEPA and on SBGNtext, which is a textual representation for SBGN-PD models, can be found in the technical report Defining a textual representation for SBGN Process Diagrams and translating it to Bio-PEPA for quantitative analysis of the MAPK signal transduction cascade.
L. Loewe, S. Moodie and J. Hillston. Technical Report EDI-INF-RR-1334, School for Informatics, University of Edinburgh, 2009.