Bio-PEPA is supported by two analysis tools which are freely available to download for all major operating systems.
The Bio-PEPA Eclipse Plug-in
The Bio-PEPA Eclipse Plug-in is a fully-featured development environment for Bio-PEPA modelling.
You can read more about the Bio-PEPA Eclipse Plug-in and download it from the Bio-PEPA Eclipse Plug-in site.
The Bio-PEPA Workbench
An alternative tool is the Bio-PEPA Workbench. In this tool, modellers write models in the Bio-PEPA language and analyse them by using different techniques, such as stochastic simulation and model checking. The Bio-PEPA Workbench compiles Bio-PEPA models to application program code in C++ and allows simulation using other numerical and stochastic simulation libraries. You can read more about the Bio-PEPA workbench and download it from the Bio-PEPA Workbench site.
PapersMore 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.
The development of the Bio-PEPA software tools has been supported by
- the SIGNAL project ("Stochastic process algebra for biochemical signalling pathway analysis") funded by the UK Engineering and Physical Sciences Research Council
- the Bio-PEPA project within the Centre for Systems Biology at Edinburgh, funded by the EPSRC and BBSRC; and
- by Pathfinder funding from the UK Biotechnology and Biological Sciences Research Council