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.

  • Built on the powerful Eclipse rich client platform
  • Implemented in Java
  • Available for Windows, Mac OS X, and Linux
  • Contains stochastic Gillespie simulation
  • Contains deterministic ODE solvers
  • Generates complete traces for Traviando
  • Strong experimentation support
  • Static analysis of models built-in
  • Model coverage analysis built-in
  • Infer conserved moieties from model stoichiometry
  • Infer invariants on model activities
  • Results visualisation built-in
  • View Bio-PEPA models as chemical reactions
  • Export Bio-PEPA models to SBML
  • Export Bio-PEPA results to CSV
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user manual

You can download the User Manual for the Bio-PEPA Eclipse Plug-in or read the manual on-line.

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.


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.

Accompanying software

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