April 22nd, 2009
A new version of the Bio-PEPA Workbench was released today, Version 1.0 "Charlie Mingus". The features offered by this release are described in the user manual. The software can be obtained from the download page.
Bio-PEPA is a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performance analysis of computer systems, in order to handle some features of biological models, such as stoichiometry and the use of general kinetic laws.
You can read about Bio-PEPA in Bio-PEPA: a framework for the modelling and analysis of biological systems by Federica Ciocchetta and Jane Hillston.
About the Bio-PEPA Workbench
The Bio-PEPA Workbench is an implementation of Bio-PEPA which allows modellers to write models in the Bio-PEPA language and to animate them using stochastic simulation.
The Bio-PEPA Workbench uses the StochKit stochastic simulation toolkit to perform exact stochastic simulations using Gillespie's SSA algorithm.
The Bio-PEPA Workbench was developed for the SIGNAL project ("Stochastic process algebra for biochemical signalling pathway analysis") funded by the UK Engineering and Physical Sciences Research Council and the Bio-PEPA project within the Centre for Systems Biology at Edinburgh, funded by the EPSRC and BBSRC.