The Bio-PEPA Tool Suite

Author

Ciocchetta, Federica ; Duguid, Adam ; Gilmore, Stephen ; Guerriero, Maria Luisa ; Hillston, Jane

Author_Institution

Centre for Syst. Biol. at Edinburgh, Univ. of Edinburgh, Edinburgh, UK

fYear

2009

fDate

13-16 Sept. 2009

Firstpage

309

Lastpage

310

Abstract

Bio-PEPA is a timed process algebra designed specifically for the description of biological phenomena and their analysis through quantitative methods such as stochastic simulation and probabilistic model-checking. Two software tools are available for modelling with Bio-PEPA, the Bio-PEPA Workbench and the Bio-PEPA Eclipse Plugin. The Bio-PEPA Workbench is the research prototype tool which allows us to try out new language features and new types of analysis through rapid prototyping. The Bio-PEPA Eclipse Plugin is a polished modelling environment which targets end-users who wish to do Bio-PEPA modelling supported by a comprehensive integrated development environment. Both modelling tools allow the user to analyse their model both in the discrete stochastic regime and in the sure continuous regime while maintaining only a single source in the Bio-PEPA language.

Keywords

biology computing; process algebra; program diagnostics; programming environments; software prototyping; software tools; specification languages; Bio-PEPA Eclipse Plugin; Bio-PEPA Workbench; Bio-PEPA tool suite; biological phenomena description; comprehensive integrated development environment; continuous regime; discrete stochastic regime; polished modelling environment; rapid prototyping; software tool; timed process algebra; Analytical models; Biological system modeling; Computational modeling; Differential equations; Kinetic theory; Mathematical model; Software prototyping; Stochastic processes; Stochastic systems; Systems biology;

fLanguage

English

Publisher

ieee

Conference_Titel

Quantitative Evaluation of Systems, 2009. QEST '09. Sixth International Conference on the

Conference_Location

Budapest

Print_ISBN

978-0-7695-3808-2

Type

conf

DOI

10.1109/QEST.2009.27

Filename

5290668