Title :
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
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;
Conference_Titel :
Quantitative Evaluation of Systems, 2009. QEST '09. Sixth International Conference on the
Conference_Location :
Budapest
Print_ISBN :
978-0-7695-3808-2
DOI :
10.1109/QEST.2009.27
