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The quantitative process algebra Bio-PEPA is a formal language for modelling biological systems at various level of abstraction. It allows for the specification of species and their interaction, supports compartments and events. Bio-PEPA models can be analysed using stochastic simulation, ordinary differential equations and model checking on continuous-time Markov chains.

Published Bio-PEPA models include Edelstein's model for the acethylcholine receptor, complex intracellular calcium oscillationsoscillation of cyclin in the cell cycle, trafficking of Src within the mammalian cell, the MAPK pathway, the gp130/JAK/STAT pathway, the yeast pheromone pathway, the Ostreococcus tauri circadian clock and the Neurospora crassa circadian network