title: Parallel stochastic systems biology in the cloud.
abstract: The stochastic modelling of biological systems, coupled with Monte Carlo simulation of models, is an increasingly popular technique in bioinformatics. The simulation-analysis workflow may result computationally expensive reducing the interactivity required in the model tuning. In this work, we advocate the high-level software design as a vehicle for building efficient and portable parallel simulators for the cloud. In particular, the Calculus of Wrapped Components (CWC) simulator for systems biology, which is designed according to the FastFlow pattern-based approach, is presented and discussed. Thanks to the FastFlow framework, the CWC simulator is designed as a high-level workflow that can simulate CWC models, merge simulation results and statistically analyse them in a single parallel workflow in the cloud. To improve interactivity, successive phases are pipelined in such a way that the workflow begins to output a stream of analysis results immediately after simulation is started. Performance and effectiveness of the CWC simulator are validated on the Amazon Elastic Compute Cloud.
authors.forename: Marco
authors.initials: M
authors.lastname: Aldinucci
authors.forename: Massimo
authors.initials: M
authors.lastname: Torquati
authors.forename: Concetto
authors.initials: C
authors.lastname: Spampinato
authors.forename: Maurizio
authors.initials: M
authors.lastname: Drocco
authors.forename: Claudia
authors.initials: C
authors.lastname: Misale
authors.forename: Cristina
authors.initials: C
authors.lastname: Calcagno
authors.forename: Mario
authors.initials: M
authors.lastname: Coppo
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D016247:Information Storage and Retrieval; D013269:Stochastic Processes; D049490:Systems Biology
keywords: cloud; distributed computing; multi-core; parallel patterns; stochastic simulation