Paper Info
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.
Year
DOI
Venue
2014
10.1093/bib/bbt040
BRIEFINGS IN BIOINFORMATICS
Keywords
Field
DocType
stochastic simulation,cloud,multi-core,distributed computing,parallel patterns
Stochastic simulation,Interactivity,Software design,Computer science,Stochastic modelling,Bioinformatics,Multi-core processor,Workflow management system,Workflow,Distributed computing,Cloud computing
Journal
Volume
Issue
ISSN
15
5
1467-5463
Citations 
PageRank 
References 
7
0.52
42
Authors
7
Name
Order
Citations
PageRank
Marco Aldinucci163859.87
Massimo Torquati243346.72
Concetto Spampinato352158.13
Maurizio Drocco48812.09
Claudia Misale5235.44
Cristina Calcagno6172.10
Mario Coppo71054148.97