cwc:cloud:bib:13 (Article)
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Author(s) | Marco Aldinucci, Massimo Torquati, Concetto Spampinato, Maurizio Drocco, Claudia Misale, Cristina Calcagno and Mario Coppo |
Title | « Parallel stochastic systems biology in the cloud » |
Journal | Briefings in Bioinformatics |
Volume | 15 |
Number | 5 |
Page(s) | 798-813 |
Year | 2014 |
ISSN number | 1467-5463 |
URL | http://calvados.di.unipi.it/storage/paper_files/2013_ff_bio_cloud_briefings.pdf |
Abstract & Keywords |
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.
Keywords: fastflow, bioinformatics, cloud
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@article{cwc:cloud:bib:13,
volume = {15},
number = {5},
issn = {1467-5463},
author = {Marco Aldinucci and Massimo Torquati and Concetto Spampinato and
Maurizio Drocco and Claudia Misale and Cristina Calcagno and Mario
Coppo},
keywords = {fastflow, bioinformatics, cloud},
url = {http://calvados.di.unipi.it/storage/paper_files/2013_ff_bio_cloud_briefings.pdf},
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.},
title = {Parallel stochastic systems biology in the cloud},
year = {2014},
journal = {Briefings in Bioinformatics},
pages = {798-813},
}
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