stochkit-ff:hibb:10 (In proceedings)
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Author(s) | Marco Aldinucci, Andrea Bracciali, Pietro Liò, Anil Sorathiya and Massimo Torquati |
Title | « StochKit-FF: Efficient Systems Biology on Multicore Architectures » |
In | Euro-Par 2010 Workshops, Proc. of the 1st Workshop on High Performance Bioinformatics and Biomedicine (HiBB) |
Series | LNCS |
Editor(s) | M. R. Guarracino, F. Vivien, J. L. Träff, M. Cannataro, M. Danelutto, A. Hast, F. Perla, A. Knüpfer, B. Di Martino and M. Alexander |
Volume | 6586 |
Page(s) | 167-175 |
Year | 2011 |
Publisher | Springer |
Address | Ischia, Italy |
URL | http://calvados.di.unipi.it/storage/paper_files/2010_stochkit-ff_hibb.pdf |
Abstract & Keywords |
The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.
Keywords: bioinformatics
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@inproceedings{stochkit-ff:hibb:10,
volume = {6586},
month = aug,
author = {Marco Aldinucci and Andrea Bracciali and Pietro Li\`o and Anil
Sorathiya and Massimo Torquati},
series = {{LNCS}},
keywords = {bioinformatics},
booktitle = {Euro-Par 2010 Workshops, Proc. of the 1st Workshop on High
Performance Bioinformatics and Biomedicine (HiBB)},
editor = {M. R. Guarracino and F. Vivien and J. L. Tr\"aff and M. Cannataro
and M. Danelutto and A. Hast and F. Perla and A. Kn\"upfer and B. Di
Martino and M. Alexander},
url = {http://calvados.di.unipi.it/storage/paper_files/2010_stochkit-ff_hibb.pdf},
title = {{StochKit-FF}: Efficient Systems Biology on Multicore Architectures},
abstract = {The stochastic modelling of biological systems is an informative,
and in some cases, very adequate technique, which may however
result in being more expensive than other modelling approaches,
such as differential equations. We present StochKit-FF, a parallel
version of StochKit, a reference toolkit for stochastic
simulations. StochKit-FF is based on the FastFlow programming
toolkit for multicores and exploits the novel concept of selective
memory. We experiment StochKit-FF on a model of HIV infection
dynamics, with the aim of extracting information from efficiently
run experiments, here in terms of average and variance and, on a
longer term, of more structured data.},
address = {Ischia, Italy},
publisher = {Springer},
year = {2011},
pages = {167-175},
}
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