stochkit-ff:tr-10-12 (Technical report)
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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 » |
Number | TR-10-12 |
Institution | Università di Pisa, Dipartimento di Informatica, Italy |
Year | 2010 |
URL | http://calvados.di.unipi.it/storage/paper_files/TR-10-12.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: fastflow
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@techreport{stochkit-ff:tr-10-12,
number = {TR-10-12},
month = jul,
author = {Marco Aldinucci and Andrea Bracciali and Pietro Li\`o and Anil
Sorathiya and Massimo Torquati},
keywords = {fastflow},
url = {http://calvados.di.unipi.it/storage/paper_files/TR-10-12.pdf},
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.},
title = {{StochKit-FF}: Efficient Systems Biology on Multicore Architectures},
institution = {Universit{\`a} di Pisa, Dipartimento di Informatica, Italy},
year = {2010},
}
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