StochKit-FF: Efficient Systems Biology on Multicore Architectures
Computational Engineering, Finance, and Science
2010-07-13 v1 Quantitative Methods
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.
Cite
@article{arxiv.1007.1768,
title = {StochKit-FF: Efficient Systems Biology on Multicore Architectures},
author = {Marco Aldinucci and Andrea Bracciali and Pietro Liò and Anil Sorathiya and Massimo Torquati},
journal= {arXiv preprint arXiv:1007.1768},
year = {2010}
}
Comments
14 pages + cover page