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Formal Methods in Computing
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stochkit-ff:hibb:10 (In proceedings)
Author(s) Marco Aldinucci, Andrea Bracciali, Pietro Liò, Anil Sorathiya and Massimo Torquati
Title« StochKit-FF: Efficient Systems Biology on Multicore Architectures »
InEuro-Par 2010 Workshops, Proc. of the 1st Workshop on High Performance Bioinformatics and Biomedicine (HiBB)
SeriesLNCS
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
Volume6586
Page(s)167-175
Year2011
PublisherSpringer
AddressIschia, Italy
URLhttp://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

BibTeX code

@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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