Chronological Overview 
 Type-Hierarchical Overview 
Formal Methods in Computing
(Most of the papers antecedent to 1995
are not included in the list)
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ff:cwc:pdp:11 (In proceedings)
Author(s) Marco Aldinucci, Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Massimo Torquati and Angelo Troina
Title« On Designing Multicore-Aware Simulators for Biological Systems »
InProc. of Intl. Euromicro PDP 2011: Parallel Distributed and network-based Processing
Editor(s) Yiannis Cotronis, Marco Danelutto and George Angelos Papadopoulos
Page(s)318-325
Year2011
PublisherIEEE
AddressAyia Napa, Cyprus
URLhttp://calvados.di.unipi.it/storage/paper_files/2011_ff_cwc_sim_PDP.pdf
Abstract & Keywords
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.

Keywords: fastflow

BibTeX code

@inproceedings{ff:cwc:pdp:11,
  month = feb,
  author = {Marco Aldinucci and Mario Coppo and Ferruccio Damiani and Maurizio
            Drocco and Massimo Torquati and Angelo Troina},
  keywords = {fastflow},
  booktitle = {Proc. of Intl. Euromicro PDP 2011: Parallel Distributed and
               network-based Processing},
  editor = {Yiannis Cotronis and Marco Danelutto and George Angelos
            Papadopoulos},
  url = {http://calvados.di.unipi.it/storage/paper_files/2011_ff_cwc_sim_PDP.pdf},
  address = {Ayia Napa, Cyprus},
  title = {On Designing Multicore-Aware Simulators for Biological Systems},
  abstract = {The stochastic simulation of biological systems is an increasingly
              popular technique in bioinformatics. It often is an enlightening
              technique, which may however result in being computational
              expensive. We discuss the main opportunities to speed it up on
              multi-core platforms, which pose new challenges for
              parallelisation techniques. These opportunities are developed in
              two general families of solutions involving both the single
              simulation and a bulk of independent simulations (either replicas
              of derived from parameter sweep). Proposed solutions are tested on
              the parallelisation of the CWC simulator (Calculus of Wrapped
              Compartments) that is carried out according to proposed solutions
              by way of the FastFlow programming framework making possible fast
              development and efficient execution on multi-cores.},
  publisher = {IEEE},
  year = {2011},
  pages = {318-325},
}


 Chronological Overview 
 Type-Hierarchical Overview 
Formal Methods in Computing
(Most of the papers antecedent to 1995
are not included in the list)
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