@article{cwc:cloud:bib:13,
  volume = {15},
  number = {5},
  issn = {1467-5463},
  author = {Marco Aldinucci and Massimo Torquati and Concetto Spampinato and
            Maurizio Drocco and Claudia Misale and Cristina Calcagno and Mario
            Coppo},
  keywords = {fastflow, bioinformatics, cloud},
  url = {http://calvados.di.unipi.it/storage/paper_files/2013_ff_bio_cloud_briefings.pdf},
  abstract = {The stochastic modelling of biological systems, coupled with Monte
              Carlo simulation of models, is an increasingly popular technique
              in bioinformatics. The simulation-analysis workflow may result
              computationally expensive reducing the interactivity required in
              the model tuning. In this work, we advocate the high-level
              software design as a vehicle for building efficient and portable
              parallel simulators for the cloud. In particular, the Calculus of
              Wrapped Components (CWC) simulator for systems biology, which is
              designed according to the FastFlow pattern-based approach, is
              presented and discussed. Thanks to the FastFlow framework, the CWC
              simulator is designed as a high-level workflow that can simulate
              CWC models, merge simulation results and statistically analyse
              them in a single parallel workflow in the cloud. To improve
              interactivity, successive phases are pipelined in such a way that
              the workflow begins to output a stream of analysis results
              immediately after simulation is started. Performance and
              effectiveness of the CWC simulator are validated on the Amazon
              Elastic Compute Cloud.},
  title = {Parallel stochastic systems biology in the cloud},
  year = {2014},
  journal = {Briefings in Bioinformatics},
  pages = {798-813},
}

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