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Simulation of P systems with active membranes on CUDA

Jose M. Cecilia, Jose M. Garcia, Gines D. Guerrero, Miguel A. Martinez-del-Amor, Ignacio Perez-Hurtado, Mario J. Perez-Jimenez
Grupo de Arquitectura y Computacion Paralela, Dpto. Ingenieria y Tecnologia de Computadores, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain
Brief Bioinform, Vol. 11, No. 3. (1 May 2010), pp. 313-322.

@conference{canales2009simulation,

   title={Simulation of P Systems with Active Membranes on CUDA},

   author={Canales, J.M.C. and Carrasco, J.M.G. and Hern{‘a}ndez, G.D.G. and del Amor, M.{‘A}.M. and de Mendoza, I.P.H. and Perez-Jimenez, M.J.},

   booktitle={Proceedings of the 2009 International Workshop on High Performance Computational Systems Biology},

   pages={61–70},

   year={2009},

   organization={IEEE Computer Society}

}

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P systems or Membrane Systems provide a high-level computational modelling framework that combines the structure and dynamic aspects of biological systems in a relevant and understandable way. They are inherently parallel and non-deterministic computing devices. In this article, we discuss the motivation, design principles and key of the implementation of a simulator for the class of recognizer P systems with active membranes running on a (GPU). We compare our parallel simulator for GPUs to the simulator developed for a single central processing unit (CPU), showing that GPUs are better suited than CPUs to simulate P systems due to their highly parallel nature. 10.1093/bib/bbp064
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