Simulation of P systems with active membranes on CUDA
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}
}
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
November 19, 2010 by hgpu
