GPU-powered Simulation Methodologies for Biological Systems

• Main Authors: Dario Pescini, Marco Nobile, Paolo Cazzaniga, Giulio Caravagna, Daniela Besozzi, Alessandro Re
• Format: Article
• Language: English
• Published: Open Publishing Association 2013-09-01
• Series: Electronic Proceedings in Theoretical Computer Science
• Online Access: http://arxiv.org/pdf/1309.7695v1

The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological systems in a quantitative manner. Computer algorithms allow to faithfully reproduce the dynamics of the corresponding biological system, and, at the price of a large number of simulations, it is possible to extensively investigate the system functioning across a wide spectrum of natural conditions. To enable multiple analysis in parallel, using cheap, diffused and highly efficient multi-core devices we developed GPU-powered simulation algorithms for stochastic, deterministic and hybrid modeling approaches, so that also users with no knowledge of GPUs hardware and programming can easily access the computing power of graphics engines.