StochKit-FF: Efficient Systems Biology on Multicore Architectures

The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.Comment: 14 pages + cover pag

Gaspar data-centric framework

This paper presents the Gaspar data-centric framework to develop high performance parallel applications in Java. Our approach is based on data iterators and on the map pattern of computation. The framework provides an efficient data Application Programming Inter-face(API) that supports flexible data layout and data tiling. Data layout and tiling enable the improvement of data locality, which is essential to foster application scalability in modern multi-core systems. The paper presents the framework data-centric concepts and shows that the performance is comparable to pure Java code.(undefined)info:eu-repo/semantics/publishedVersio