gpusmoldyn Files

This folder contains the documentation (paper and slides) relative to our project of porting core portions of the Smoldyn code (www.smoldyn.org) to CUDA, the NVIDIA programming environment for GPU Computing.

Smoldyn is an algorithm and computer program for stochastic simulations of biochemical systems. In Smoldyn, the user (usually, a theoretical biologist or a researcher in systems biology) enters informations about a system of reactions that can happen in a model organism (for example, a bacteria). Information includes: the geometry of the reaction chamber (shape, walls), biochemical species, reactions, diffusion rates. Smoldyn simulates the behaviour in time of molecules of different species, how they react and interact.

This project is a study on how the Smoldyn algorithm, which was strictly sequential, can be rewritten using a data parallel approach, and run on the GPU to provide great speed-ups of the simulation. The method is explained in the paper, accepted and presented at the 2010 Conference on High Performance Computing for Systems Biology (HIBI) and in teh related set of slides.