Exact stochastic simulation of intracellular transport
A C++ implementation of the hybrid continuous-discrete stochastic simulation algorithm for intracellular transport can be downloaded here. The code was written by Jo Helmuth as part of his PhD project at the MOSAIC Group:
J. A. Helmuth. Computational Methods for Analyzing and Simulating Intra-Cellular Transport Processes. PhD thesis, Diss. ETH No. 19190, ETH Zürich, 2010. (PDF)
The method and algorithm implemented in this toolbox are described and benchmarked in the following publication:
J. A. Helmuth, S. Reboux, and I. F. Sbalzarini. Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors. J. Comput. Sci., doi: 10.1016/j.jocs.2011.08.006, 2011. (PDF)
In order to ensure financial support for our project and allow further development of this software, please cite above publications in all your documents and manuscripts that made use of this software. Thanks a lot!
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