RDSIM

This repository contains the source code, model files, mesh files, Matlab scripts, and bash scripts that we used to generate and analyze the data for the manuscript "Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning", submitted to the Journal of Chemical Physics, 2017.

Please note that the code is not stable; it is under continuing development and we ask that any potential user contacts us before using this release of the code for research purposes. We may have found unresolved bugs or other issues since this release, that could potentially affect the results in a significant way. By contacting us, we can advise on such issues, as well as on how to best use the code.

We have tested this code on a clean Ubuntu 16.04 install. It may work on some versions of Mac OS as well; note however that some parts of the code utilizes OpenMP. Note that some of the examples require days of computational time. The authors tested the code and scripts on a 4 core, 8GB Ubuntu 16.04 instance in an OpenStack cloud; all the simulations would require on the order of a week of computational time on such a set up.

You are more than welcome to contact us with questions or comments. If you are interested in using this method for research, please contact us as well. We may be able to help you get started, or possibly collaborate.

st.hellander@gmail.com

Stefan Hellander
Andreas Hellander
Linda Petzold

Download source code, scripts, and data (1.42GB)

The repository is public on Bitbucket (with instructions on how to run the solver as a plugin solver to PyURDME): RDSIM on Bitbucket.