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Bioinformatics Advance Access originally published online on April 7, 2005
Bioinformatics 2005 21(12):2923-2924; doi:10.1093/bioinformatics/bti431
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Stochastic reaction-diffusion simulation with MesoRD

Johan Hattne {dagger}, David Fange and Johan Elf *

Department of Cell and Molecular Biology, BMC, Uppsala University 75124 Uppsala, Sweden

*To whom correspondence should be addressed.

Summary: MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular, it is an implementation of the next subvolume method, which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation.

Availability: MesoRD is free software, written in C++ and licensed under the GNU general public license (GPL). MesoRD runs on Linux, Mac OS X, NetBSD, Solaris and Windows XP. It can be downloaded from http://mesord.sourceforge.net.

Contact: johan.elf{at}icm.uu.se; johan.hattne{at}embl-hamburg.de

Supplementary information: ‘MesoRD User's Guide’ and other documents are available at http://mesord.sourceforge.net.


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