MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit.

Fange D, Mahmutovic A, Elf J

Bioinformatics 28 (23) 3155-3157 [2012-12-01; online 2012-10-07]

MesoRD is a tool for simulating stochastic reaction-diffusion systems as modeled by the reaction diffusion master equation. The simulated systems are defined in the Systems Biology Markup Language with additions to define compartment geometries. MesoRD 1.0 supports scale-dependent reaction rate constants and reactions between reactants in neighbouring subvolumes. These new features make it possible to construct physically consistent models of diffusion-controlled reactions also at fine spatial discretization. MesoRD is written in C++ and licensed under the GNU general public license (GPL). MesoRD can be downloaded at http://mesord.sourceforge.net. The MesoRD homepage, http://mesord.sourceforge.net, contains detailed documentation and news about recently implemented features. johan.elf@icm.uu.se.

Affiliated researcher

PubMed 23044538

DOI 10.1093/bioinformatics/bts584

Crossref 10.1093/bioinformatics/bts584

pii: bts584


Publications 7.1.2