title: MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  johan.elf@icm.uu.se.
authors.affiliation: Department of Cell & Molecular Biology, Science for Life Laboratory, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden.
authors.forename: David
authors.initials: D
authors.lastname: Fange
authors.forename: Anel
authors.initials: A
authors.lastname: Mahmutovic
authors.forename: Johan
authors.initials: J
authors.lastname: Elf
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004058:Diffusion; D008956:Models, Chemical; D012984:Software; D013269:Stochastic Processes; D049490:Systems Biology