Skip to main content

Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Table 3 A comparison of features of RDME simulation software

From: URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

  URDME 1.1 MesoRD 1.0 STEPS 1.3
Interface Matlab & Comsol Command line Python
   Simple GUI (Windows)  
Visualization Matlab & Comsol OpenGL tool PyOpenGL tool
   Matlab toolbox  
Post-processing Matlab 3rd party Python
SBML support Conversion tool SBML L2v4 Import module
  (no geometry) + CSG geometry (no geometry)
Edit Geometry Comsol SBML 3rd party
Mesh Type Vertex centered Uniform Cartesian Body centered
  Tetrahedrons   Tetrahedrons
Algorithms NSM, DFSP NSM Spatial-SSA
  + extendable +non-local extension  
Propensity types All SBML (MathML) Mass-action
Model Features compartments compartments compartments
  surfaces   surfaces
  volume diffusion volume diffusion volume diffusion
  surface diffusion   
  directed transport   
  1. This table summarizes the main differences and similarities between the software packages URDME, MesoRD and STEPS.
Back to article page