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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.
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BMC Systems Biology

ISSN: 1752-0509

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