JDesigner is a graphical modeling environment for biochemical reaction networks. It allows drawing the network on screen and selecting the appropriate kinetic laws from a wide selection of inbuilt rate laws or defining new user defined rate laws. JDesigner is probably the module that profits the most from SBW. Via the previously described auto-layout and SBML Layout extension modules, it is able to render any SBML file. Using the SBW menu, it allows passing on the current model to a wide variety of analysis tools. It also allows for time-course simulation and steady state analysis using either roadRunner or Jarnac. Furthermore, it uses Metatool for structural analysis. Finally, it dynamically finds modules from the SBML Exporter category at runtime to allow exporting the model into a variety of file formats including Matlab, Java, or XPP.

Visual Modeling Environment