SBMLsimulator Version 2.0

New features

• Support for SBML files up to the latest release of Level 3 Version 2 thanks to the updated JSBML library
  • The graphical user interface was extended to support new model components, including various SBML extension packages, such as Groups, Layout (see further description below), Flux Balance Constraints, etc.
• Improved simulation capabilities using release 1.5 of the simulation backend SBSCL.
• Garuda support: SBMLsimulator 2.0 comes with a Garuda archive file and can, therefore, be directly used from the Garuda workbench.
• Support for model displays as SBGN Process Diagrams using yFiles for Java™:
  • If a model contains a diagram (in the format of the SBML Layout Extension), SBMLsimulator 2.0 can now display this layout in an interactive map.
  • SBMLsimulator automatically generates a map representation for models without graphical information.
  • In either case, the new tab Graph can be clicked to access the model's display.
• Mapping of experimental or simulation data to an interactive map: The model display (be it defined in the model or automatically generated) takes simulation data (the result of a numerical calculation) or loaded experimental data and maps it to the nodes and arrows.
  • Several different ways of data mapping have been implemented and are accessible from the graphical user interface: node size, node color, absolute size and relative color, relative size and absolute color values, relative filling levels with absolute color gradients. Further details are described in this article.
  • An export function allows users to save the display as an image, e.g., for publication or analysis in scalable vector format (SVG) or as a portable network graphics file (PNG).
  • Time-series data can be visualized as a dynamically animated video that can be played in several speeds. While the video is playing, users can zoom and pan on the map and analyze areas of interest. To this end, the animation can play in an ongoing loop. Optionally, the exact values of fluxes and concentrations can be displayed directly on the graph.
  • An animated sliding camera window can automatically move the viewport through the graph while the animation is playing. To this end, users can define coordinates in a simple text file format. The user can also adjust the speed of the sliding window.
  • Optionally, a diagram with a moving red line can be displayed while the animation is running to indicate where in the diagram the animation is.
  • An export function saves the generated animations to a variety of standard video file formats, including MOV, AVI, MPG, WMV, FLV.

Bug fixes

• The application has generally become more stable and sophisticated, thanks to updated third-party apps and minor improvements.