The simulation tools now display an animated "fire" on top of items after a simulation. The purpose of the fire is to highlight upregulated and downregulated molecules. The size of the fire is proportional to the final output in the simulation.
These fires can be created from Python or Octave scripts using the tc_burn( item, intensity ) command, where intensity is a number in the range (0,1). From C++, a tool can connect to signals in the LabelingTool (in TinkerCellCore library) in order to create these effects.
The fire feature can be completely inactivated from C++ by setting the LabelingTool::ENABLE_FIRE to false.