File -> Import (BNGL files)

BNGL is the Bio Net Gen Language that is a native format for storing rule-based models used in BioNetGen and NFSim simulators. VCell supports import of models encoded in BNGL.

To import a file into the Virtual Cell, choose File -> Import. This opens a "Choose File" dialog. Navigate to the folder where the file to be imported is stored. Click Open to import the file or Cancel to cancel the operation.

If some features in BNGL file are not supported by VCell, a pop-up window is launched with a suggestion to correct unsupported features. In some cases, when some features in BNGL file (such as fixed value of concentration) are supported by BioNetGen but not NFsim, only a single deterministic rule-based application will be created.

Unit conversions from SBML

BNGL does not have defined units (units are implicit and must be consistent), while VCell must have a defined unit system. During import, a user must define a default substance units for the imported model as either Concentrations or Molecules. Note that Virtual Cell internally represents species and kinetic laws only in terms of concentration, thus every number of molecules is converted to concentration units in the Virtual Cell by dividing the quantity in substance units by the size of the compartment in which the species is located. Also, reaction rates in SBML are defined in terms of substance/time, which are converted to concentration/time while importing into the Virtual Cell.