Atomizer can be invoked from BioNetGen in order to use an SBML file as part of a BioNetGen simulation protocol


This will populate BioNetGen species and reactions with a structureless version of the SBML model. In order to recover structure information you can use the following command

readFile({file=>"<filename.xml>", atomize=>1})

You can also include other Atomizer command line options using the BioNetGen option syntax.