I installed BioNetGen as well as I could on Windows, but it doesn't seem to work right. However, you can use RuleBuilder and you are welcome to try BioNetGen -- maybe you'll have better luck. At least one of the students in the workshop was able to get it to run on a PC.
Note: When I use pointy brackets around a word or phrase, it means you should change the entire word or phrase, including the pointy brackets, to the thing I'm describing. For example, since my loginname is nancyg, I would use C:\Users\nancyg and C:\Users\nancyg\Desktop in place of the above.
Wherever you put the file, figure out the absolute path to the directory. This is the sequence of directories, separated by "\" characters, and beginning with C:
Inside the BioNetGen directory are a number of subdirectories -- the most interesting are Models2, which contains a collection of models including toy-jim.bngl; Perl2, which contains a number of programs, most importantly BNG2.pl; and bin, which contains some more important programs. I have already put run_network.exe and run_network_MSWin32.exe in it for you.
To run BioNetGen, all you have to do is type BNG2.pl <modelfile>.bngl.