A BioNetGen@VCell automatically generates a biochemical reaction network from user-specified rules for biomolecular interactions. BioNetGen@VCell provides all capabilities of BioNetGen stand-alone. For the full list of capabilities, check http://vcell.org/bionetgen or http://bionetgen.org. Additionally, BioNetGen@VCell provides:
Rule-based Modeling With BioNetGen
Rules are specified in the BioNetGen language (BNGL). A user can explicitly indicate the parts of proteins involved in an interaction, the conditions upon which an interaction depends, the connectivity of proteins in a complex, and other aspects of protein-protein interactions. BioNetGen is useful when one needs to account for effects of combinatorial complexity, when a small number of interactions generates a much larger number of chemical species and reactions. For example, a receptor that contains N sites at which phosphate can be added or removed can occupy 2^N different states.
Clicking the Launch BioNetGen menu item invokes a window with 4 tabs: