Launch BioNetGen

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:

Generation of compartmental Virtual Cell BioModels from the BioNetGen-generated reaction network.
A convenient interface to view results.
Different results export options.

BioNetGen runs locally on your computer, so performance depends on your machine performance. No jobs are sent to the Virtual Cell server and no model is uploaded to the Virtual Cell Database Server unless specifically requested.

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:

Rules editor - editor to write a set of rules in BioNetGen Language.
Messages - view detailed information about BioNetGen network generation and simulation.
Output - view and save generated model and simulation results, create VCell BioModel.
Help - links to web resources about BioNetGen.