BioNetGen at Virtual Cell
Rule-based modeling tutorial April 8-10th, 2013 at NIMBioS!
BioNetGen is now available to run from the Virtual Cell. You need to register for the Virtual Cell, then you may call BioNetGen window and create a mathematical model.
BioNetGen@VCell is a web-based tool for automatically generating a biochemical reaction networks from user-specified rules for biomolecular interactions.
Rules are specified in the BioNetGen language (BNGL) designed with protein-protein interactions in mind. 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 will generate a model that accounts comprehensively for the full spectrum of chemical species and reactions implied by the rules that define the model.
BioNetGen has been used to generate models for reaction networks with hundreds of thousands of species and reactions. It is one of the few software tools available for generating physicochemical models of systems marked by combinatorial complexity - a hallmark of cellular signaling.
The latest BioNetGen tutorial - book chapter
TUTORIAL at ICSB 2010
STEP-BY-STEP TUTORIAL at ICSB 2007
EXAMPLES FOR THE TUTORIAL at ICSB 2007
BioNetGen - Biological Motivation
BioNetGen - Formal Tutorial
BioNetGen - EGFR Tutorial