Virtual Cell at UConn


BioNetGen at Los Alamos

BioNetGen at Virtual Cell


RELEASED October 6th, 2006 in VCell 4.3 BETA

 

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.


TUTORIAL at ICSB October 1st, 2007
EXAMPLES FOR THE TUTORIAL at ICSB October 1st, 2007


Resources for starting with BioNetGen (updated 06/07/07)


Biological Motivation for Rule-based modeling (pdf)

Science STKE review of rule-based modeling(pdf)

BioNetGen - powerpoint tutorial (pdf)

BioNetGen - powerpoint Tutorial on EGFR (pdf)

BioNetGen@VCell UserGuide

Detailed BioNetGen modeling tutorial (html)

Tutorial at q-bio Santa Fe, 08/08/2007