Tutorial

A BioNetGen2 Tutorial Jim Faeder Theoretical Biology and Biophysics Group Los Alamos National Laboratory How to find BioNetGen• Web site is http://cellsignaling.lanl.gov• Web interface is athttp://cellsignaling.lanl.gov/bionetgen/bionetgen2.html• Send email to faeder@lanl.gov torequest an account, source code, or forother questions.Introduction to the GraphicalRepresentationSignaling proteins and theircomplexes are represented asGraphsA multi-subunit receptor~Y ~Y Component states~pY ~pYMoleculeComponentsFcεRIThe high affinityreceptor for IgEα β γβ γβ γA kinasetSH2 L~YL~pYLA~YAA~pYSykSyk!!!!A molecular complexLig%~P%~P !#~U $ $ !#~UFc!"RI Fc!"RItSH2L~UA~PSyk!!!!!!!!Patterns select groups ofchemical speciesA pattern that selects a receptorwith free ligand binding siteList of selected species "%~U !$~U "Unspecified Fc!#RIcomponents Fc!#RImay be in any binding or %~P !$~U "internal state.Fc!#RI...%~P $~U "Fc!#RItSH2L~UList contains 24 speciesA~Pfor 354 state model.Syk!!!!!!!!!!Another pattern exampleA pattern that selects a receptorwith bound ligand siteList of selected species $LigFilled circle Fc!"RI %~U #~U $indicates that component has Fc!"RIone or more ...unspecified bonds. LigThis species is %~P%~P !#~U $ $ !#~Uselected twice becuaseit contains two Fc!"RIFc!"RI Fc!"RI molecules that match... the pattern. Lig%~P !#~U $Fc!"RItSH2List contains ...