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Models with extremely high symmetry in the molecule definition bog down BioNetGen #165

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jjtapia opened this issue Mar 2, 2016 · 0 comments

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@jjtapia
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jjtapia commented Mar 2, 2016

Attaching model that reproduces the isse. The culprit seems to be

Species __ErbB3_ErbB2___P_GAP_Grb2_Gab1_P_PI3K___PIP2__6_plasma_membrane @plasma_membrane:ErB2(_p~_P,atp1_2e9,b~B,cpp,erb2,erb3!27,erb4,erbb1,erk,gab1!47,gap!38,grb2!46,inh,pase9t,pi!64,pi!65,pi!66,pi!67,pi!68,pi!69,pi3k!59,ras,rtk_pase,shc,shp2).Gab1(Gab1_Pm~0,Gab1_Psh~0,_P,_p~_P,erb2!47,erbb1,m,p~0).PI(PIP2~0,akt,erb2!64,erbb1,p3~P3,pdk1,pten,shp).PI(PIP2~0,akt,erb2!65,erbb1,p3~P3,pdk1,pten,shp).PI(PIP2~0,akt,erb2!66,erbb1,p3~P3,pdk1,pten,shp).PI(PIP2~0,akt,erb2!67,erbb1,p3~P3,pdk1,pten,shp).PI(PIP2~0,akt,erb2!68,erbb1,p3~P3,pdk1,pten,shp).PI(PIP2~0,akt,erb2!69,erbb1,p3~P3,pdk1,pten,shp).ErB3(_p~0,b~B,erb2!27,erb3,erbb1,hrg,inh).Grb2(erb2!46,erbb1,shc,sos).GAP(erb2!38,erbb1).PI3K(erb2!59,erbb1) #(ErbB3:ErbB2)_P:GAP:Grb2:Gab1_P:PI3K:(PIP2)6

and similar molecules

Reference model:
https://dl.dropboxusercontent.com/u/7096948/bmd255.bngl

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