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Merged
JoshLoecker merged 2 commits into from
Dec 9, 2024
Merged

Add boundary column #196

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f72eff9
feat: add boundary column
JoshLoecker Dec 9, 2024
7b58147
fix: allow new boundary column
JoshLoecker Dec 9, 2024
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1 change: 1 addition & 0 deletions main/como/create_context_specific_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -550,6 +550,7 @@ def _collect_boundary_reactions(path: Path) -> _BoundaryReactions:
df = _create_df(path)
for column in df.columns:
if column not in [
"boundary",
"reaction",
"abbreviation",
"compartment",
Expand Down
140 changes: 70 additions & 70 deletions main/data/boundary_rxns/naiveB_boundary_rxns.csv
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Original file line number Diff line number Diff line change
@@ -1,70 +1,70 @@
Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
Exchange,glc_D,Extracellular,-100,1000
Exchange,fe2,Extracellular,-1000,1000
Exchange,gal,Extracellular,0,1000
Exchange,zn2,Extracellular,-1000,1000
Exchange,ca2,Extracellular,-1000,1000
Exchange,na1,Extracellular,-1000,1000
Exchange,cl,Extracellular,-1000,1000
Exchange,k,Extracellular,-1000,1000
Exchange,h,Extracellular,-1000,1000
Exchange,h2o,Extracellular,-1000,1000
Exchange,o2,Extracellular,-1000,1000
Exchange,pi,Extracellular,-1000,1000
Exchange,ppi,Extracellular,-1000,1000
Exchange,co2,Extracellular,-1000,1000
Exchange,nh4,Extracellular,-1000,1000
Exchange,no2,Extracellular,-1000,1000
Exchange,co,Extracellular,-1000,1000
Exchange,asn_L,Extracellular,-1,1000
Exchange,asp_L,Extracellular,-1,1000
Exchange,glu_L,Extracellular,-1,1000
Exchange,ile_L,Extracellular,-1,1000
Exchange,leu_L,Extracellular,-1,1000
Exchange,lys_L,Extracellular,-1,1000
Exchange,met_L,Extracellular,-1,1000
Exchange,pro_L,Extracellular,-1,1000
Exchange,ser_L,Extracellular,-1,1000
Exchange,val_L,Extracellular,-1,1000
Exchange,gly,Extracellular,-1,1000
Exchange,cys_L,Extracellular,-1,1000
Exchange,ala_L,Extracellular,-1,1000
Exchange,his_L,Extracellular,-1,1000
Exchange,thr_L,Extracellular,-1,1000
Exchange,gln_L,Extracellular,-1,1000
Exchange,phe_L,Extracellular,-1,1000
Exchange,tyr_L,Extracellular,-1,1000
Exchange,arg_L,Extracellular,-1,1000
Exchange,trp_L,Extracellular,-1,1000
Exchange,eicostet,Extracellular,-1,1000
Exchange,hdca,Extracellular,-1,1000
Exchange,hdcea,Extracellular,-1,1000
Exchange,lnlc,Extracellular,-1,1000
Exchange,lnlnca,Extracellular,-1,1000
Exchange,lnlncg,Extracellular,-1,1000
Exchange,ocdca,Extracellular,-1,1000
Exchange,ocdcea,Extracellular,-1,1000
Exchange,thmmp,Extracellular,0,1000
Exchange,thmtp,Extracellular,0,1000
Exchange,ncam,Extracellular,0,1000
Exchange,pnto_R,Extracellular,0,1000
Exchange,pydxn,Extracellular,0,1000
Exchange,pydx,Extracellular,0,1000
Exchange,pydam,Extracellular,0,1000
Exchange,btn,Extracellular,0,1000
Exchange,fol,Extracellular,-10,1000
Exchange,aqcobal,Extracellular,0,1000
Exchange,vitd3,Extracellular,-1,1000
Exchange,ascb_L,Extracellular,0,1000
Exchange,retinol,Extracellular,-10,1000
Exchange,retinal,Extracellular,-10,1000
Exchange,ala_B,Extracellular,-1,1000
Exchange,ala_D,Extracellular,-1,1000
Exchange,h2co3,Extracellular,-1000,1000
Exchange,h2o2,Extracellular,-1000,1000
Exchange,hco3,Extracellular,-1000,1000
Exchange,orn,Extracellular,-1,1000
Exchange,orn_D,Extracellular,-1,1000
Exchange,so4,Extracellular,-1000,1000
Exchange,ribflv,Extracellular,-1,1000
Exchange,Lcystin,Extracellular,-1,1000
Boundary,Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
Demand,Exchange,glc_D,Extracellular,-100,1000
Demand,Exchange,fe2,Extracellular,-1000,1000
Demand,Exchange,gal,Extracellular,0,1000
Demand,Exchange,zn2,Extracellular,-1000,1000
Demand,Exchange,ca2,Extracellular,-1000,1000
Demand,Exchange,na1,Extracellular,-1000,1000
Demand,Exchange,cl,Extracellular,-1000,1000
Demand,Exchange,k,Extracellular,-1000,1000
Demand,Exchange,h,Extracellular,-1000,1000
Demand,Exchange,h2o,Extracellular,-1000,1000
Demand,Exchange,o2,Extracellular,-1000,1000
Demand,Exchange,pi,Extracellular,-1000,1000
Demand,Exchange,ppi,Extracellular,-1000,1000
Demand,Exchange,co2,Extracellular,-1000,1000
Demand,Exchange,nh4,Extracellular,-1000,1000
Demand,Exchange,no2,Extracellular,-1000,1000
Demand,Exchange,co,Extracellular,-1000,1000
Demand,Exchange,asn_L,Extracellular,-1,1000
Demand,Exchange,asp_L,Extracellular,-1,1000
Demand,Exchange,glu_L,Extracellular,-1,1000
Demand,Exchange,ile_L,Extracellular,-1,1000
Demand,Exchange,leu_L,Extracellular,-1,1000
Demand,Exchange,lys_L,Extracellular,-1,1000
Demand,Exchange,met_L,Extracellular,-1,1000
Demand,Exchange,pro_L,Extracellular,-1,1000
Demand,Exchange,ser_L,Extracellular,-1,1000
Demand,Exchange,val_L,Extracellular,-1,1000
Demand,Exchange,gly,Extracellular,-1,1000
Demand,Exchange,cys_L,Extracellular,-1,1000
Demand,Exchange,ala_L,Extracellular,-1,1000
Demand,Exchange,his_L,Extracellular,-1,1000
Demand,Exchange,thr_L,Extracellular,-1,1000
Demand,Exchange,gln_L,Extracellular,-1,1000
Demand,Exchange,phe_L,Extracellular,-1,1000
Demand,Exchange,tyr_L,Extracellular,-1,1000
Demand,Exchange,arg_L,Extracellular,-1,1000
Demand,Exchange,trp_L,Extracellular,-1,1000
Demand,Exchange,eicostet,Extracellular,-1,1000
Demand,Exchange,hdca,Extracellular,-1,1000
Demand,Exchange,hdcea,Extracellular,-1,1000
Demand,Exchange,lnlc,Extracellular,-1,1000
Demand,Exchange,lnlnca,Extracellular,-1,1000
Demand,Exchange,lnlncg,Extracellular,-1,1000
Demand,Exchange,ocdca,Extracellular,-1,1000
Demand,Exchange,ocdcea,Extracellular,-1,1000
Demand,Exchange,thmmp,Extracellular,0,1000
Demand,Exchange,thmtp,Extracellular,0,1000
Demand,Exchange,ncam,Extracellular,0,1000
Demand,Exchange,pnto_R,Extracellular,0,1000
Demand,Exchange,pydxn,Extracellular,0,1000
Demand,Exchange,pydx,Extracellular,0,1000
Demand,Exchange,pydam,Extracellular,0,1000
Demand,Exchange,btn,Extracellular,0,1000
Demand,Exchange,fol,Extracellular,-10,1000
Demand,Exchange,aqcobal,Extracellular,0,1000
Demand,Exchange,vitd3,Extracellular,-1,1000
Demand,Exchange,ascb_L,Extracellular,0,1000
Demand,Exchange,retinol,Extracellular,-10,1000
Demand,Exchange,retinal,Extracellular,-10,1000
Demand,Exchange,ala_B,Extracellular,-1,1000
Demand,Exchange,ala_D,Extracellular,-1,1000
Demand,Exchange,h2co3,Extracellular,-1000,1000
Demand,Exchange,h2o2,Extracellular,-1000,1000
Demand,Exchange,hco3,Extracellular,-1000,1000
Demand,Exchange,orn,Extracellular,-1,1000
Demand,Exchange,orn_D,Extracellular,-1,1000
Demand,Exchange,so4,Extracellular,-1000,1000
Demand,Exchange,ribflv,Extracellular,-1,1000
Demand,Exchange,Lcystin,Extracellular,-1,1000
140 changes: 70 additions & 70 deletions main/data/boundary_rxns/smB_boundary_rxns.csv
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,70 +1,70 @@
Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
Exchange,glc_D,Extracellular,-100,1000
Exchange,fe2,Extracellular,-1000,1000
Exchange,gal,Extracellular,0,1000
Exchange,zn2,Extracellular,-1000,1000
Exchange,ca2,Extracellular,-1000,1000
Exchange,na1,Extracellular,-1000,1000
Exchange,cl,Extracellular,-1000,1000
Exchange,k,Extracellular,-1000,1000
Exchange,h,Extracellular,-1000,1000
Exchange,h2o,Extracellular,-1000,1000
Exchange,o2,Extracellular,-1000,1000
Exchange,pi,Extracellular,-1000,1000
Exchange,ppi,Extracellular,-1000,1000
Exchange,co2,Extracellular,-1000,1000
Exchange,nh4,Extracellular,-1000,1000
Exchange,no2,Extracellular,-1000,1000
Exchange,co,Extracellular,-1000,1000
Exchange,asn_L,Extracellular,-1,1000
Exchange,asp_L,Extracellular,-1,1000
Exchange,glu_L,Extracellular,-1,1000
Exchange,ile_L,Extracellular,-1,1000
Exchange,leu_L,Extracellular,-1,1000
Exchange,lys_L,Extracellular,-1,1000
Exchange,met_L,Extracellular,-1,1000
Exchange,pro_L,Extracellular,-1,1000
Exchange,ser_L,Extracellular,-1,1000
Exchange,val_L,Extracellular,-1,1000
Exchange,gly,Extracellular,-1,1000
Exchange,cys_L,Extracellular,-1,1000
Exchange,ala_L,Extracellular,-1,1000
Exchange,his_L,Extracellular,-1,1000
Exchange,thr_L,Extracellular,-1,1000
Exchange,gln_L,Extracellular,-1,1000
Exchange,phe_L,Extracellular,-1,1000
Exchange,tyr_L,Extracellular,-1,1000
Exchange,arg_L,Extracellular,-1,1000
Exchange,trp_L,Extracellular,-1,1000
Exchange,eicostet,Extracellular,-1,1000
Exchange,hdca,Extracellular,-1,1000
Exchange,hdcea,Extracellular,-1,1000
Exchange,lnlc,Extracellular,-1,1000
Exchange,lnlnca,Extracellular,-1,1000
Exchange,lnlncg,Extracellular,-1,1000
Exchange,ocdca,Extracellular,-1,1000
Exchange,ocdcea,Extracellular,-1,1000
Exchange,thmmp,Extracellular,0,1000
Exchange,thmtp,Extracellular,0,1000
Exchange,ncam,Extracellular,0,1000
Exchange,pnto_R,Extracellular,0,1000
Exchange,pydxn,Extracellular,0,1000
Exchange,pydx,Extracellular,0,1000
Exchange,pydam,Extracellular,0,1000
Exchange,btn,Extracellular,0,1000
Exchange,fol,Extracellular,-10,1000
Exchange,aqcobal,Extracellular,0,1000
Exchange,vitd3,Extracellular,-1,1000
Exchange,ascb_L,Extracellular,0,1000
Exchange,retinol,Extracellular,-10,1000
Exchange,retinal,Extracellular,-10,1000
Exchange,ala_B,Extracellular,-1,1000
Exchange,ala_D,Extracellular,-1,1000
Exchange,h2co3,Extracellular,-1000,1000
Exchange,h2o2,Extracellular,-1000,1000
Exchange,hco3,Extracellular,-1000,1000
Exchange,orn,Extracellular,-1,1000
Exchange,orn_D,Extracellular,-1,1000
Exchange,so4,Extracellular,-1000,1000
Exchange,ribflv,Extracellular,-1,1000
Exchange,Lcystin,Extracellular,-1,1000
Boundary,Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
Demand,Exchange,glc_D,Extracellular,-100,1000
Demand,Exchange,fe2,Extracellular,-1000,1000
Demand,Exchange,gal,Extracellular,0,1000
Demand,Exchange,zn2,Extracellular,-1000,1000
Demand,Exchange,ca2,Extracellular,-1000,1000
Demand,Exchange,na1,Extracellular,-1000,1000
Demand,Exchange,cl,Extracellular,-1000,1000
Demand,Exchange,k,Extracellular,-1000,1000
Demand,Exchange,h,Extracellular,-1000,1000
Demand,Exchange,h2o,Extracellular,-1000,1000
Demand,Exchange,o2,Extracellular,-1000,1000
Demand,Exchange,pi,Extracellular,-1000,1000
Demand,Exchange,ppi,Extracellular,-1000,1000
Demand,Exchange,co2,Extracellular,-1000,1000
Demand,Exchange,nh4,Extracellular,-1000,1000
Demand,Exchange,no2,Extracellular,-1000,1000
Demand,Exchange,co,Extracellular,-1000,1000
Demand,Exchange,asn_L,Extracellular,-1,1000
Demand,Exchange,asp_L,Extracellular,-1,1000
Demand,Exchange,glu_L,Extracellular,-1,1000
Demand,Exchange,ile_L,Extracellular,-1,1000
Demand,Exchange,leu_L,Extracellular,-1,1000
Demand,Exchange,lys_L,Extracellular,-1,1000
Demand,Exchange,met_L,Extracellular,-1,1000
Demand,Exchange,pro_L,Extracellular,-1,1000
Demand,Exchange,ser_L,Extracellular,-1,1000
Demand,Exchange,val_L,Extracellular,-1,1000
Demand,Exchange,gly,Extracellular,-1,1000
Demand,Exchange,cys_L,Extracellular,-1,1000
Demand,Exchange,ala_L,Extracellular,-1,1000
Demand,Exchange,his_L,Extracellular,-1,1000
Demand,Exchange,thr_L,Extracellular,-1,1000
Demand,Exchange,gln_L,Extracellular,-1,1000
Demand,Exchange,phe_L,Extracellular,-1,1000
Demand,Exchange,tyr_L,Extracellular,-1,1000
Demand,Exchange,arg_L,Extracellular,-1,1000
Demand,Exchange,trp_L,Extracellular,-1,1000
Demand,Exchange,eicostet,Extracellular,-1,1000
Demand,Exchange,hdca,Extracellular,-1,1000
Demand,Exchange,hdcea,Extracellular,-1,1000
Demand,Exchange,lnlc,Extracellular,-1,1000
Demand,Exchange,lnlnca,Extracellular,-1,1000
Demand,Exchange,lnlncg,Extracellular,-1,1000
Demand,Exchange,ocdca,Extracellular,-1,1000
Demand,Exchange,ocdcea,Extracellular,-1,1000
Demand,Exchange,thmmp,Extracellular,0,1000
Demand,Exchange,thmtp,Extracellular,0,1000
Demand,Exchange,ncam,Extracellular,0,1000
Demand,Exchange,pnto_R,Extracellular,0,1000
Demand,Exchange,pydxn,Extracellular,0,1000
Demand,Exchange,pydx,Extracellular,0,1000
Demand,Exchange,pydam,Extracellular,0,1000
Demand,Exchange,btn,Extracellular,0,1000
Demand,Exchange,fol,Extracellular,-10,1000
Demand,Exchange,aqcobal,Extracellular,0,1000
Demand,Exchange,vitd3,Extracellular,-1,1000
Demand,Exchange,ascb_L,Extracellular,0,1000
Demand,Exchange,retinol,Extracellular,-10,1000
Demand,Exchange,retinal,Extracellular,-10,1000
Demand,Exchange,ala_B,Extracellular,-1,1000
Demand,Exchange,ala_D,Extracellular,-1,1000
Demand,Exchange,h2co3,Extracellular,-1000,1000
Demand,Exchange,h2o2,Extracellular,-1000,1000
Demand,Exchange,hco3,Extracellular,-1000,1000
Demand,Exchange,orn,Extracellular,-1,1000
Demand,Exchange,orn_D,Extracellular,-1,1000
Demand,Exchange,so4,Extracellular,-1000,1000
Demand,Exchange,ribflv,Extracellular,-1,1000
Demand,Exchange,Lcystin,Extracellular,-1,1000