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JoshLoeckerJoshLoecker
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Merge pull request #196 from HelikarLab/hotfix
Add boundary column
2 parents 38c7aa9 + c299b64 commit fcd6857

3 files changed

Lines changed: 141 additions & 140 deletions

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‎main/como/create_context_specific_model.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -550,6 +550,7 @@ def _collect_boundary_reactions(path: Path) -> _BoundaryReactions:
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df = _create_df(path)
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for column in df.columns:
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if column not in [
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"boundary",
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"reaction",
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"abbreviation",
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"compartment",

‎main/data/boundary_rxns/naiveB_boundary_rxns.csv‎

Lines changed: 70 additions & 70 deletions
Original file line numberDiff line numberDiff line change
@@ -1,70 +1,70 @@
1-
Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
2-
Exchange,glc_D,Extracellular,-100,1000
3-
Exchange,fe2,Extracellular,-1000,1000
4-
Exchange,gal,Extracellular,0,1000
5-
Exchange,zn2,Extracellular,-1000,1000
6-
Exchange,ca2,Extracellular,-1000,1000
7-
Exchange,na1,Extracellular,-1000,1000
8-
Exchange,cl,Extracellular,-1000,1000
9-
Exchange,k,Extracellular,-1000,1000
10-
Exchange,h,Extracellular,-1000,1000
11-
Exchange,h2o,Extracellular,-1000,1000
12-
Exchange,o2,Extracellular,-1000,1000
13-
Exchange,pi,Extracellular,-1000,1000
14-
Exchange,ppi,Extracellular,-1000,1000
15-
Exchange,co2,Extracellular,-1000,1000
16-
Exchange,nh4,Extracellular,-1000,1000
17-
Exchange,no2,Extracellular,-1000,1000
18-
Exchange,co,Extracellular,-1000,1000
19-
Exchange,asn_L,Extracellular,-1,1000
20-
Exchange,asp_L,Extracellular,-1,1000
21-
Exchange,glu_L,Extracellular,-1,1000
22-
Exchange,ile_L,Extracellular,-1,1000
23-
Exchange,leu_L,Extracellular,-1,1000
24-
Exchange,lys_L,Extracellular,-1,1000
25-
Exchange,met_L,Extracellular,-1,1000
26-
Exchange,pro_L,Extracellular,-1,1000
27-
Exchange,ser_L,Extracellular,-1,1000
28-
Exchange,val_L,Extracellular,-1,1000
29-
Exchange,gly,Extracellular,-1,1000
30-
Exchange,cys_L,Extracellular,-1,1000
31-
Exchange,ala_L,Extracellular,-1,1000
32-
Exchange,his_L,Extracellular,-1,1000
33-
Exchange,thr_L,Extracellular,-1,1000
34-
Exchange,gln_L,Extracellular,-1,1000
35-
Exchange,phe_L,Extracellular,-1,1000
36-
Exchange,tyr_L,Extracellular,-1,1000
37-
Exchange,arg_L,Extracellular,-1,1000
38-
Exchange,trp_L,Extracellular,-1,1000
39-
Exchange,eicostet,Extracellular,-1,1000
40-
Exchange,hdca,Extracellular,-1,1000
41-
Exchange,hdcea,Extracellular,-1,1000
42-
Exchange,lnlc,Extracellular,-1,1000
43-
Exchange,lnlnca,Extracellular,-1,1000
44-
Exchange,lnlncg,Extracellular,-1,1000
45-
Exchange,ocdca,Extracellular,-1,1000
46-
Exchange,ocdcea,Extracellular,-1,1000
47-
Exchange,thmmp,Extracellular,0,1000
48-
Exchange,thmtp,Extracellular,0,1000
49-
Exchange,ncam,Extracellular,0,1000
50-
Exchange,pnto_R,Extracellular,0,1000
51-
Exchange,pydxn,Extracellular,0,1000
52-
Exchange,pydx,Extracellular,0,1000
53-
Exchange,pydam,Extracellular,0,1000
54-
Exchange,btn,Extracellular,0,1000
55-
Exchange,fol,Extracellular,-10,1000
56-
Exchange,aqcobal,Extracellular,0,1000
57-
Exchange,vitd3,Extracellular,-1,1000
58-
Exchange,ascb_L,Extracellular,0,1000
59-
Exchange,retinol,Extracellular,-10,1000
60-
Exchange,retinal,Extracellular,-10,1000
61-
Exchange,ala_B,Extracellular,-1,1000
62-
Exchange,ala_D,Extracellular,-1,1000
63-
Exchange,h2co3,Extracellular,-1000,1000
64-
Exchange,h2o2,Extracellular,-1000,1000
65-
Exchange,hco3,Extracellular,-1000,1000
66-
Exchange,orn,Extracellular,-1,1000
67-
Exchange,orn_D,Extracellular,-1,1000
68-
Exchange,so4,Extracellular,-1000,1000
69-
Exchange,ribflv,Extracellular,-1,1000
70-
Exchange,Lcystin,Extracellular,-1,1000
1+
Boundary,Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
2+
Demand,Exchange,glc_D,Extracellular,-100,1000
3+
Demand,Exchange,fe2,Extracellular,-1000,1000
4+
Demand,Exchange,gal,Extracellular,0,1000
5+
Demand,Exchange,zn2,Extracellular,-1000,1000
6+
Demand,Exchange,ca2,Extracellular,-1000,1000
7+
Demand,Exchange,na1,Extracellular,-1000,1000
8+
Demand,Exchange,cl,Extracellular,-1000,1000
9+
Demand,Exchange,k,Extracellular,-1000,1000
10+
Demand,Exchange,h,Extracellular,-1000,1000
11+
Demand,Exchange,h2o,Extracellular,-1000,1000
12+
Demand,Exchange,o2,Extracellular,-1000,1000
13+
Demand,Exchange,pi,Extracellular,-1000,1000
14+
Demand,Exchange,ppi,Extracellular,-1000,1000
15+
Demand,Exchange,co2,Extracellular,-1000,1000
16+
Demand,Exchange,nh4,Extracellular,-1000,1000
17+
Demand,Exchange,no2,Extracellular,-1000,1000
18+
Demand,Exchange,co,Extracellular,-1000,1000
19+
Demand,Exchange,asn_L,Extracellular,-1,1000
20+
Demand,Exchange,asp_L,Extracellular,-1,1000
21+
Demand,Exchange,glu_L,Extracellular,-1,1000
22+
Demand,Exchange,ile_L,Extracellular,-1,1000
23+
Demand,Exchange,leu_L,Extracellular,-1,1000
24+
Demand,Exchange,lys_L,Extracellular,-1,1000
25+
Demand,Exchange,met_L,Extracellular,-1,1000
26+
Demand,Exchange,pro_L,Extracellular,-1,1000
27+
Demand,Exchange,ser_L,Extracellular,-1,1000
28+
Demand,Exchange,val_L,Extracellular,-1,1000
29+
Demand,Exchange,gly,Extracellular,-1,1000
30+
Demand,Exchange,cys_L,Extracellular,-1,1000
31+
Demand,Exchange,ala_L,Extracellular,-1,1000
32+
Demand,Exchange,his_L,Extracellular,-1,1000
33+
Demand,Exchange,thr_L,Extracellular,-1,1000
34+
Demand,Exchange,gln_L,Extracellular,-1,1000
35+
Demand,Exchange,phe_L,Extracellular,-1,1000
36+
Demand,Exchange,tyr_L,Extracellular,-1,1000
37+
Demand,Exchange,arg_L,Extracellular,-1,1000
38+
Demand,Exchange,trp_L,Extracellular,-1,1000
39+
Demand,Exchange,eicostet,Extracellular,-1,1000
40+
Demand,Exchange,hdca,Extracellular,-1,1000
41+
Demand,Exchange,hdcea,Extracellular,-1,1000
42+
Demand,Exchange,lnlc,Extracellular,-1,1000
43+
Demand,Exchange,lnlnca,Extracellular,-1,1000
44+
Demand,Exchange,lnlncg,Extracellular,-1,1000
45+
Demand,Exchange,ocdca,Extracellular,-1,1000
46+
Demand,Exchange,ocdcea,Extracellular,-1,1000
47+
Demand,Exchange,thmmp,Extracellular,0,1000
48+
Demand,Exchange,thmtp,Extracellular,0,1000
49+
Demand,Exchange,ncam,Extracellular,0,1000
50+
Demand,Exchange,pnto_R,Extracellular,0,1000
51+
Demand,Exchange,pydxn,Extracellular,0,1000
52+
Demand,Exchange,pydx,Extracellular,0,1000
53+
Demand,Exchange,pydam,Extracellular,0,1000
54+
Demand,Exchange,btn,Extracellular,0,1000
55+
Demand,Exchange,fol,Extracellular,-10,1000
56+
Demand,Exchange,aqcobal,Extracellular,0,1000
57+
Demand,Exchange,vitd3,Extracellular,-1,1000
58+
Demand,Exchange,ascb_L,Extracellular,0,1000
59+
Demand,Exchange,retinol,Extracellular,-10,1000
60+
Demand,Exchange,retinal,Extracellular,-10,1000
61+
Demand,Exchange,ala_B,Extracellular,-1,1000
62+
Demand,Exchange,ala_D,Extracellular,-1,1000
63+
Demand,Exchange,h2co3,Extracellular,-1000,1000
64+
Demand,Exchange,h2o2,Extracellular,-1000,1000
65+
Demand,Exchange,hco3,Extracellular,-1000,1000
66+
Demand,Exchange,orn,Extracellular,-1,1000
67+
Demand,Exchange,orn_D,Extracellular,-1,1000
68+
Demand,Exchange,so4,Extracellular,-1000,1000
69+
Demand,Exchange,ribflv,Extracellular,-1,1000
70+
Demand,Exchange,Lcystin,Extracellular,-1,1000

‎main/data/boundary_rxns/smB_boundary_rxns.csv‎

Lines changed: 70 additions & 70 deletions
Original file line numberDiff line numberDiff line change
@@ -1,70 +1,70 @@
1-
Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
2-
Exchange,glc_D,Extracellular,-100,1000
3-
Exchange,fe2,Extracellular,-1000,1000
4-
Exchange,gal,Extracellular,0,1000
5-
Exchange,zn2,Extracellular,-1000,1000
6-
Exchange,ca2,Extracellular,-1000,1000
7-
Exchange,na1,Extracellular,-1000,1000
8-
Exchange,cl,Extracellular,-1000,1000
9-
Exchange,k,Extracellular,-1000,1000
10-
Exchange,h,Extracellular,-1000,1000
11-
Exchange,h2o,Extracellular,-1000,1000
12-
Exchange,o2,Extracellular,-1000,1000
13-
Exchange,pi,Extracellular,-1000,1000
14-
Exchange,ppi,Extracellular,-1000,1000
15-
Exchange,co2,Extracellular,-1000,1000
16-
Exchange,nh4,Extracellular,-1000,1000
17-
Exchange,no2,Extracellular,-1000,1000
18-
Exchange,co,Extracellular,-1000,1000
19-
Exchange,asn_L,Extracellular,-1,1000
20-
Exchange,asp_L,Extracellular,-1,1000
21-
Exchange,glu_L,Extracellular,-1,1000
22-
Exchange,ile_L,Extracellular,-1,1000
23-
Exchange,leu_L,Extracellular,-1,1000
24-
Exchange,lys_L,Extracellular,-1,1000
25-
Exchange,met_L,Extracellular,-1,1000
26-
Exchange,pro_L,Extracellular,-1,1000
27-
Exchange,ser_L,Extracellular,-1,1000
28-
Exchange,val_L,Extracellular,-1,1000
29-
Exchange,gly,Extracellular,-1,1000
30-
Exchange,cys_L,Extracellular,-1,1000
31-
Exchange,ala_L,Extracellular,-1,1000
32-
Exchange,his_L,Extracellular,-1,1000
33-
Exchange,thr_L,Extracellular,-1,1000
34-
Exchange,gln_L,Extracellular,-1,1000
35-
Exchange,phe_L,Extracellular,-1,1000
36-
Exchange,tyr_L,Extracellular,-1,1000
37-
Exchange,arg_L,Extracellular,-1,1000
38-
Exchange,trp_L,Extracellular,-1,1000
39-
Exchange,eicostet,Extracellular,-1,1000
40-
Exchange,hdca,Extracellular,-1,1000
41-
Exchange,hdcea,Extracellular,-1,1000
42-
Exchange,lnlc,Extracellular,-1,1000
43-
Exchange,lnlnca,Extracellular,-1,1000
44-
Exchange,lnlncg,Extracellular,-1,1000
45-
Exchange,ocdca,Extracellular,-1,1000
46-
Exchange,ocdcea,Extracellular,-1,1000
47-
Exchange,thmmp,Extracellular,0,1000
48-
Exchange,thmtp,Extracellular,0,1000
49-
Exchange,ncam,Extracellular,0,1000
50-
Exchange,pnto_R,Extracellular,0,1000
51-
Exchange,pydxn,Extracellular,0,1000
52-
Exchange,pydx,Extracellular,0,1000
53-
Exchange,pydam,Extracellular,0,1000
54-
Exchange,btn,Extracellular,0,1000
55-
Exchange,fol,Extracellular,-10,1000
56-
Exchange,aqcobal,Extracellular,0,1000
57-
Exchange,vitd3,Extracellular,-1,1000
58-
Exchange,ascb_L,Extracellular,0,1000
59-
Exchange,retinol,Extracellular,-10,1000
60-
Exchange,retinal,Extracellular,-10,1000
61-
Exchange,ala_B,Extracellular,-1,1000
62-
Exchange,ala_D,Extracellular,-1,1000
63-
Exchange,h2co3,Extracellular,-1000,1000
64-
Exchange,h2o2,Extracellular,-1000,1000
65-
Exchange,hco3,Extracellular,-1000,1000
66-
Exchange,orn,Extracellular,-1,1000
67-
Exchange,orn_D,Extracellular,-1,1000
68-
Exchange,so4,Extracellular,-1000,1000
69-
Exchange,ribflv,Extracellular,-1,1000
70-
Exchange,Lcystin,Extracellular,-1,1000
1+
Boundary,Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
2+
Demand,Exchange,glc_D,Extracellular,-100,1000
3+
Demand,Exchange,fe2,Extracellular,-1000,1000
4+
Demand,Exchange,gal,Extracellular,0,1000
5+
Demand,Exchange,zn2,Extracellular,-1000,1000
6+
Demand,Exchange,ca2,Extracellular,-1000,1000
7+
Demand,Exchange,na1,Extracellular,-1000,1000
8+
Demand,Exchange,cl,Extracellular,-1000,1000
9+
Demand,Exchange,k,Extracellular,-1000,1000
10+
Demand,Exchange,h,Extracellular,-1000,1000
11+
Demand,Exchange,h2o,Extracellular,-1000,1000
12+
Demand,Exchange,o2,Extracellular,-1000,1000
13+
Demand,Exchange,pi,Extracellular,-1000,1000
14+
Demand,Exchange,ppi,Extracellular,-1000,1000
15+
Demand,Exchange,co2,Extracellular,-1000,1000
16+
Demand,Exchange,nh4,Extracellular,-1000,1000
17+
Demand,Exchange,no2,Extracellular,-1000,1000
18+
Demand,Exchange,co,Extracellular,-1000,1000
19+
Demand,Exchange,asn_L,Extracellular,-1,1000
20+
Demand,Exchange,asp_L,Extracellular,-1,1000
21+
Demand,Exchange,glu_L,Extracellular,-1,1000
22+
Demand,Exchange,ile_L,Extracellular,-1,1000
23+
Demand,Exchange,leu_L,Extracellular,-1,1000
24+
Demand,Exchange,lys_L,Extracellular,-1,1000
25+
Demand,Exchange,met_L,Extracellular,-1,1000
26+
Demand,Exchange,pro_L,Extracellular,-1,1000
27+
Demand,Exchange,ser_L,Extracellular,-1,1000
28+
Demand,Exchange,val_L,Extracellular,-1,1000
29+
Demand,Exchange,gly,Extracellular,-1,1000
30+
Demand,Exchange,cys_L,Extracellular,-1,1000
31+
Demand,Exchange,ala_L,Extracellular,-1,1000
32+
Demand,Exchange,his_L,Extracellular,-1,1000
33+
Demand,Exchange,thr_L,Extracellular,-1,1000
34+
Demand,Exchange,gln_L,Extracellular,-1,1000
35+
Demand,Exchange,phe_L,Extracellular,-1,1000
36+
Demand,Exchange,tyr_L,Extracellular,-1,1000
37+
Demand,Exchange,arg_L,Extracellular,-1,1000
38+
Demand,Exchange,trp_L,Extracellular,-1,1000
39+
Demand,Exchange,eicostet,Extracellular,-1,1000
40+
Demand,Exchange,hdca,Extracellular,-1,1000
41+
Demand,Exchange,hdcea,Extracellular,-1,1000
42+
Demand,Exchange,lnlc,Extracellular,-1,1000
43+
Demand,Exchange,lnlnca,Extracellular,-1,1000
44+
Demand,Exchange,lnlncg,Extracellular,-1,1000
45+
Demand,Exchange,ocdca,Extracellular,-1,1000
46+
Demand,Exchange,ocdcea,Extracellular,-1,1000
47+
Demand,Exchange,thmmp,Extracellular,0,1000
48+
Demand,Exchange,thmtp,Extracellular,0,1000
49+
Demand,Exchange,ncam,Extracellular,0,1000
50+
Demand,Exchange,pnto_R,Extracellular,0,1000
51+
Demand,Exchange,pydxn,Extracellular,0,1000
52+
Demand,Exchange,pydx,Extracellular,0,1000
53+
Demand,Exchange,pydam,Extracellular,0,1000
54+
Demand,Exchange,btn,Extracellular,0,1000
55+
Demand,Exchange,fol,Extracellular,-10,1000
56+
Demand,Exchange,aqcobal,Extracellular,0,1000
57+
Demand,Exchange,vitd3,Extracellular,-1,1000
58+
Demand,Exchange,ascb_L,Extracellular,0,1000
59+
Demand,Exchange,retinol,Extracellular,-10,1000
60+
Demand,Exchange,retinal,Extracellular,-10,1000
61+
Demand,Exchange,ala_B,Extracellular,-1,1000
62+
Demand,Exchange,ala_D,Extracellular,-1,1000
63+
Demand,Exchange,h2co3,Extracellular,-1000,1000
64+
Demand,Exchange,h2o2,Extracellular,-1000,1000
65+
Demand,Exchange,hco3,Extracellular,-1000,1000
66+
Demand,Exchange,orn,Extracellular,-1,1000
67+
Demand,Exchange,orn_D,Extracellular,-1,1000
68+
Demand,Exchange,so4,Extracellular,-1000,1000
69+
Demand,Exchange,ribflv,Extracellular,-1,1000
70+
Demand,Exchange,Lcystin,Extracellular,-1,1000

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