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chore: update file format for ecoli 0.2.1 #40

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f4fb931
feat: reverse directionality of HSDy
KennetLindquist Oct 30, 2025
08fff45
chore: add macaw test result
KennetLindquist Oct 30, 2025
ba4efb1
feat: reverse directionality of HSDy
KennetLindquist Jan 21, 2026
034d763
fix: make succt1pp irreversible in the forward direction
KennetLindquist Feb 4, 2026
4fc2c45
chore: add macaw test result
KennetLindquist Feb 4, 2026
5df5a9b
fix: make succt1pp irreversible forward direction
KennetLindquist Feb 11, 2026
769d196
fix: Resolve merge conflict from model date
KennetLindquist Feb 19, 2026
366a54e
ci(memote): add Memote HTML report [skip ci]
KennetLindquist Feb 19, 2026
257a1d5
fix: Remove extra model file formats
KennetLindquist Feb 19, 2026
5d9faac
chore: update file format for Ecoli 0.2.1
KennetLindquist Feb 19, 2026
3895faf
ci(memote): add Memote HTML report [skip ci]
KennetLindquist Feb 19, 2026
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20 changes: 10 additions & 10 deletions data/testResults/macaw_results.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -623,7 +623,7 @@ CYSItpp,cysi__L_c --> cysi__L_p,cysi__L_c;cysi__L_p,ok,ok,ok,N/A
CYSS,acser_c + h2s_c --> ac_c + cys__L_c + h_c,ok,ok,ok,ok,N/A
CYSSADS,3sala_c + 2.0 h_c --> ala__L_c + so2_c,3sala_c;so2_c,ok,ok,ok,N/A
CYSTA,akg_c + cys__L_c --> glu__L_c + mercppyr_c,mercppyr_c,ok,ok,ok,N/A
CYSTL,cyst__L_c + h2o_c --> hcys__L_c + nh4_c + pyr_c,cyst__L_c,ok,ok,ok,N/A
CYSTL,cyst__L_c + h2o_c --> hcys__L_c + nh4_c + pyr_c,ok,ok,ok,ok,N/A
CYSabc2pp,atp_c + cys__L_c + h2o_c --> adp_c + cys__L_p + h_c + pi_c,ok,ok,ok,CYSabcpp,N/A
CYSabcpp,atp_c + cys__L_p + h2o_c --> adp_c + cys__L_c + h_c + pi_c,ok,ok,ok,CYSabc2pp,N/A
CYStex,cys__L_e <=> cys__L_p,only when going forwards,ok,ok,ok,N/A
Expand Down Expand Up @@ -1037,7 +1037,7 @@ EX_hdca_e,hdca_e --> ,hdca_e,ok,ok,ok,N/A
EX_hdcea_e,hdcea_e --> ,hdcea_e,ok,ok,ok,N/A
EX_hg2_e,hg2_e --> ,hg2_e,ok,ok,ok,N/A
EX_his__L_e,his__L_e --> ,ok,ok,ok,ok,N/A
EX_hom__L_e,hom__L_e --> ,hom__L_e,ok,ok,ok,N/A
EX_hom__L_e,hom__L_e --> ,ok,ok,ok,ok,N/A
EX_hxa_e,hxa_e --> ,ok,ok,ok,ok,N/A
EX_hxan_e,hxan_e --> ,ok,ok,ok,ok,N/A
EX_idon__L_e,idon__L_e --> ,ok,ok,ok,ok,N/A
Expand Down Expand Up @@ -1589,8 +1589,8 @@ HKNDDH,h2o_c + hkndd_c --> h_c + op4en_c + succ_c,hkndd_c;op4en_c,ok,ok,ok,N/A
HKNTDH,h2o_c + hkntd_c --> fum_c + h_c + op4en_c,hkntd_c;op4en_c,ok,ok,ok,N/A
HMBS,h2o_c + 4.0 ppbng_c --> hmbil_c + 4.0 nh4_c,ok,ok,ok,ok,N/A
HMPK1,4ahmmp_c + atp_c --> 4ampm_c + adp_c + h_c,4ahmmp_c,ok,ok,ok,N/A
HOMt2pp,h_p + hom__L_c --> h_c + hom__L_p,hom__L_c;hom__L_p,ok,ok,ok,N/A
HOMtex,hom__L_e <=> hom__L_p,hom__L_e;hom__L_p,ok,ok,ok,N/A
HOMt2pp,h_p + hom__L_c --> h_c + hom__L_p,ok,ok,ok,ok,N/A
HOMtex,hom__L_e <=> hom__L_p,only when going forwards,ok,ok,ok,N/A
HOPNTAL,4h2opntn_c --> acald_c + pyr_c,4h2opntn_c,ok,ok,ok,N/A
HPACOAT,34dphacoa_c + h2o_c --> 34dhpha_c + coa_c + h_c,34dhpha_c;34dphacoa_c,ok,ok,ok,N/A
HPPK2,6hmhpt_c + atp_c --> 6hmhptpp_c + amp_c + h_c,ok,ok,ok,ok,N/A
Expand All @@ -1601,9 +1601,9 @@ HPYRI,hpyr_c <=> 2h3oppan_c,ok,ok,ok,ok,N/A
HPYRP,3php_c + h2o_c --> hpyr_c + pi_c,ok,ok,ok,ok,N/A
HPYRRx,h_c + hpyr_c + nadh_c --> glyc__R_c + nad_c,ok,ok,ok,ok,N/A
HPYRRy,h_c + hpyr_c + nadph_c --> glyc__R_c + nadp_c,ok,ok,ok,ok,N/A
HSDy,hom__L_c + nadp_c --> aspsa_c + h_c + nadph_c,hom__L_c,ok,ok,ok,N/A
HSK,atp_c + hom__L_c --> adp_c + h_c + phom_c,hom__L_c;phom_c,ok,ok,ok,N/A
HSST,hom__L_c + succoa_c --> coa_c + suchms_c,hom__L_c;suchms_c,ok,ok,ok,N/A
HSDy,aspsa_c + h_c + nadph_c --> hom__L_c + nadp_c,ok,ok,ok,ok,N/A
HSK,atp_c + hom__L_c --> adp_c + h_c + phom_c,ok,ok,ok,ok,N/A
HSST,hom__L_c + succoa_c --> coa_c + suchms_c,ok,ok,ok,ok,N/A
HSTPT,glu__L_c + imacp_c --> akg_c + hisp_c,ok,ok,ok,ok,N/A
HXAND,h2o_c + hxan_c + nad_c --> h_c + nadh_c + xan_c,ok,ok,ok,ok,N/A
HXAtex,hxa_e <=> hxa_p,only when going forwards,ok,ok,ok,N/A
Expand Down Expand Up @@ -2472,7 +2472,7 @@ SHCHF,fe2_c + scl_c --> 3.0 h_c + sheme_c,ok,ok,ok,ok,N/A
SHGO,S2hglut_c + o2_c --> akg_c + h2o2_c,ok,ok,ok,ok,N/A
SHK3Dr,3dhsk_c + h_c + nadph_c <=> nadp_c + skm_c,only when going backwards,ok,ok,ok,N/A
SHKK,atp_c + skm_c --> adp_c + h_c + skm5p_c,ok,ok,ok,ok,N/A
SHSL1,cys__L_c + suchms_c --> cyst__L_c + h_c + succ_c,cyst__L_c;suchms_c,ok,ok,ok,N/A
SHSL1,cys__L_c + suchms_c --> cyst__L_c + h_c + succ_c,ok,ok,ok,ok,N/A
SKMt2pp,h_p + skm_p --> h_c + skm_c,skm_p,ok,ok,ok,N/A
SKMtex,skm_e <=> skm_p,skm_e;skm_p,ok,ok,ok,N/A
SLNTabcpp,atp_c + h2o_c + slnt_p --> adp_c + h_c + pi_c + slnt_c,slnt_c;slnt_p,ok,ok,ok,N/A
Expand Down Expand Up @@ -2500,7 +2500,7 @@ SSALy,h2o_c + nadp_c + sucsal_c --> 2.0 h_c + nadph_c + succ_c,ok,ok,ok,ok,N/A
SUCASPtpp,asp__L_p + succ_c <=> asp__L_c + succ_p,ok,ok,ok,ok,N/A
SUCBZL,atp_c + coa_c + sucbz_c --> amp_c + ppi_c + sbzcoa_c,ok,ok,ok,ok,N/A
SUCBZS,2shchc_c --> h2o_c + sucbz_c,ok,ok,ok,ok,N/A
SUCCt1pp,succ_p --> succ_c,ok,ok,ok,ok,N/A
SUCCt1pp,succ_c --> succ_p,ok,ok,ok,ok,N/A
SUCCt2_2pp,2.0 h_p + succ_p --> 2.0 h_c + succ_c,ok,ok,ok,SUCCt2_3pp,N/A
SUCCt2_3pp,3.0 h_p + succ_p --> 3.0 h_c + succ_c,ok,ok,ok,SUCCt2_2pp,N/A
SUCCtex,succ_e <=> succ_p,only when going forwards,ok,ok,ok,N/A
Expand Down Expand Up @@ -2552,7 +2552,7 @@ THRA2,athr__L_c --> acald_c + gly_c,ok,ok,ok,ok,N/A
THRD,nad_c + thr__L_c --> 2aobut_c + h_c + nadh_c,ok,ok,ok,ok,N/A
THRD_L,thr__L_c --> 2obut_c + nh4_c,ok,ok,ok,ok,N/A
THRPtex,thrp_e <=> thrp_p,thrp_e;thrp_p,ok,ok,ok,N/A
THRS,h2o_c + phom_c --> pi_c + thr__L_c,phom_c,ok,ok,ok,N/A
THRS,h2o_c + phom_c --> pi_c + thr__L_c,ok,ok,ok,ok,N/A
THRabcpp,atp_c + h2o_c + thr__L_p --> adp_c + h_c + pi_c + thr__L_c,ok,ok,ok,ok,N/A
THRt2pp,h_p + thr__L_c --> h_c + thr__L_p,ok,ok,ok,THRt2rpp,N/A
THRt2rpp,h_p + thr__L_p --> h_c + thr__L_c,ok,ok,ok,THRt2pp,N/A
Expand Down
6 changes: 3 additions & 3 deletions data/testResults/macaw_summary.md
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Starting dead-end test...
- Found 688 dead-end metabolites.
- Found 875 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 244 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
- Found 682 dead-end metabolites.
- Found 866 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 245 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
- Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
- Found 77 reactions that were some type of duplicate:
Expand Down
2 changes: 1 addition & 1 deletion memote_report.html
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16 changes: 8 additions & 8 deletions model/Ecoli-GEM.json
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Original file line number Diff line number Diff line change
Expand Up @@ -91664,11 +91664,11 @@
"id":"HSDy",
"name":"Homoserine dehydrogenase (NADPH)",
"metabolites":{
"aspsa_c":1.0,
"h_c":1.0,
"hom__L_c":-1.0,
"nadp_c":-1.0,
"nadph_c":1.0
"aspsa_c":-1.0,
"h_c":-1.0,
"hom__L_c":1.0,
"nadp_c":1.0,
"nadph_c":-1.0
},
"lower_bound":0.0,
"upper_bound":1000.0,
Expand Down Expand Up @@ -116294,8 +116294,8 @@
"id":"SUCCt1pp",
"name":"Succinate transport via diffusion in (periplasm)",
"metabolites":{
"succ_c":1.0,
"succ_p":-1.0
"succ_c":-1.0,
"succ_p":1.0
},
"lower_bound":0.0,
"upper_bound":1000.0,
Expand Down Expand Up @@ -151226,7 +151226,7 @@
}
}
],
"id":"Ecoli-GEM",
"id":null,
"compartments":{
"c":"cytosol",
"e":"extracellular space",
Expand Down
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4 changes: 2 additions & 2 deletions model/Ecoli-GEM.txt
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Expand Up @@ -1601,7 +1601,7 @@ R_HPYRI Hydroxypyruvate[c] <=> 2-Hydroxy-3-oxopropanoate[c] G_b0508 -1000.00 10
R_HPYRP 3-Phosphohydroxypyruvate[c] + H2O H2O[c] => Hydroxypyruvate[c] + Phosphate[c] G_b1813 0.00 1000.00 0.00
R_HPYRRx H+[c] + Hydroxypyruvate[c] + Nicotinamide adenine dinucleotide - reduced[c] => (R)-Glycerate[c] + Nicotinamide adenine dinucleotide[c] G_b1033 or G_b3553 0.00 1000.00 0.00
R_HPYRRy H+[c] + Hydroxypyruvate[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => (R)-Glycerate[c] + Nicotinamide adenine dinucleotide phosphate[c] G_b1033 or G_b3553 0.00 1000.00 0.00
R_HSDy L-Homoserine[c] + Nicotinamide adenine dinucleotide phosphate[c] => L-Aspartate 4-semialdehyde[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] G_b3940 or G_b0002 0.00 1000.00 0.00
R_HSDy L-Aspartate 4-semialdehyde[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => L-Homoserine[c] + Nicotinamide adenine dinucleotide phosphate[c] G_b3940 or G_b0002 0.00 1000.00 0.00
R_HSK ATP C10H12N5O13P3[c] + L-Homoserine[c] => ADP C10H12N5O10P2[c] + H+[c] + O-Phospho-L-homoserine[c] G_b0003 0.00 1000.00 0.00
R_HSST L-Homoserine[c] + Succinyl-CoA[c] => Coenzyme A[c] + O-Succinyl-L-homoserine[c] G_b4013 0.00 1000.00 0.00
R_HSTPT L-Glutamate[c] + 3-(Imidazol-4-yl)-2-oxopropyl phosphate[c] => 2-Oxoglutarate[c] + L-Histidinol phosphate[c] G_b2021 0.00 1000.00 0.00
Expand Down Expand Up @@ -2500,7 +2500,7 @@ R_SSALy H2O H2O[c] + Nicotinamide adenine dinucleotide phosphate[c] + Succinic s
R_SUCASPtpp L-Aspartate[p] + Succinate[c] <=> L-Aspartate[c] + Succinate[p] G_b4138 or G_b4123 or G_b0621 -1000.00 1000.00 0.00
R_SUCBZL ATP C10H12N5O13P3[c] + Coenzyme A[c] + O-Succinylbenzoate[c] => AMP C10H12N5O7P[c] + Diphosphate[c] + O-Succinylbenzoyl-CoA[c] G_b2260 0.00 1000.00 0.00
R_SUCBZS 2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate[c] => H2O H2O[c] + O-Succinylbenzoate[c] G_b2261 0.00 1000.00 0.00
R_SUCCt1pp Succinate[p] => Succinate[c] G_b1206 0.00 1000.00 0.00
R_SUCCt1pp Succinate[c] => Succinate[p] G_b1206 0.00 1000.00 0.00
R_SUCCt2_2pp 2 H+[p] + Succinate[p] => 2 H+[c] + Succinate[c] G_b3528 or G_b0010 0.00 1000.00 0.00
R_SUCCt2_3pp 3 H+[p] + Succinate[p] => 3 H+[c] + Succinate[c] G_b4123 or G_b4138 0.00 1000.00 0.00
R_SUCCtex Succinate[e] <=> Succinate[p] G_b0241 or G_b0929 or G_b1377 or G_b2215 -1000.00 1000.00 0.00
Expand Down
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