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chore: update file format for Ecoli 0.2.0 #33

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Merged
KennetLindquist merged 9 commits into from
Sep 8, 2025
Merged

chore: update file format for Ecoli 0.2.0 #33

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85dee07
chore: update file format for Ecoli 0.2.0
KennetLindquist Sep 1, 2025
9ad4336
ci(memote): add Memote HTML report [skip ci]
KennetLindquist Sep 1, 2025
992906f
chore: update frog report
mihai-sysbio Sep 6, 2025
1148c2d
ci(memote): add Memote HTML report [skip ci]
mihai-sysbio Sep 6, 2025
11b7b62
docs: expand notes on the frog files
mihai-sysbio Sep 8, 2025
21eb140
ci(memote): add Memote HTML report [skip ci]
mihai-sysbio Sep 8, 2025
c798737
chore: version in yml
KennetLindquist Sep 8, 2025
2d0af61
chore: version text file
KennetLindquist Sep 8, 2025
21a9138
ci(memote): add Memote HTML report [skip ci]
KennetLindquist Sep 8, 2025
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2 changes: 1 addition & 1 deletion memote_report.html
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115 changes: 21 additions & 94 deletions model/Ecoli-GEM.json
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Original file line number Diff line number Diff line change
Expand Up @@ -50553,7 +50553,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b4213 or b0383 or b0383",
"gene_reaction_rule":"b0383 or b4213 or b2744",
"subsystem":"Nucleotide Salvage Pathway",
"annotation":{
"bigg.reaction":"3NTD4pp",
Expand Down Expand Up @@ -59044,7 +59044,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"(b2308 and b2306 and b2310 and b2307) or (b0864 and b0860 and b0863 and b0862 and b0861)",
"gene_reaction_rule":"(b2310 and b2308 and b2306 and b2307) or (b0862 and b0860 and b0864 and b0861) or (b0862 and b0864 and b0863 and b0861)",
"subsystem":"Transport, Inner Membrane",
"annotation":{
"bigg.reaction":"ARGabcpp",
Expand Down Expand Up @@ -60717,7 +60717,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b3857 or (b3857 and b3856)",
"gene_reaction_rule":"b3857",
"subsystem":"Cofactor and Prosthetic Group Biosynthesis",
"annotation":{
"bigg.reaction":"BMOGDS1",
Expand All @@ -60737,7 +60737,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"(b3857 and b3856) or b3857",
"gene_reaction_rule":"b3857",
"subsystem":"Cofactor and Prosthetic Group Biosynthesis",
"annotation":{
"bigg.reaction":"BMOGDS2",
Expand Down Expand Up @@ -61033,7 +61033,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"(b3857 and b3856) or b3857",
"gene_reaction_rule":"b3857",
"subsystem":"Cofactor and Prosthetic Group Biosynthesis",
"annotation":{
"bigg.reaction":"BWCOGDS1",
Expand All @@ -61053,7 +61053,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"(b3857 and b3856) or b3857",
"gene_reaction_rule":"b3857",
"subsystem":"Cofactor and Prosthetic Group Biosynthesis",
"annotation":{
"bigg.reaction":"BWCOGDS2",
Expand Down Expand Up @@ -70285,7 +70285,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b3785 and b3793",
"gene_reaction_rule":"b3785 and b3793 and b3792",
"subsystem":"Lipopolysaccharide Biosynthesis / Recycling",
"annotation":{
"bigg.reaction":"ECAP1pp",
Expand All @@ -70305,7 +70305,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b3785 and b3793",
"gene_reaction_rule":"b3785 and b3793 and b3792",
"subsystem":"Lipopolysaccharide Biosynthesis / Recycling",
"annotation":{
"bigg.reaction":"ECAP2pp",
Expand All @@ -70325,7 +70325,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b3785 and b3793",
"gene_reaction_rule":"b3785 and b3793 and b3792",
"subsystem":"Lipopolysaccharide Biosynthesis / Recycling",
"annotation":{
"bigg.reaction":"ECAP3pp",
Expand Down Expand Up @@ -80146,7 +80146,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b2764 and b2763",
"gene_reaction_rule":"b2764",
"subsystem":"Cofactor and Prosthetic Group Biosynthesis",
"annotation":{
"bigg.reaction":"FADRx2",
Expand Down Expand Up @@ -82109,7 +82109,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b3844 or b0937 or (b2764 and b2763)",
"gene_reaction_rule":"b0937 or b3844 or b2764",
"subsystem":"Cofactor and Prosthetic Group Biosynthesis",
"annotation":{
"bigg.reaction":"FMNRx2",
Expand Down Expand Up @@ -85180,7 +85180,7 @@
"ser__L_c":-1.0,
"thf_c":-1.0
},
"lower_bound":-1000.0,
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b2551",
"subsystem":"Glycine and Serine Metabolism",
Expand Down Expand Up @@ -86122,7 +86122,7 @@
},
"lower_bound":-1000.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b1761 or (b3213 and b3212)",
"gene_reaction_rule":"b1761",
"subsystem":"Glutamate Metabolism",
"annotation":{
"bigg.reaction":"GLUDy",
Expand Down Expand Up @@ -87002,51 +87002,6 @@
}
},
{
"id":"GLYCK",
"name":"Glycerate kinase",
"metabolites":{
"3pg_c":1.0,
"adp_c":1.0,
"atp_c":-1.0,
"glyc__R_c":-1.0,
"h_c":1.0
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b0514",
"subsystem":"Glyoxylate Metabolism",
"annotation":{
"bigg.reaction":"GLYCK",
"biocyc":"META:GLY3KIN-RXN",
"ec-code":"2.7.1.31",
"kegg.reaction":"R01514",
"metanetx.reaction":"MNXR100328",
"reactome.reaction":[
"R-MMU-6799495",
"R-TGU-6799495",
"R-DME-6799495",
"R-GGA-6799495",
"R-RNO-6799495",
"R-XTR-6799495",
"R-DRE-6799495",
"R-HSA-6799495",
"R-SSC-6799495",
"R-BTA-6799495",
"R-CEL-6799495",
"R-CFA-6799495"
],
"rhea":[
"23518",
"23519",
"23516",
"23517"
],
"sabiork":"428",
"sbo":"SBO:0000176",
"seed.reaction":"rxn01102"
}
},
{
"id":"GLYCK2",
"name":"Glycerate kinase",
"metabolites":{
Expand All @@ -87058,7 +87013,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b3124",
"gene_reaction_rule":"b3124 or b0514",
"subsystem":"Glycine and Serine Metabolism",
"annotation":{
"bigg.reaction":"GLYCK2",
Expand Down Expand Up @@ -91715,7 +91670,7 @@
"nadp_c":-1.0,
"nadph_c":1.0
},
"lower_bound":-1000.0,
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b3940 or b0002",
"subsystem":"Threonine and Lysine Metabolism",
Expand Down Expand Up @@ -100167,7 +100122,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"(b3857 and b3856) or b3857",
"gene_reaction_rule":"b3857",
"subsystem":"Cofactor and Prosthetic Group Biosynthesis",
"annotation":{
"bigg.reaction":"MOGDS",
Expand Down Expand Up @@ -116342,7 +116297,7 @@
"succ_c":1.0,
"succ_p":-1.0
},
"lower_bound":-1000.0,
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b1206",
"subsystem":"Transport, Inner Membrane",
Expand Down Expand Up @@ -117348,8 +117303,8 @@
"id":"THD2pp",
"name":"NAD(P) transhydrogenase (periplasm)",
"metabolites":{
"h_c":2.0,
"h_p":-2.0,
"h_c":1.0,
"h_p":-1.0,
"nad_c":1.0,
"nadh_c":-1.0,
"nadp_c":-1.0,
Expand Down Expand Up @@ -117943,7 +117898,7 @@
},
"lower_bound":0.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b0423 and b3990 and b2530 and b3992 and b4407",
"gene_reaction_rule":"b3992 and b3990 and b0423 and b2530 and b4407 and b3991",
"subsystem":"Cofactor and Prosthetic Group Biosynthesis",
"annotation":{
"bigg.reaction":"THZPSN3",
Expand Down Expand Up @@ -121868,7 +121823,7 @@
"biocyc":"META:XYLISOM-RXN",
"ec-code":"5.3.1.5",
"kegg.reaction":"R01432",
"metanetx.reaction":"MNXR105253",
"metanetx.reaction":"MNXR146751",
"rhea":[
"22818",
"22816",
Expand All @@ -121880,34 +121835,6 @@
}
},
{
"id":"XYLI2",
"name":"Xylose isomerase",
"metabolites":{
"fru_c":1.0,
"glc__D_c":-1.0
},
"lower_bound":-1000.0,
"upper_bound":1000.0,
"gene_reaction_rule":"b3565",
"subsystem":"Alternate Carbon Metabolism",
"annotation":{
"bigg.reaction":"XYLI2",
"biocyc":"META:GLUCISOM-RXN",
"ec-code":"5.3.1.5",
"kegg.reaction":"R00307",
"metanetx.reaction":"MNXR105254",
"rhea":[
"28546",
"28547",
"28549",
"28548"
],
"sabiork":"800",
"sbo":"SBO:0000176",
"seed.reaction":"rxn00223"
}
},
{
"id":"XYLK",
"name":"Xylulokinase",
"metabolites":{
Expand Down
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