chore: round of model I/O

SysBioChalmers · Nov 23, 2024 · e4a3d59 · e4a3d59
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diff --git a/README.md b/README.md
@@ -39,7 +39,7 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |
 |:-------|:--------------|:------|:------|:----------|:-----|
-| _Saccharomyces cerevisiae_ | 14-Nov-2024 | develop | 4131 | 2806 | 1161 |
+| _Saccharomyces cerevisiae_ | 23-Nov-2024 | develop | 4131 | 2806 | 1161 |
 
 # Installation & usage
 

diff --git a/model/dependencies.txt b/model/dependencies.txt
@@ -1,4 +1,4 @@
 MATLAB	24.1.0.2568132 (R2024a) Update 1
 libSBML	5.20.2
-RAVEN_toolbox	commit c90390e
+RAVEN_toolbox	2.10.2
 COBRA_toolbox	3.4
diff --git a/model/yeast-GEM.txt b/model/yeast-GEM.txt
@@ -653,7 +653,7 @@ r_0810	GDP[g] + H2O[g] => GMP[g] + H+[g] + phosphate[g] 	YEL042W	  0.00	1000.00
 r_0811	ATP[c] + UDP[c] => ADP[c] + UTP[c] 	YKL067W	  0.00	1000.00	  0.00
 r_0812	methanethiol[c] + O-acetyl-L-homoserine[c] => acetate[c] + H+[c] + L-methionine[c] 	YLR303W	  0.00	1000.00	  0.00
 r_0813	hydrogen sulfide[c] + O-acetyl-L-homoserine[c] => acetate[c] + L-homocysteine[c] 	YLR303W	  0.00	1000.00	  0.00
-r_0815	L-cysteine[c] + O-succinyl-L-homoserine[c] <=> H+[c] + L-cystathionine[c] + succinate[c] 	YLL058W or YML082W or YAL012W	  0.00	1000.00	  0.00
+r_0815	L-cysteine[c] + O-succinyl-L-homoserine[c] => H+[c] + L-cystathionine[c] + succinate[c] 	YLL058W or YML082W or YAL012W	  0.00	1000.00	  0.00
 r_0816	carbamoyl phosphate[c] + ornithine[c] => H+[c] + L-citrulline[c] + phosphate[c] 	YJL088W	  0.00	1000.00	  0.00
 r_0817	H+[c] + ornithine[c] => carbon dioxide[c] + putrescine[c] 	YKL184W	  0.00	1000.00	  0.00
 r_0818	L-glutamate[m] + N(2)-acetyl-L-ornithine[m] => N-acetyl-L-glutamate[m] + ornithine[m] 	YMR062C	  0.00	1000.00	  0.00
@@ -4050,7 +4050,7 @@ r_4699	ethyl propionate[e] =>  		  0.00	1000.00	  0.00
 r_4700	hydrogen sulfide[c] => hydrogen sulfide[e] 	YIL166C	  0.00	1000.00	  0.00
 r_4701	H2O[m] + L-cysteine[m] <=> ammonium[m] + pyruvate[m] + hydrogen sulfide[m] 	YFR055W	-1000.00	1000.00	  0.00
 r_4702	2-oxoglutarate[c] + L-cysteine[c] <=> L-glutamate[c] + 3-mercaptopyruvate[c] 		-1000.00	1000.00	  0.00
-r_4703	TRX1[c] + 3-mercaptopyruvate[c] <=> hydrogen sulfide[c] + pyruvate[c] + TRX1 disulphide[c] 	YOR251C	  0.00	1000.00	  0.00
+r_4703	TRX1[c] + 3-mercaptopyruvate[c] => hydrogen sulfide[c] + pyruvate[c] + TRX1 disulphide[c] 	YOR251C	  0.00	1000.00	  0.00
 r_4704	alkanesulfonate[e] => alkanesulfonate[c] 	YIL166C	  0.00	1000.00	  0.00
 r_4705	taurocholate[e] => taurocholate[c] 	YIL166C	  0.00	1000.00	  0.00
 r_4706	2-oxoglutarate[c] + oxygen[c] + alkanesulfonate[c] <=> aminoacetaldehyde[c] + carbon dioxide[c] + succinate[c] + sulphite[c] 	YLL057C	-1000.00	1000.00	  0.00

diff --git a/model/yeast-GEM.xml b/model/yeast-GEM.xml
@@ -24,10 +24,10 @@
             </rdf:Bag>
           </dcterms:creator>
           <dcterms:created rdf:parseType="Resource">
-            <dcterms:W3CDTF>2024-11-14T21:12:33Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2024-11-23T16:03:25Z</dcterms:W3CDTF>
           </dcterms:created>
           <dcterms:modified rdf:parseType="Resource">
-            <dcterms:W3CDTF>2024-11-14T21:12:33Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2024-11-23T16:03:25Z</dcterms:W3CDTF>
           </dcterms:modified>
           <bqbiol:is>
             <rdf:Bag>
@@ -65955,7 +65955,7 @@
           <fbc:geneProductRef fbc:geneProduct="YLR303W"/>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="r_0815" sboTerm="SBO:0000176" id="r_0815" name="O-succinylhomoserine lyase (L-cysteine)" reversible="true" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
+      <reaction metaid="r_0815" sboTerm="SBO:0000176" id="r_0815" name="O-succinylhomoserine lyase (L-cysteine)" reversible="false" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
             <p>Confidence Level: 3</p>
@@ -166516,7 +166516,7 @@
           <speciesReference species="s_4264" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="r_4703" sboTerm="SBO:0000176" id="r_4703" name="3-mercaptopyruvate sulfurtransferase" reversible="true" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
+      <reaction metaid="r_4703" sboTerm="SBO:0000176" id="r_4703" name="3-mercaptopyruvate sulfurtransferase" reversible="false" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
             <p>AUTHORS: 10.1093/femsyr/foy046</p>

diff --git a/model/yeast-GEM.yml b/model/yeast-GEM.yml
@@ -4,7 +4,7 @@
     id: "yeastGEM_develop"
     name: "The Consensus Genome-Scale Metabolic Model of Yeast"
     version: ""
-    date: "2024-11-14"
+    date: "2024-11-23"
     defaultLB: "-1000"
     defaultUB: "1000"
     givenName: "Eduard"