chore: version 9.0.1

SysBioChalmers · Aug 14, 2024 · 2c9db41 · 2c9db41
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diff --git a/README.md b/README.md
@@ -39,15 +39,15 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |
 |:-------|:--------------|:------|:------|:----------|:-----|
-| _Saccharomyces cerevisiae_ | 04-Dec-2023 | 9.0.0 | 4130 | 2805 | 1162 |
+| _Saccharomyces cerevisiae_ | 14-Aug-2024 | 9.0.1 | 4130 | 2805 | 1162 |
 
 ### Gene essentiality prediction
 
-- Accuracy: 0.882
-- True non-essential genes: 928
-- True essential genes: 63
-- False non-essential genes: 95
-- False essential genes: 38
+- Accuracy: 0.899
+- True non-essential genes: 953
+- True essential genes: 58
+- False non-essential genes: 100
+- False essential genes: 13
 
 ### Growth prediction
 

diff --git a/history.md b/history.md
@@ -1,5 +1,13 @@
 # History
 
+### yeast 9.0.1:
+- Features:
+  - Provide reference metabolite concentration from YMDB, which can be loaded with `code/missingFields/addYMDBconcentrations.m`. (PR #364)
+- Documentation:
+  - Update citation and `README.md`. (PR #368)
+- Chore:
+  - Use latest RAVEN (2.9.3) for import/export (resolved bug https://github.com/SysBioChalmers/RAVEN/issues/529 results in higher accuracy in gene essentiality prediction).
+
 ### yeast 9.0.0:
 - Fixes:
   - Correct unbalanced reactions `r_4196` (closes #358), `r_4240`, `r_4722`. (PR #360)

diff --git a/model/dependencies.txt b/model/dependencies.txt
@@ -1,4 +1,4 @@
-MATLAB	9.12.0.2039608 (R2022a) Update 5
-libSBML	5.19.0
-RAVEN_toolbox	2.8.6
-COBRA_toolbox	commit 28acb94
+MATLAB	24.1.0.2568132 (R2024a) Update 1
+libSBML	5.20.2
+RAVEN_toolbox	2.9.3
+COBRA_toolbox	3.4
diff --git a/model/yeast-GEM.mat b/model/yeast-GEM.mat
diff --git a/model/yeast-GEM.xlsx b/model/yeast-GEM.xlsx
diff --git a/model/yeast-GEM.xml b/model/yeast-GEM.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" level="3" version="1" fbc:required="false" groups:required="false">
-  <model metaid="yeastGEM_v9.0.0" id="yeastGEM_v9__46__0__46__0" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
+  <model metaid="yeastGEM_v9.0.1" id="yeastGEM_v9__46__0__46__1" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <p>Saccharomyces cerevisiae - strain S288C</p>
       </body>
     </notes>
     <annotation>
       <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-        <rdf:Description rdf:about="#yeastGEM_v9.0.0">
+        <rdf:Description rdf:about="#yeastGEM_v9.0.1">
           <dcterms:creator>
             <rdf:Bag>
               <rdf:li rdf:parseType="Resource">
@@ -24,10 +24,10 @@
             </rdf:Bag>
           </dcterms:creator>
           <dcterms:created rdf:parseType="Resource">
-            <dcterms:W3CDTF>2023-12-04T09:40:27Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2024-08-14T16:00:24Z</dcterms:W3CDTF>
           </dcterms:created>
           <dcterms:modified rdf:parseType="Resource">
-            <dcterms:W3CDTF>2023-12-04T09:40:27Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2024-08-14T16:00:24Z</dcterms:W3CDTF>
           </dcterms:modified>
           <bqbiol:is>
             <rdf:Bag>

diff --git a/model/yeast-GEM.yml b/model/yeast-GEM.yml
@@ -1,10 +1,10 @@
 ---
 !!omap
 - metaData:
-    id: "yeastGEM_v9.0.0"
+    id: "yeastGEM_v9.0.1"
     name: "The Consensus Genome-Scale Metabolic Model of Yeast"
-    version: "9.0.0"
-    date: "2023-12-04"
+    version: "9.0.1"
+    date: "2024-08-14"
     defaultLB: "-1000"
     defaultUB: "1000"
     givenName: "Eduard"

diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-9.0.0
+9.0.1