chore: version 9.0.0

SysBioChalmers · Dec 4, 2023 · 1bda758 · 1bda758
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Showing 9 changed files with 313 additions and 10 deletions.
diff --git a/.gitignore b/.gitignore
@@ -49,7 +49,6 @@ Thumbs.db
 *.mex*
 *.mlappinstall
 *.mltbx
-*.mat
 helpsearch*/
 
 # Python-related things #
@@ -60,7 +59,6 @@ helpsearch*/
 
 # Non-complying tables and files #
 ##################################
-*.xls*
 *.tab
 *.doc*
 *.ppt*

diff --git a/README.md b/README.md
@@ -33,7 +33,21 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |
 |:-------|:--------------|:------|:------|:----------|:-----|
-| _Saccharomyces cerevisiae_ | 02-Dec-2023 | develop | 4130 | 2805 | 1162 |
+| _Saccharomyces cerevisiae_ | 04-Dec-2023 | 9.0.0 | 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
+
+### Growth prediction
+
+- Correlation coefficient R<sup>2</sup>: 0.880
+
+![Growth curve](growth.png)
 
 # Installation & usage
 

diff --git a/growth.png b/growth.png
diff --git a/history.md b/history.md
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_develop" id="yeastGEM_develop" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
+  <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">
     <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_develop">
+        <rdf:Description rdf:about="#yeastGEM_v9.0.0">
           <dcterms:creator>
             <rdf:Bag>
               <rdf:li rdf:parseType="Resource">
@@ -24,10 +24,10 @@
             </rdf:Bag>
           </dcterms:creator>
           <dcterms:created rdf:parseType="Resource">
-            <dcterms:W3CDTF>2023-12-02T23:21:12Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2023-12-04T09:40:27Z</dcterms:W3CDTF>
           </dcterms:created>
           <dcterms:modified rdf:parseType="Resource">
-            <dcterms:W3CDTF>2023-12-02T23:21:12Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2023-12-04T09:40:27Z</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_develop"
+    id: "yeastGEM_v9.0.0"
     name: "The Consensus Genome-Scale Metabolic Model of Yeast"
-    version: ""
-    date: "2023-12-02"
+    version: "9.0.0"
+    date: "2023-12-04"
     defaultLB: "-1000"
     defaultUB: "1000"
     givenName: "Eduard"

diff --git a/version.txt b/version.txt
@@ -0,0 +1 @@
+9.0.0