chore: new version

SysBioChalmers · May 14, 2018 · b331d49 · b331d49
1 parent e537a13
commit b331d49
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Showing 6 changed files with 17 additions and 9 deletions.
diff --git a/ComplementaryScripts/newRelease.m b/ComplementaryScripts/newRelease.m
@@ -17,7 +17,7 @@ function newRelease(bumpType)
 end
 
 %Bump version number:
-oldModel   = load('ModelFiles/mat/Sco.mat');
+oldModel   = load('../ModelFiles/mat/Sco.mat');
 oldVersion = oldModel.model.description;
 oldVersion = oldVersion(strfind(oldVersion,'_v')+2:end);
 oldVersion = str2double(strsplit(oldVersion,'.'));
@@ -38,24 +38,24 @@ function newRelease(bumpType)
 newVersion = num2str(newVersion,'%d.%d.%d');
 
 %Check if history has been updated:
-fid     = fopen('history.md','r');
+fid     = fopen('../history.md','r');
 history = fscanf(fid,'%s');
 fclose(fid);
 if ~contains(history,['Sco' newVersion ':'])
     error('ERROR: update history.md first')
 end
 
 %Load model:
-model = importModel('ModelFiles/xml/Sco.xml');
+model = importModel('../ModelFiles/xml/Sco.xml');
 
 %Include tag and save model:
-model.description = ['v' newVersion];
+model.description = ['Streptomyces coelicolor-GEM_v' newVersion];
 
 %Save model
-exportForGit(model,'Sco','',{'mat', 'txt', 'xlsx', 'xml', 'yml'});
+exportForGit(model,'Sco','..',{'mat', 'txt', 'xlsx', 'xml', 'yml'});
 
 %Update version file:
-fid = fopen('version.txt','wt');
+fid = fopen('../version.txt','wt');
 fprintf(fid,newVersion);
 fclose(fid);
 end
diff --git a/ModelFiles/mat/Sco.mat b/ModelFiles/mat/Sco.mat
diff --git a/ModelFiles/xlsx/Sco.xlsx b/ModelFiles/xlsx/Sco.xlsx
diff --git a/ModelFiles/xml/Sco.xml b/ModelFiles/xml/Sco.xml
@@ -1,6 +1,6 @@
 <?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="Sco" id="Sco" name="Streptomyces coelicolor genome-scale model" fbc:strict="true">
+  <model metaid="Sco" id="Sco" name="Streptomyces coelicolor-GEM_v4.0.0" fbc:strict="true">
     <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="#Sco">
@@ -19,10 +19,10 @@
             </rdf:Bag>
           </dcterms:creator>
           <dcterms:created rdf:parseType="Resource">
-            <dcterms:W3CDTF>2018-05-14T11:27:30Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2018-05-14T14:37:43Z</dcterms:W3CDTF>
           </dcterms:created>
           <dcterms:modified rdf:parseType="Resource">
-            <dcterms:W3CDTF>2018-05-14T11:27:30Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2018-05-14T14:37:43Z</dcterms:W3CDTF>
           </dcterms:modified>
           <bqbiol:is>
             <rdf:Bag>

diff --git a/history.md b/history.md
@@ -0,0 +1,7 @@
+Sco 4.0.0:
+New _S. coelicolor_ genome scale model, based on iMK1208.
+* New features:
+  * Extended with reactions from MetaCyc- and KEGG-based reconstructions with [RAVEN Toolbox 2](https://github.com/SysBioChalmers/RAVEN).
+  * Updated annotation of metabolites and reactions
+  * SBML L3V1 FBCv2 compatible
+  * Standardized GitHub repository for easy collaboration, with `newCommit` and `newRelease` functions
diff --git a/version.txt b/version.txt
@@ -0,0 +1 @@
+4.0.0