chore: new version

SysBioChalmers · Jan 15, 2021 · 69ec18c · 69ec18c
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diff --git a/README.md b/README.md
@@ -35,7 +35,7 @@ Manuscript under preparation
 
 |Taxonomy | Template Model | Reactions | Metabolites| Genes |
 | ------------- |:-------------:|:-------------:|:-------------:|:-----:|
-|_Mus musculus_ |   Human-GEM |  13093  | 8404 | 3510 |
+|_Mus musculus_ |   Human-GEM |  13094  | 8404 | 3510 |
 
 
 ## Installation

diff --git a/model/Mouse-GEM.mat b/model/Mouse-GEM.mat
diff --git a/model/Mouse-GEM.xml b/model/Mouse-GEM.xml
@@ -13,10 +13,10 @@
             <rdf:Bag/>
           </dcterms:creator>
           <dcterms:created rdf:parseType="Resource">
-            <dcterms:W3CDTF>2020-10-24T12:15:21Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2021-01-15T15:41:00Z</dcterms:W3CDTF>
           </dcterms:created>
           <dcterms:modified rdf:parseType="Resource">
-            <dcterms:W3CDTF>2020-10-24T12:15:21Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2021-01-15T15:41:00Z</dcterms:W3CDTF>
           </dcterms:modified>
           <bqbiol:is>
             <rdf:Bag>
@@ -239191,7 +239191,7 @@
           </fbc:or>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="R_biomass_components" sboTerm="SBO:0000176" id="R_biomass_components" reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB2N0">
+      <reaction metaid="R_biomass_components" sboTerm="SBO:0000176" id="R_biomass_components" reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
             <p>Confidence Level: 0</p>
@@ -333113,7 +333113,7 @@
           <speciesReference species="M_m10012c" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="R_biomass_human" sboTerm="SBO:0000176" id="R_biomass_human" name="Generic human cell biomass reaction" reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
+      <reaction metaid="R_biomass_human" sboTerm="SBO:0000176" id="R_biomass_human" name="Generic human cell biomass reaction" reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB2N0">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
             <p>Confidence Level: 0</p>
@@ -334649,11 +334649,24 @@
           <fbc:geneProductRef fbc:geneProduct="Sult3a1"/>
         </fbc:geneProductAssociation>
       </reaction>
+      <reaction metaid="R_MA_20016" sboTerm="SBO:0000176" id="R_MA_20016" reversible="false" fast="false" fbc:lowerFluxBound="FB2N0" fbc:upperFluxBound="FB3N1000">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+            <p>Confidence Level: 0</p>
+          </body>
+        </notes>
+        <listOfReactants>
+          <speciesReference species="M_m01368r" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_m01368c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
     </listOfReactions>
     <fbc:listOfObjectives fbc:activeObjective="obj">
       <fbc:objective fbc:id="obj" fbc:type="maximize">
         <fbc:listOfFluxObjectives>
-          <fbc:fluxObjective fbc:reaction="R_biomass_human" fbc:coefficient="1"/>
+          <fbc:fluxObjective fbc:reaction="R_biomass_components" fbc:coefficient="1"/>
         </fbc:listOfFluxObjectives>
       </fbc:objective>
     </fbc:listOfObjectives>
@@ -347095,6 +347108,7 @@
         <groups:listOfMembers>
           <groups:member groups:idRef="R_MA_20005"/>
           <groups:member groups:idRef="R_MA_20006"/>
+          <groups:member groups:idRef="R_MA_20016"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group sboTerm="SBO:0000633" groups:id="group131" groups:name="Transport reactions" groups:kind="partonomy">

diff --git a/model/Mouse-GEM.yml b/model/Mouse-GEM.yml
@@ -3,8 +3,8 @@
 - metaData:
     short_name: "Mouse-GEM"
     full_name: ""
-    version: ""
-    date: "2020-10-24"
+    version: "1.1.0"
+    date: "2021-01-15"
     authors: ""
     email: ""
     organization: ""
@@ -194144,8 +194144,9 @@
           - m03161c: -1
           - temp001c: 1
       - lower_bound: 0
-      - upper_bound: 0
+      - upper_bound: 1000
       - gene_reaction_rule: ""
+      - objective_coefficient: 1
       - eccodes: ""
       - references: ""
       - subsystem:
@@ -270615,9 +270616,8 @@
           - m10015c: -0.4835
           - temp001c: 1
       - lower_bound: 0
-      - upper_bound: 1000
+      - upper_bound: 0
       - gene_reaction_rule: ""
-      - objective_coefficient: 1
       - eccodes: ""
       - references: ""
       - subsystem:
@@ -271889,6 +271889,20 @@
       - subsystem:
           - "Amine sulfotransferase"
       - confidence_score: 2
+    - !!omap
+      - id: "MA_20016"
+      - name: ""
+      - metabolites: !!omap
+          - m01368c: 1
+          - m01368r: -1
+      - lower_bound: 0
+      - upper_bound: 1000
+      - gene_reaction_rule: ""
+      - eccodes: ""
+      - references: ""
+      - subsystem:
+          - "Transport"
+      - confidence_score: 0
 - genes:
     - !!omap
       - id: "A4galt"

diff --git a/model/dependencies.txt b/model/dependencies.txt
@@ -1,5 +1,5 @@
 MATLAB	9.8.0.1323502 (R2020a)
 libSBML	5.17.0
-RAVEN_toolbox	2.4.0
+RAVEN_toolbox	2.4.2
 COBRA_toolbox	commit c317723
 Human-GEM	1.5.0
diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-1.0.0
+1.1.0