Merge pull request #183 from SysBioChalmers/fix-biomass

Fix biomass: Add Ca(2+) into Biomass
SysBioChalmers · Dec 6, 2018 · 8aef65c · 8aef65c
2 parents 34a34fc + c1ecddc
commit 8aef65c
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Showing 11 changed files with 67 additions and 30 deletions.
diff --git a/ComplementaryData/modelCuration/Biomass_newRxnMatrix.tsv b/ComplementaryData/modelCuration/Biomass_newRxnMatrix.tsv
@@ -26,3 +26,4 @@ Cu2(+) exchange	1	Cu2(+)	reactant	extracellular
 Mn(2+) exchange	1	Mn(2+)	reactant	extracellular
 Zn(2+) exchange	1	Zn(2+)	reactant	extracellular
 Mg(2+) exchange	1	Mg(2+)	reactant	extracellular
+Ca(2+) exchange	1	Ca(2+)	reactant	extracellular
diff --git a/ComplementaryData/modelCuration/Biomass_newRxnProp.tsv b/ComplementaryData/modelCuration/Biomass_newRxnProp.tsv
@@ -10,3 +10,4 @@ Cu2(+) exchange	1		Cu2(+) exchange
 Mn(2+) exchange	1		Mn(2+) exchange
 Zn(2+) exchange	1		Zn(2+) exchange
 Mg(2+) exchange	1		Mg(2+) exchange
+Ca(2+) exchange	1		Ca(2+) exchange
diff --git a/ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv b/ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv
@@ -1,3 +1,4 @@
+model_id	name	abundance_mmol/gDW	MW_g/mol	group	reference
 s_3880[c]	Ca(2+) 	2.17E-04	40.08	ion	DOI: 10.22161/ijeab/2.2.2
 s_3778[c]	chloride 	1.29E-03	35.45	ion	DOI: 10.3103/S106836741702015X
 s_4019[c]	Cu2(+) 	6.59E-04	63.55	ion	DOI: 10.22161/ijeab/2.2.2

diff --git a/ComplementaryScripts/modelCuration/addBiomassUpdate.m b/ComplementaryScripts/modelCuration/addBiomassUpdate.m
@@ -142,6 +142,8 @@
     model.rxnNotes{rxnIndex} = 'NOTES:added for BiomassUpdate (PR #174)';
     if ~isempty(model.rules{rxnIndex})
         model.rxnConfidenceScores(rxnIndex) = 2;   %reactions has GPR rules
+    elseif contains(model.rxnNames(rxnIndex),'exchange')
+        model.rxnConfidenceScores(rxnIndex) = NaN; %exchange rxns
     else
         model.rxnConfidenceScores(rxnIndex) = 1;   %reactions without gene but needed for modelling
     end
@@ -213,6 +215,7 @@
         rxnIndex = strcmp(model.rxns,rxnID);
     end
     model.rxnNotes{rxnIndex} = 'NOTES:added for BiomassUpdate (PR #174)';
+    model.rxnConfidenceScores(rxnIndex) = 1; %needed for modeling
     model = rmfield(model,'grRules');
 end
 

diff --git a/ComplementaryScripts/modelCuration/minimal_Y6.m b/ComplementaryScripts/modelCuration/minimal_Y6.m
@@ -27,6 +27,7 @@
                     'r_4597'; ... % Mg(2+) exchange
                     'r_2049'; ... % sodium exchange
                     'r_4594'; ... % Cu(2+) exchange
+                    'r_4600'; ... % Ca(2+) exchange
                     'r_2020' };   % potassium exchange
 
 blockedExchanges = {'r_1663'; ... % bicarbonate exchange
@@ -39,7 +40,7 @@
 glucoseExchangeIndex = findRxnIDs(model,glucoseExchange);
 BlockedRxnIndex      = findRxnIDs(model,blockedExchanges);
 
-if length(find(uptakeRxnIndexes~= 0)) ~= 14
+if length(find(uptakeRxnIndexes~= 0)) ~= 15
     warning('Not all exchange reactions were found.')
 end
 

diff --git a/ModelFiles/boundaryMets.txt b/ModelFiles/boundaryMets.txt
@@ -243,3 +243,4 @@ s_4201[e]	Cu2(+) [extracellular]
 s_4202[e]	Mn(2+) [extracellular]
 s_4203[e]	Zn(2+) [extracellular]
 s_4204[e]	Mg(2+) [extracellular]
+s_4199[e]	Ca(2+) [extracellular]
diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt
@@ -1,7 +1,7 @@
-MATLAB	9.5.0.944444 (R2018b)
+MATLAB	9.1.0.441655 (R2016b)
 libSBML	5.17.0
 RAVEN_toolbox	2.1.0
-COBRA_toolbox	3.0.2
+COBRA_toolbox	3.0.3
 SBML_level	3
 SBML_version	1
 fbc_version	2
diff --git a/ModelFiles/txt/yeastGEM.txt b/ModelFiles/txt/yeastGEM.txt
@@ -3415,7 +3415,7 @@ r_4044	s_3716[e]  -> 		  0.00	1000.00	  0.00
 r_4041	55.3 s_0434[c] + 55.3 s_0803[c] + s_1096[c] + s_3717[c] + s_3718[c] + s_3719[c] + s_3720[c] + s_4205[c] + s_4206[c]  -> 55.3 s_0394[c] + s_0450[c] + 55.3 s_0794[c] + 55.3 s_1322[c] 		  0.00	1000.00	  0.00
 r_4046	s_0434[c] + s_0803[c]  -> s_0394[c] + s_0794[c] + s_1322[c] 		  0.70	  0.70	  0.00
 r_4047	0.527012 s_0404[c] + 0.184592 s_0428[c] + 0.11682 s_0430[c] + 0.341731 s_0432[c] + 0.00758126 s_0542[c] + 0.12107 s_0747[c] + 0.34667 s_0748[c] + 0.333575 s_0757[c] + 0.0761572 s_0832[c] + 0.22135 s_0847[c] + 0.340467 s_1077[c] + 0.328751 s_1099[c] + 0.0582379 s_1148[c] + 0.153808 s_1314[c] + 0.189187 s_1379[c] + 0.212964 s_1428[c] + 0.219857 s_1491[c] + 0.0326224 s_1527[c] + 0.117165 s_1533[c] + 0.30394 s_1561[c]  -> 0.527012 s_1582[c] + 0.184592 s_1583[c] + 0.11682 s_1585[c] + 0.341731 s_1587[c] + 0.00758126 s_1589[c] + 0.12107 s_1590[c] + 0.34667 s_1591[c] + 0.333575 s_1593[c] + 0.0761572 s_1594[c] + 0.22135 s_1596[c] + 0.340467 s_1598[c] + 0.328751 s_1600[c] + 0.0582379 s_1602[c] + 0.153808 s_1604[c] + 0.189187 s_1606[c] + 0.212964 s_1607[c] + 0.219857 s_1608[c] + 0.0326224 s_1610[c] + 0.117165 s_1612[c] + 0.30394 s_1614[c] + s_3717[c] 		  0.00	1000.00	  0.00
-r_4048	0.748532 s_0001[ce] + 0.250097 s_0004[ce] + 0.361423 s_0773[c] + 0.710956 s_1107[c] + 0.138279 s_1520[c]  -> s_3718[c] 		  0.00	1000.00	  0.00
+r_4048	0.748515 s_0001[ce] + 0.250092 s_0004[ce] + 0.361415 s_0773[c] + 0.71094 s_1107[c] + 0.138276 s_1520[c]  -> s_3718[c] 		  0.00	1000.00	  0.00
 r_4049	0.0445348 s_0423[c] + 0.0432762 s_0526[c] + 0.0445348 s_0782[c] + 0.0579921 s_1545[c]  -> s_3719[c] 		  0.00	1000.00	  0.00
 r_4050	0.0036 s_0584[c] + 0.0024 s_0589[c] + 0.0024 s_0615[c] + 0.0036 s_0649[c]  -> s_3720[c] 		  0.00	1000.00	  0.00
 r_4051	s_3721[g]  -> s_3722[c] 		  0.00	1000.00	  0.00
@@ -3960,4 +3960,5 @@ r_4595	s_4202[e]  <=> 		-1000.00	1000.00	  0.00
 r_4596	s_4203[e]  <=> 		-1000.00	1000.00	  0.00
 r_4597	s_4204[e]  <=> 		-1000.00	1000.00	  0.00
 r_4598	0.00019 s_0529[c] + 1e-05 s_0687[c] + 0.00265 s_1198[c] + 0.00015 s_1203[c] + 0.00057 s_1207[c] + 0.0027 s_1212[c] + 0.00099 s_1405[c] + 1.2e-06 s_1475[c] + 6.34e-05 s_1487[c] + 1e-06 s_3714[c]  -> s_4205[c] 		  0.00	1000.00	  0.00
-r_4599	3.04e-05 s_0924[c] + 0.00363 s_1373[c] + 0.00397 s_1437[c] + 0.02 s_1467[c] + 0.00129 s_3778[c] + 0.00273 s_3801[c] + 0.000748 s_3822[c] + 0.00124254 s_4013[c] + 0.000659 s_4019[c]  -> s_4206[c] 		  0.00	1000.00	  0.00
+r_4599	3.04e-05 s_0924[c] + 0.00363 s_1373[c] + 0.00397 s_1437[c] + 0.02 s_1467[c] + 0.00129 s_3778[c] + 0.00273 s_3801[c] + 0.000748 s_3822[c] + 0.000217 s_3880[c] + 0.00124254 s_4013[c] + 0.000659 s_4019[c]  -> s_4206[c] 		  0.00	1000.00	  0.00
+r_4600	s_4199[e]  <=> 		-1000.00	1000.00	  0.00
diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml
@@ -175476,11 +175476,11 @@
           </rdf:RDF>
         </annotation>
         <listOfReactants>
-          <speciesReference species="s_0001__91__ce__93__" stoichiometry="0.748532066067701" constant="true"/>
-          <speciesReference species="s_0004__91__ce__93__" stoichiometry="0.250097368470812" constant="true"/>
-          <speciesReference species="s_0773__91__c__93__" stoichiometry="0.361422785012112" constant="true"/>
-          <speciesReference species="s_1107__91__c__93__" stoichiometry="0.710955868599178" constant="true"/>
-          <speciesReference species="s_1520__91__c__93__" stoichiometry="0.13827887134841" constant="true"/>
+          <speciesReference species="s_0001__91__ce__93__" stoichiometry="0.748514964334505" constant="true"/>
+          <speciesReference species="s_0004__91__ce__93__" stoichiometry="0.25009165448919" constant="true"/>
+          <speciesReference species="s_0773__91__c__93__" stoichiometry="0.361414527575564" constant="true"/>
+          <speciesReference species="s_1107__91__c__93__" stoichiometry="0.710939625370425" constant="true"/>
+          <speciesReference species="s_1520__91__c__93__" stoichiometry="0.138275712087142" constant="true"/>
         </listOfReactants>
         <listOfProducts>
           <speciesReference species="s_3718__91__c__93__" stoichiometry="1" constant="true"/>
@@ -192501,7 +192501,7 @@
       <reaction metaid="r_4593" sboTerm="SBO:0000627" id="r_4593" name="chloride exchange" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
-            <p>Confidence Level: 1</p>
+            <p>Confidence Level: NaN</p>
             <p>NOTES:added for BiomassUpdate (PR #174)</p>
           </body>
         </notes>
@@ -192523,7 +192523,7 @@
       <reaction metaid="r_4594" sboTerm="SBO:0000627" id="r_4594" name="Cu2(+) exchange" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
-            <p>Confidence Level: 1</p>
+            <p>Confidence Level: NaN</p>
             <p>NOTES:added for BiomassUpdate (PR #174)</p>
           </body>
         </notes>
@@ -192545,7 +192545,7 @@
       <reaction metaid="r_4595" sboTerm="SBO:0000627" id="r_4595" name="Mn(2+) exchange" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
-            <p>Confidence Level: 1</p>
+            <p>Confidence Level: NaN</p>
             <p>NOTES:added for BiomassUpdate (PR #174)</p>
           </body>
         </notes>
@@ -192567,7 +192567,7 @@
       <reaction metaid="r_4596" sboTerm="SBO:0000627" id="r_4596" name="Zn(2+) exchange" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
-            <p>Confidence Level: 1</p>
+            <p>Confidence Level: NaN</p>
             <p>NOTES:added for BiomassUpdate (PR #174)</p>
           </body>
         </notes>
@@ -192589,7 +192589,7 @@
       <reaction metaid="r_4597" sboTerm="SBO:0000627" id="r_4597" name="Mg(2+) exchange" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
-            <p>Confidence Level: 1</p>
+            <p>Confidence Level: NaN</p>
             <p>NOTES:added for BiomassUpdate (PR #174)</p>
           </body>
         </notes>
@@ -192611,7 +192611,7 @@
       <reaction metaid="r_4598" sboTerm="SBO:0000395" id="r_4598" name="cofactor pseudoreaction" reversible="false" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
-            <p>Confidence Level: 0</p>
+            <p>Confidence Level: 1</p>
             <p>NOTES:added for BiomassUpdate (PR #174)</p>
           </body>
         </notes>
@@ -192645,7 +192645,7 @@
       <reaction metaid="r_4599" sboTerm="SBO:0000395" id="r_4599" name="ion pseudoreaction" reversible="false" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
-            <p>Confidence Level: 0</p>
+            <p>Confidence Level: 1</p>
             <p>NOTES:added for BiomassUpdate (PR #174)</p>
           </body>
         </notes>
@@ -192668,13 +192668,36 @@
           <speciesReference species="s_3778__91__c__93__" stoichiometry="0.00129000004380941" constant="true"/>
           <speciesReference species="s_3801__91__c__93__" stoichiometry="0.00273000006563962" constant="true"/>
           <speciesReference species="s_3822__91__c__93__" stoichiometry="0.000747999991290271" constant="true"/>
+          <speciesReference species="s_3880__91__c__93__" stoichiometry="0.000216999993426725" constant="true"/>
           <speciesReference species="s_4013__91__c__93__" stoichiometry="0.0012425429886207" constant="true"/>
           <speciesReference species="s_4019__91__c__93__" stoichiometry="0.000659000012092292" constant="true"/>
         </listOfReactants>
         <listOfProducts>
           <speciesReference species="s_4206__91__c__93__" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
+      <reaction metaid="r_4600" sboTerm="SBO:0000627" id="r_4600" name="Ca(2+) exchange" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+            <p>Confidence Level: NaN</p>
+            <p>NOTES:added for BiomassUpdate (PR #174)</p>
+          </body>
+        </notes>
+        <annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <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="#r_4600">
+              <bqbiol:hasProperty>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000627"/>
+                </rdf:Bag>
+              </bqbiol:hasProperty>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="s_4199__91__e__93__" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
     </listOfReactions>
     <fbc:listOfObjectives fbc:activeObjective="obj">
       <fbc:objective fbc:id="obj" fbc:type="maximize">

diff --git a/ModelFiles/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml
@@ -86148,10 +86148,10 @@
     - id: r_4048
     - name: carbohydrate pseudoreaction
     - metabolites: !!omap
-      - s_0001: -0.74853
-      - s_0004: -0.2501
-      - s_0773: -0.36142
-      - s_1107: -0.71096
+      - s_0001: -0.74851
+      - s_0004: -0.25009
+      - s_0773: -0.36141
+      - s_1107: -0.71094
       - s_1520: -0.13828
       - s_3718: 1
     - lower_bound: 0
@@ -93915,7 +93915,6 @@
     - upper_bound: 1000
     - annotation: !!omap
       - sbo: SBO:0000627
-    - confidence_score: 1
   - !!omap
     - id: r_4594
     - name: Cu2(+) exchange
@@ -93925,7 +93924,6 @@
     - upper_bound: 1000
     - annotation: !!omap
       - sbo: SBO:0000627
-    - confidence_score: 1
   - !!omap
     - id: r_4595
     - name: Mn(2+) exchange
@@ -93935,7 +93933,6 @@
     - upper_bound: 1000
     - annotation: !!omap
       - sbo: SBO:0000627
-    - confidence_score: 1
   - !!omap
     - id: r_4596
     - name: Zn(2+) exchange
@@ -93945,7 +93942,6 @@
     - upper_bound: 1000
     - annotation: !!omap
       - sbo: SBO:0000627
-    - confidence_score: 1
   - !!omap
     - id: r_4597
     - name: Mg(2+) exchange
@@ -93955,7 +93951,6 @@
     - upper_bound: 1000
     - annotation: !!omap
       - sbo: SBO:0000627
-    - confidence_score: 1
   - !!omap
     - id: r_4598
     - name: cofactor pseudoreaction
@@ -93975,7 +93970,7 @@
     - upper_bound: 1000
     - annotation: !!omap
       - sbo: SBO:0000395
-    - confidence_score: 0
+    - confidence_score: 1
   - !!omap
     - id: r_4599
     - name: ion pseudoreaction
@@ -93987,14 +93982,24 @@
       - s_3778: -0.00129
       - s_3801: -0.00273
       - s_3822: -0.000748
+      - s_3880: -0.000217
       - s_4013: -0.0012425
       - s_4019: -0.000659
       - s_4206: 1
     - lower_bound: 0
     - upper_bound: 1000
     - annotation: !!omap
       - sbo: SBO:0000395
-    - confidence_score: 0
+    - confidence_score: 1
+  - !!omap
+    - id: r_4600
+    - name: Ca(2+) exchange
+    - metabolites: !!omap
+      - s_4199: -1
+    - lower_bound: -1000
+    - upper_bound: 1000
+    - annotation: !!omap
+      - sbo: SBO:0000627
 - genes:
   - !!omap
     - id: GR191W

diff --git a/README.md b/README.md
@@ -10,13 +10,13 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 **GEM Category:** species; **Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** reconstruction, curated; **Model Source:** YeastMetabolicNetwork; **Omic Source:** genomics, metabolomics; **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** general metabolism; **Bioreactor**; **Strain:** S288C; **Condition:** aerobic, glucose-limited, defined media;
 
-* Last update: 2018-11-26
+* Last update: 2018-12-05
 
 * Main Model Descriptors:
 
 |Taxonomy | Template Model | Reactions | Metabolites| Genes |
 |:-------:|:--------------:|:---------:|:----------:|:-----:|
-|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3962|2691|1139|
+|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3963|2691|1139|
 
 This repository is administered by Benjamín J. Sánchez ([@BenjaSanchez](https://github.com/benjasanchez)), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.