Merge pull request #139 from SysBioChalmers/devel

yeast 8.1.3

ComplementaryScripts/increaseVersion.m

@@ -14,7 +14,7 @@ function increaseVersion(bumpType)
 
 %Bump version number:
 oldModel   = load('../ModelFiles/mat/yeastGEM.mat');
-oldVersion = oldModel.model.description;
+oldVersion = oldModel.model.modelID;
 oldVersion = oldVersion(strfind(oldVersion,'_v')+2:end);
 oldVersion = str2double(strsplit(oldVersion,'.'));
 newVersion = oldVersion;
@@ -49,6 +49,31 @@ function increaseVersion(bumpType)
 model.modelID = ['yeastGEM_v' newVersion];
 saveYeastModel(model,false)
 
+%Check if any file changed (except for history.md and 1 line in yeastGEM.xml):
+diff   = git('diff --numstat');
+diff   = strsplit(diff,'\n');
+change = false;
+for i = 1:length(diff)
+    diff_i = strsplit(diff{i},'\t');
+    if length(diff_i) == 3
+        %.xml file: 1 line should be added & 1 line should be deleted
+        if strcmp(diff_i{3},'ModelFiles/xml/yeastGEM.xml')
+            if eval([diff_i{1} ' > 1']) || eval([diff_i{2} ' > 1'])
+                disp(['NOTE: File ' diff_i{3} ' is changing more than expected'])
+                change = true;
+            end
+        %Any other file except for history.md: no changes should be detected
+        elseif ~strcmp(diff_i{3},{'history.md'})
+            disp(['NOTE: File ' diff_i{3} ' is changing'])
+            change = true;
+        end
+    end
+end
+if change
+    error(['Some files are changing from devel. To fix, first update devel, ' ...
+        'then merge to master, and try again.'])
+end
+
 %Allow .mat & .xls storage:
 copyfile('../.gitignore','backup')
 fin  = fopen('backup','r');

ComplementaryScripts/missingFields/addSBOterms.m

@@ -0,0 +1,61 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% model = addSBOterms(model)
+%
+% Benjamín J. Sánchez
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function model = addSBOterms(model)
+
+%Get RAVEN model for matching names & compartments
+model_r = ravenCobraWrapper(model);
+
+%Add SBO terms for mets:
+model.metSBOTerms = cell(size(model.mets));
+for i = 1:length(model.mets)
+    metName = model_r.metNames{i};
+    if ismember(metName,{'biomass','DNA','RNA','protein','carbohydrate','lipid'}) ...
+            || endsWith(metName,' backbone') || endsWith(metName,' chain')
+        model.metSBOTerms{i} = 'SBO:0000649';     %Biomass
+    else
+        model.metSBOTerms{i} = 'SBO:0000247';     %Simple chemical
+    end
+end
+
+%Add SBO terms for rxns:
+model.rxnSBOTerms = cell(size(model.rxns));
+for i = 1:length(model.rxns)
+    rxnName   = model_r.rxnNames{i};
+    metNames  = model_r.metNames(model.S(:,i) ~= 0);
+    metComps  = model_r.metComps(model.S(:,i) ~= 0);
+    metStoich = model_r.S(model.S(:,i) ~= 0,i);
+
+    if length(metNames) == 1
+        if strcmp(model_r.comps{metComps},'e')
+            model.rxnSBOTerms{i} = 'SBO:0000627';	%Exchange rxn
+
+        elseif metStoich > 0
+            model.rxnSBOTerms{i} = 'SBO:0000628';	%Demand rxn
+        else
+            model.rxnSBOTerms{i} = 'SBO:0000632';	%Sink rxn
+        end
+
+    elseif strcmp(rxnName,'biomass pseudoreaction')
+        model.rxnSBOTerms{i} = 'SBO:0000629';       %Biomass pseudo-rxn
+
+    elseif strcmp(rxnName,'non-growth associated maintenance reaction')
+        model.rxnSBOTerms{i} = 'SBO:0000630';       %ATP maintenance
+
+    elseif contains(rxnName,'pseudoreaction') || contains(rxnName,'SLIME rxn')
+        model.rxnSBOTerms{i} = 'SBO:0000395';       %Encapsulating process
+
+    elseif length(unique(metComps)) > 1 && length(unique(metNames)) < length(metNames)
+        model.rxnSBOTerms{i} = 'SBO:0000655';       %Transport rxn
+
+    else
+        model.rxnSBOTerms{i} = 'SBO:0000176';       %Metabolic rxn
+    end
+end
+
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

ComplementaryScripts/saveYeastModel.m

@@ -20,6 +20,11 @@ function saveYeastModel(model,upDATE)
 scriptFolder = fileparts(which(mfilename));
 currentDir = cd(scriptFolder);
 
+%Update SBO terms in model:
+cd missingFields
+model = addSBOterms(model);
+cd ..
+
 %Check if model is a valid SBML structure:
 writeCbModel(model,'sbml','tempModel.xml');
 [~,errors] = TranslateSBML('tempModel.xml');

ModelFiles/boundaryMets.txt

@@ -164,5 +164,5 @@ s_2826[e]	oleate [extracellular]
 s_1163[e]	myristate [extracellular]
 s_3715[e]	raffinose [extracellular]
 s_3716[e]	melibiose [extracellular]
-s_3746[c]	lipid - backbones [cytoplasm]
-s_3747[c]	lipid - tails [cytoplasm]
+s_3746[c]	lipid backbone [cytoplasm]
+s_3747[c]	lipid chain [cytoplasm]

ModelFiles/dependencies.txt

@@ -1,7 +1,7 @@
 MATLAB	9.4.0.813654 (R2018a)
 libSBML	5.17.0
 RAVEN_toolbox	2.0.0
-COBRA_toolbox	commit c72a7bd
+COBRA_toolbox	commit 1361503
 SBML_level	3
 SBML_version	1
 fbc_version	2

ModelFiles/yml/yeastGEM.yml

@@ -18374,11 +18374,11 @@
     - formula: C26H52O2
   - !!omap
     - id: s_3746
-    - name: lipid - backbones
+    - name: lipid backbone
     - compartment: c
   - !!omap
     - id: s_3747
-    - name: lipid - tails
+    - name: lipid chain
     - compartment: c
 - reactions:
   - !!omap
@@ -71614,14 +71614,14 @@
     - confidence_score: 1
   - !!omap
     - id: r_4062
-    - name: lipid - backbones exchange
+    - name: lipid backbone exchange
     - metabolites: !!omap
       - s_3746: -1
     - lower_bound: 0
     - upper_bound: 0
   - !!omap
     - id: r_4063
-    - name: lipid pseudoreaction - backbone
+    - name: lipid backbone pseudoreaction
     - metabolites: !!omap
       - s_0089: -0.0069103
       - s_0666: -0.026583
@@ -71637,14 +71637,14 @@
     - confidence_score: 1
   - !!omap
     - id: r_4064
-    - name: lipid - tails exchange
+    - name: lipid chain exchange
     - metabolites: !!omap
       - s_3747: -1
     - lower_bound: 0
     - upper_bound: 0
   - !!omap
     - id: r_4065
-    - name: lipid pseudoreaction - tail
+    - name: lipid chain pseudoreaction
     - metabolites: !!omap
       - s_3740: -0.0080858
       - s_3741: -0.02373

README.md

@@ -10,7 +10,7 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 **GEM Category:** Species; **Utilisation:** predictive simulation, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** curated, reconstruction; **Model Source:** [Yeast 7.6](https://sourceforge.net/projects/yeast/); **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** General Metabolism; **Condition:** aerobic, glucose-limited, defined media, maximization of growth.
 
-* Last update: 2018-06-26
+* Last update: 2018-07-13
 
 * Main Model Descriptors:
 
@@ -66,6 +66,7 @@ The model is available in `.xml`, `.txt`, `.yml`, `.mat` and `.xlsx` (the last 2
 * `missingFields`: Folder with functions for adding missing fields to the model.
   * `addGeneNames.m`: Adds the field `geneNames` by extracting the data from KEGG.
   * `addConfidenceScores.m`: Adds confidence scores based in a basic automatic criteria.
+  * `addSBOterms.m`: Adds SBO terms to metabolites and reactions based on the corresponding names.
   * `getMissingFields.m`: Retrieves missing information (`rxnECNumbers` and `subSystems`) from KEGG & Swissprot. It uses `changeRules.m` for properly reading the gene-reaction rules, and `findInDB.m`, `getAllPath.m`, `findSubSystem.m` & `deleteRepeated.m` for reading the databases. The latter 4 functions are adapted versions of functions from the [GECKO toolbox](https://github.com/SysBioChalmers/GECKO).
 * `modelCuration`: Folder with curation functions.
   * `addiSce926changes.m`: Updates the model to include curation from [the iSce926 model](http://www.maranasgroup.com/submission_models/iSce926.htm).