SysBioChalmers · edkerk · Jun 30, 2023 · Jun 26, 2023 · Jun 26, 2023 · Jun 26, 2023
diff --git a/doc/index.html b/doc/index.html
diff --git a/doc/src/geckomat/gather_kcats/fuzzyKcatMatching.html b/doc/src/geckomat/gather_kcats/fuzzyKcatMatching.html
@@ -181,7 +181,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0085 <span class="keyword">else</span>
 0086     rxnNames = extractAfter(model.ec.rxns, 4);
 0087 <span class="keyword">end</span>
-0088 originalRxns = getIndexes(model,rxnNames(ecRxns),<span class="string">'rxns'</span>);
+0088 [~,originalRxns] = ismember(rxnNames(ecRxns),model.rxns);
 0089 <span class="keyword">for</span> i = 1:length(ecRxns)
 0090     sel = find(model.S(:,originalRxns(i)) &lt; 0);
 0091     substrates{i}  = model.metNames(sel); 

diff --git a/doc/src/geckomat/gather_kcats/getStandardKcat.html b/doc/src/geckomat/gather_kcats/getStandardKcat.html
diff --git a/doc/src/geckomat/get_enzyme_data/getECfromGEM.html b/doc/src/geckomat/get_enzyme_data/getECfromGEM.html
@@ -98,7 +98,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0033     rxnNames = extractAfter(model.ec.rxns, 4);
 0034 <span class="keyword">end</span>
 0035 
-0036 rxnIdxs = getIndexes(model,rxnNames,<span class="string">'rxns'</span>);
+0036 [~,rxnIdxs] = ismember(rxnNames,model.rxns);
 0037 
 0038 <span class="comment">% Check if eccodes are valid</span>
 0039 eccodes = model.eccodes;

diff --git a/doc/src/geckomat/utilities/getSubsetEcModel.html b/doc/src/geckomat/utilities/getSubsetEcModel.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+                "http://www.w3.org/TR/REC-html40/loose.dtd">
+<html>
+<head>
+  <title>Description of getSubsetEcModel</title>
+  <meta name="keywords" content="getSubsetEcModel">
+  <meta name="description" content="getSubset_ecModel">
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+  <meta name="generator" content="m2html v1.5 &copy; 2003-2005 Guillaume Flandin">
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+<body>
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+<div><a href="../../../index.html">Home</a> &gt;  <a href="#">src</a> &gt; <a href="#">geckomat</a> &gt; <a href="index.html">utilities</a> &gt; getSubsetEcModel.m</div>
+
+<!--<table width="100%"><tr><td align="left"><a href="../../../index.html"><img alt="<" border="0" src="../../../left.png">&nbsp;Master index</a></td>
+<td align="right"><a href="index.html">Index for src\geckomat\utilities&nbsp;<img alt=">" border="0" src="../../../right.png"></a></td></tr></table>-->
+
+<h1>getSubsetEcModel
+</h1>
+
+<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../../../up.png"></a></h2>
+<div class="box"><strong>getSubset_ecModel</strong></div>
+
+<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../../../up.png"></a></h2>
+<div class="box"><strong>function smallEcModel = getSubsetEcModel(bigEcModel,smallGEM) </strong></div>
+
+<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../../../up.png"></a></h2>
+<div class="fragment"><pre class="comment"> getSubset_ecModel
+   Generate a context-specific ecModel (strain/cell-line/tissue) by
+   mapping reactions and genes from a conventional context-specific GEM to
+   a general ecModel (bigEcModel), to yield a context-specific ecModel.
+
+ Input:
+   bigEcModel  enzyme-constrained version of conventional model of
+                  metabolism for a given species
+   smallGEM       Reduced model (subset of the general model) for a
+                  specific strain (microbes) or cell-line/tissues (mammals)
+
+ Output:
+   smallEcModel  Enzyme-constrained version of the context-specific model
+
+ Usage: smallEcModel = getSubsetEcModel(smallGEM,bigEcModel)</pre></div>
+
+<!-- crossreference -->
+<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../../../up.png"></a></h2>
+This function calls:
+<ul style="list-style-image:url(../../../matlabicon.gif)">
+</ul>
+This function is called by:
+<ul style="list-style-image:url(../../../matlabicon.gif)">
+</ul>
+<!-- crossreference -->
+
+
+
+<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../../../up.png"></a></h2>
+<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function smallEcModel = getSubsetEcModel(bigEcModel,smallGEM)</a>
+0002 <span class="comment">% getSubset_ecModel</span>
+0003 <span class="comment">%   Generate a context-specific ecModel (strain/cell-line/tissue) by</span>
+0004 <span class="comment">%   mapping reactions and genes from a conventional context-specific GEM to</span>
+0005 <span class="comment">%   a general ecModel (bigEcModel), to yield a context-specific ecModel.</span>
+0006 <span class="comment">%</span>
+0007 <span class="comment">% Input:</span>
+0008 <span class="comment">%   bigEcModel  enzyme-constrained version of conventional model of</span>
+0009 <span class="comment">%                  metabolism for a given species</span>
+0010 <span class="comment">%   smallGEM       Reduced model (subset of the general model) for a</span>
+0011 <span class="comment">%                  specific strain (microbes) or cell-line/tissues (mammals)</span>
+0012 <span class="comment">%</span>
+0013 <span class="comment">% Output:</span>
+0014 <span class="comment">%   smallEcModel  Enzyme-constrained version of the context-specific model</span>
+0015 <span class="comment">%</span>
+0016 <span class="comment">% Usage: smallEcModel = getSubsetEcModel(smallGEM,bigEcModel)</span>
+0017 
+0018 <span class="comment">% Check if original bigEcModel contains context-dependent protein constraints</span>
+0019 <span class="keyword">if</span> any(bigEcModel.lb(startsWith(bigEcModel.rxns,<span class="string">'usage_prot_'</span>)) ~= -1000)
+0020     disp([<span class="string">'The bigEcModel is constraint by protein concentrations that are '</span> <span class="keyword">...</span>
+0021              <span class="string">'likely not relevant in the constructed smallEcModel.'</span>])
+0022 <span class="keyword">end</span>
+0023 
+0024 <span class="comment">% Remove genes (and associated reactions) that are absent in smallGEM</span>
+0025 genesToRemove  = setdiff(bigEcModel.genes,smallGEM.genes);
+0026 smallEcModel = removeGenes(bigEcModel,genesToRemove,true,true,false);
+0027 
+0028 <span class="comment">% Remove genes from ec-structure</span>
+0029 enzToRemove = ismember(smallEcModel.ec.genes,genesToRemove);
+0030 smallEcModel.ec.genes(enzToRemove)       = [];
+0031 smallEcModel.ec.enzymes(enzToRemove)     = [];
+0032 smallEcModel.ec.concs(enzToRemove)       = [];
+0033 smallEcModel.ec.mw(enzToRemove)          = [];
+0034 smallEcModel.ec.sequence(enzToRemove)    = [];
+0035 smallEcModel.ec.rxnEnzMat(:,enzToRemove) = [];
+0036 
+0037 <span class="comment">% Remove any reaction (except prot_ associated) that is absent from smallGEM</span>
+0038 trimRxns = regexprep(smallEcModel.rxns,<span class="string">'_REV|_EXP_\d+'</span>,<span class="string">''</span>);
+0039 protRxns = startsWith(smallEcModel.rxns,{<span class="string">'usage_prot_'</span>,<span class="string">'prot_pool_exchange'</span>});
+0040 keepRxns = ismember(trimRxns,smallGEM.rxns) | protRxns;
+0041 smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);
+0042 
+0043 <span class="comment">% Remove reactions from ec-structure</span>
+0044 ecRxnsToRemove = ~ismember(smallEcModel.ec.rxns,smallEcModel.rxns);
+0045 
+0046 smallEcModel.ec.rxns(ecRxnsToRemove)        = [];
+0047 smallEcModel.ec.kcat(ecRxnsToRemove)        = [];
+0048 smallEcModel.ec.source(ecRxnsToRemove)      = [];
+0049 smallEcModel.ec.notes(ecRxnsToRemove)       = [];
+0050 smallEcModel.ec.eccodes(ecRxnsToRemove)     = [];
+0051 smallEcModel.ec.rxnEnzMat(ecRxnsToRemove,:) = [];
+0052 
+0053 smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);
+0054 <span class="keyword">end</span>
+0055</pre></div>
+<hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+</body>
+</html>
diff --git a/doc/src/geckomat/utilities/index.html b/doc/src/geckomat/utilities/index.html
@@ -19,7 +19,7 @@ <h1>Index for src\geckomat\utilities</h1>
 
 <h2>Matlab files in this directory:</h2>
 <table>
-<tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="ecFVA.html">ecFVA</a></td><td>ecFVA </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="enzymeUsage.html">enzymeUsage</a></td><td>enzymeUsage </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="findGECKOroot.html">findGECKOroot</a></td><td>findGECKOroot </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getFluxTarget.html">getFluxTarget</a></td><td>getFluxTarget </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="loadConventionalGEM.html">loadConventionalGEM</a></td><td>loadConventionalGEM </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="loadEcModel.html">loadEcModel</a></td><td>loadEcModel </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="loadFluxData.html">loadFluxData</a></td><td>loadFluxData </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="loadProtData.html">loadProtData</a></td><td>loadProtData </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="mapRxnsToConv.html">mapRxnsToConv</a></td><td>mapRxnsToConv </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="plotEcFVA.html">plotEcFVA</a></td><td>plotEcFVA </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="reportEnzymeUsage.html">reportEnzymeUsage</a></td><td>reportEnzymeUsage </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="saveEcModel.html">saveEcModel</a></td><td>saveECmodel </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="startGECKOproject.html">startGECKOproject</a></td><td>startGECKOproject </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="updateGECKOdoc.html">updateGECKOdoc</a></td><td>updateGeckoDoc </td></tr></table>
+<tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="ecFVA.html">ecFVA</a></td><td>ecFVA </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="enzymeUsage.html">enzymeUsage</a></td><td>enzymeUsage </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="findGECKOroot.html">findGECKOroot</a></td><td>findGECKOroot </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getFluxTarget.html">getFluxTarget</a></td><td>getFluxTarget </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getSubsetEcModel.html">getSubsetEcModel</a></td><td>getSubset_ecModel </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="loadConventionalGEM.html">loadConventionalGEM</a></td><td>loadConventionalGEM </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="loadEcModel.html">loadEcModel</a></td><td>loadEcModel </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="loadFluxData.html">loadFluxData</a></td><td>loadFluxData </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="loadProtData.html">loadProtData</a></td><td>loadProtData </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="mapRxnsToConv.html">mapRxnsToConv</a></td><td>mapRxnsToConv </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="plotEcFVA.html">plotEcFVA</a></td><td>plotEcFVA </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="reportEnzymeUsage.html">reportEnzymeUsage</a></td><td>reportEnzymeUsage </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="saveEcModel.html">saveEcModel</a></td><td>saveECmodel </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="startGECKOproject.html">startGECKOproject</a></td><td>startGECKOproject </td></tr><tr><td><img src="../../../matlabicon.gif" alt="" border="">&nbsp;<a href="updateGECKOdoc.html">updateGECKOdoc</a></td><td>updateGeckoDoc </td></tr></table>
 
 
 <h2>Subsequent directories:</h2>

diff --git a/src/geckomat/gather_kcats/getStandardKcat.m b/src/geckomat/gather_kcats/getStandardKcat.m
@@ -150,14 +150,13 @@
 
 % Only add if not geckoLight & getStandardKcat was not run earlier
 if ~any(strcmp(model.mets,'prot_standard'))
-    % Add a new gene to be consistent with ec field named standard
-    proteinStdGenes.genes = 'standard';
-    if isfield(model,'geneShortNames')
-        proteinStdGenes.geneShortNames = 'std';
-    end
-    model = addGenesRaven(model, proteinStdGenes);
-
     if ~model.ec.geckoLight
+        % Add a new gene to be consistent with ec field named standard
+        proteinStdGenes.genes = 'standard';
+        if isfield(model,'geneShortNames')
+            proteinStdGenes.geneShortNames = 'std';
+        end
+        model = addGenesRaven(model, proteinStdGenes);
         % Add a new metabolite named prot_standard
         proteinStdMets.mets         = 'prot_standard';
         proteinStdMets.metNames     = proteinStdMets.mets;

diff --git a/src/geckomat/utilities/getSubsetEcModel.m b/src/geckomat/utilities/getSubsetEcModel.m
@@ -0,0 +1,55 @@
+function smallEcModel = getSubsetEcModel(bigEcModel,smallGEM)
+% getSubset_ecModel
+%   Generate a context-specific ecModel (strain/cell-line/tissue) by
+%   mapping reactions and genes from a conventional context-specific GEM to
+%   a general ecModel (bigEcModel), to yield a context-specific ecModel.
+% 
+% Input:
+%   bigEcModel  enzyme-constrained version of conventional model of
+%                  metabolism for a given species
+%   smallGEM       Reduced model (subset of the general model) for a
+%                  specific strain (microbes) or cell-line/tissues (mammals)
+% 
+% Output:
+%   smallEcModel  Enzyme-constrained version of the context-specific model
+% 
+% Usage: smallEcModel = getSubsetEcModel(smallGEM,bigEcModel)
+
+% Check if original bigEcModel contains context-dependent protein constraints
+if any(bigEcModel.lb(startsWith(bigEcModel.rxns,'usage_prot_')) ~= -1000)
+    disp(['The bigEcModel is constraint by protein concentrations that are ' ...
+             'likely not relevant in the constructed smallEcModel.'])
+end
+
+% Remove genes (and associated reactions) that are absent in smallGEM
+genesToRemove  = setdiff(bigEcModel.genes,smallGEM.genes);
+smallEcModel = removeGenes(bigEcModel,genesToRemove,true,true,false);
+
+% Remove genes from ec-structure
+enzToRemove = ismember(smallEcModel.ec.genes,genesToRemove);
+smallEcModel.ec.genes(enzToRemove)       = [];
+smallEcModel.ec.enzymes(enzToRemove)     = [];
+smallEcModel.ec.concs(enzToRemove)       = [];
+smallEcModel.ec.mw(enzToRemove)          = [];
+smallEcModel.ec.sequence(enzToRemove)    = [];
+smallEcModel.ec.rxnEnzMat(:,enzToRemove) = [];
+
+% Remove any reaction (except prot_ associated) that is absent from smallGEM
+trimRxns = regexprep(smallEcModel.rxns,'_REV|_EXP_\d+','');
+protRxns = startsWith(smallEcModel.rxns,{'usage_prot_','prot_pool_exchange'});
+keepRxns = ismember(trimRxns,smallGEM.rxns) | protRxns;
+smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);
+
+% Remove reactions from ec-structure
+ecRxnsToRemove = ~ismember(smallEcModel.ec.rxns,smallEcModel.rxns);
+
+smallEcModel.ec.rxns(ecRxnsToRemove)        = [];
+smallEcModel.ec.kcat(ecRxnsToRemove)        = [];
+smallEcModel.ec.source(ecRxnsToRemove)      = [];
+smallEcModel.ec.notes(ecRxnsToRemove)       = [];
+smallEcModel.ec.eccodes(ecRxnsToRemove)     = [];
+smallEcModel.ec.rxnEnzMat(ecRxnsToRemove,:) = [];
+
+smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);
+end
+
diff --git a/tutorials/light_ecModel/code/HT29_ftINIT.m b/tutorials/light_ecModel/code/HT29_ftINIT.m
@@ -0,0 +1,46 @@
+% For reference, code is provided here that was used to make a cell-line
+% specific (HT-29) model of human-GEM with the ftINIT function of RAVEN.
+% This model, stored at tutorials/light_ecModel/models/HT-29-GEM.yml, is
+% for demontration purposes only. The intention of the code in this file is
+% not to routinely regenerate this model file, but merely as reference how
+% the HT-29-GEM was constructed.
+
+% Have the Human-GEM repo at release 1.15.0, and added to the MATLAB path.
+humanGEMroot = HumanGEMInstaller.getHumanGEMMainPath;
+load(fullfile(humanGEMroot,'model','Human-GEM.mat');
+m = ihuman;
+m.grRules = simplifyGrRules(m.grRules, true);
+
+prepDataHumanGEM = prepHumanModelForftINIT(m, true, ...
+                    fullfile(humanGEMroot,'data','metabolicTasks','metabolicTasks_Essential.txt'), ...
+                    fullfile(humanGEMroot,'model','reactions.tsv'));
+save('prepDataHumanGEMGeneSymbols.mat','prepDataHumanGEM');
+
+% Use RNA-seq data of cell line HT-29 (ACH-000552) from DepMap, downloaded
+% from here: https://depmap.org/portal/download/all/.
+
+tbl = readtable('OmicsExpressionProteinCodingGenesTPMLogp1.csv');
+% Cell lines are per row, genes are columns.
+sel = strcmp(tbl.Var1, 'ACH-000552');
+genes = tbl.Properties.VariableNames(2:end);
+for x = 1:length(genes)
+     a = split(genes{x}, '_');
+     genes{x} = a{1};
+end
+
+% Invert Logp1
+dataTmp = table2array(tbl(sel,2:end));
+data = 2.^dataTmp - 1;
+
+arrayData = struct(); 
+arrayData.genes = genes.';
+arrayData.levels = data.';
+arrayData.tissues = {'1'};
+arrayData.threshold = 1;
+HT29 = ftINIT(prepDataHumanGEM,arrayData.tissues{1},[],[],arrayData,{},getHumanGEMINITSteps('1+1'),false,true,[]);
+
+% Restore ENSEMBL gene identifiers and remove unnecessary fields
+[HT29.grRules,HT29.genes,HT29.rxnGeneMat] = translateGrRules(HT29.grRules,'ENSG','Symbol');
+HT29 = rmfield(HT29,{'geneShortNames','rxnReferences','rxnFrom','metFrom','rxnConfidenceScores','rxnNotes','metCharges','inchis','metFormulas','subSystems','eccodes'});
+HT29.name = 'GEM of HT-29 cell-line, for use in GECKO3 tutorial';
+writeYAMLmodel(HT29,fullfile('..','models','HT29-GEM.yml'));
diff --git a/tutorials/light_ecModel/data/smilesDB.tsv b/tutorials/light_ecModel/data/smilesDB.tsv
@@ -3498,3 +3498,4 @@ ximenic acid	CCCCCCCCC=CCCCCCCCCCCCCCCCC(=O)O
 xylitol	C(C(C(C(CO)O)O)O)O
 zinc	[Zn]
 zymosterol	CC(CCC=C(C)C)C1CCC2C1(CCC3=C2CCC4C3(CCC(C4)O)C)C
+