SysBioChalmers · edkerk · Jun 7, 2026 · Jun 7, 2026 · Jun 7, 2026
diff --git a/core/FSEOF.m → analysis/FSEOF.m b/core/FSEOF.m → analysis/FSEOF.m
diff --git a/core/analyzeSampling.m → analysis/analyzeSampling.m b/core/analyzeSampling.m → analysis/analyzeSampling.m
diff --git a/core/findGeneDeletions.m → analysis/findGeneDeletions.m b/core/findGeneDeletions.m → analysis/findGeneDeletions.m
diff --git a/core/followChanged.m → analysis/followChanged.m b/core/followChanged.m → analysis/followChanged.m
diff --git a/core/followFluxes.m → analysis/followFluxes.m b/core/followFluxes.m → analysis/followFluxes.m
diff --git a/core/getAllSubGraphs.m → analysis/getAllSubGraphs.m b/core/getAllSubGraphs.m → analysis/getAllSubGraphs.m
diff --git a/core/getAllowedBounds.m → analysis/getAllowedBounds.m b/core/getAllowedBounds.m → analysis/getAllowedBounds.m
diff --git a/core/getEssentialRxns.m → analysis/getEssentialRxns.m b/core/getEssentialRxns.m → analysis/getEssentialRxns.m
diff --git a/core/getFluxZ.m → analysis/getFluxZ.m b/core/getFluxZ.m → analysis/getFluxZ.m
diff --git a/core/getMinNrFluxes.m → analysis/getMinNrFluxes.m b/core/getMinNrFluxes.m → analysis/getMinNrFluxes.m
diff --git a/core/haveFlux.m → analysis/haveFlux.m b/core/haveFlux.m → analysis/haveFlux.m
diff --git a/core/randomSampling.m → analysis/randomSampling.m b/core/randomSampling.m → analysis/randomSampling.m
diff --git a/core/reporterMetabolites.m → analysis/reporterMetabolites.m b/core/reporterMetabolites.m → analysis/reporterMetabolites.m
diff --git a/core/runDynamicFBA.m → analysis/runDynamicFBA.m b/core/runDynamicFBA.m → analysis/runDynamicFBA.m
diff --git a/core/runPhenotypePhasePlane.m → analysis/runPhenotypePhasePlane.m b/core/runPhenotypePhasePlane.m → analysis/runPhenotypePhasePlane.m
diff --git a/core/runProductionEnvelope.m → analysis/runProductionEnvelope.m b/core/runProductionEnvelope.m → analysis/runProductionEnvelope.m
diff --git a/core/runRobustnessAnalysis.m → analysis/runRobustnessAnalysis.m b/core/runRobustnessAnalysis.m → analysis/runRobustnessAnalysis.m
diff --git a/core/runSimpleOptKnock.m → analysis/runSimpleOptKnock.m b/core/runSimpleOptKnock.m → analysis/runSimpleOptKnock.m
diff --git a/core/assignSBOterms.m → annotation/assignSBOterms.m b/core/assignSBOterms.m → annotation/assignSBOterms.m
diff --git a/struct_conversion/editMiriam.m → annotation/editMiriam.m b/struct_conversion/editMiriam.m → annotation/editMiriam.m
diff --git a/struct_conversion/extractMiriam.m → annotation/extractMiriam.m b/struct_conversion/extractMiriam.m → annotation/extractMiriam.m
diff --git a/io/loadDeltaGfromCSV.m → annotation/loadDeltaGfromCSV.m b/io/loadDeltaGfromCSV.m → annotation/loadDeltaGfromCSV.m
diff --git a/io/saveDeltaGtoCSV.m → annotation/saveDeltaGtoCSV.m b/io/saveDeltaGtoCSV.m → annotation/saveDeltaGtoCSV.m
diff --git a/core/fitParameters.m → biomass/fitParameters.m b/core/fitParameters.m → biomass/fitParameters.m
diff --git a/core/getBiomassFractions.m → biomass/getBiomassFractions.m b/core/getBiomassFractions.m → biomass/getBiomassFractions.m
diff --git a/core/scaleBiomassFraction.m → biomass/scaleBiomassFraction.m b/core/scaleBiomassFraction.m → biomass/scaleBiomassFraction.m
diff --git a/core/scaleBiomassPseudoreaction.m → biomass/scaleBiomassPseudoreaction.m b/core/scaleBiomassPseudoreaction.m → biomass/scaleBiomassPseudoreaction.m
diff --git a/core/setGAM.m → biomass/setGAM.m b/core/setGAM.m → biomass/setGAM.m
diff --git a/core/compareMultipleModels.m → comparison/compareMultipleModels.m b/core/compareMultipleModels.m → comparison/compareMultipleModels.m
diff --git a/core/compareRxnsGenesMetsComps.m → comparison/compareRxnsGenesMetsComps.m b/core/compareRxnsGenesMetsComps.m → comparison/compareRxnsGenesMetsComps.m
diff --git a/core/applyCondition.m → conditions/applyCondition.m b/core/applyCondition.m → conditions/applyCondition.m
diff --git a/struct_conversion/COBRA_structure_fields.csv → conversion/COBRA_structure_fields.csv b/struct_conversion/COBRA_structure_fields.csv → conversion/COBRA_structure_fields.csv
diff --git a/struct_conversion/addIdentifierPrefix.m → conversion/addIdentifierPrefix.m b/struct_conversion/addIdentifierPrefix.m → conversion/addIdentifierPrefix.m
diff --git a/struct_conversion/cobraNamespaces.csv → conversion/cobraNamespaces.csv b/struct_conversion/cobraNamespaces.csv → conversion/cobraNamespaces.csv
diff --git a/struct_conversion/orderRavenFields.csv → conversion/orderRavenFields.csv b/struct_conversion/orderRavenFields.csv → conversion/orderRavenFields.csv
diff --git a/struct_conversion/ravenCobraWrapper.m → conversion/ravenCobraWrapper.m b/struct_conversion/ravenCobraWrapper.m → conversion/ravenCobraWrapper.m
@@ -38,7 +38,7 @@
 ravenPath=findRAVENroot();
 
 % Load COBRA field information
-fid             = fopen(fullfile(ravenPath,'struct_conversion','COBRA_structure_fields.csv')); % Taken from https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/definitions/COBRA_structure_fields.csv
+fid             = fopen(fullfile(ravenPath,'conversion','COBRA_structure_fields.csv')); % Taken from https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/definitions/COBRA_structure_fields.csv
 fieldFile       = textscan(fid,repmat('%s',1,15),'Delimiter','\t','HeaderLines',1);
 dbFields        = ~cellfun(@isempty,fieldFile{5}); % Only keep fields with database annotations that should be translated to xxxMiriams
 dbFields        = dbFields & ~contains(fieldFile{1},{'metInChIString','metKEGGID','metPubChemID','rxnECNumbers'});
@@ -48,7 +48,7 @@
 fclose(fid);
 
 % Load conversion between additional COBRA fields and namespaces:
-fid             = fopen(fullfile(ravenPath,'struct_conversion','cobraNamespaces.csv'));
+fid             = fopen(fullfile(ravenPath,'conversion','cobraNamespaces.csv'));
 fieldFile       = textscan(fid,'%s %s','Delimiter',',','HeaderLines',0);
 COBRAfields     = [COBRAfields; fieldFile{1}];
 COBRAnamespace  = [COBRAnamespace; fieldFile{2}];

diff --git a/struct_conversion/removeIdentifierPrefix.m → conversion/removeIdentifierPrefix.m b/struct_conversion/removeIdentifierPrefix.m → conversion/removeIdentifierPrefix.m
diff --git a/...t_conversion/standardizeModelFieldOrder.m → conversion/standardizeModelFieldOrder.m b/...t_conversion/standardizeModelFieldOrder.m → conversion/standardizeModelFieldOrder.m
@@ -16,12 +16,12 @@
 ravenPath=findRAVENroot();
 
 if ~isfield(model,'rules') % Check if model is RAVEN
-    fid = fopen(fullfile(ravenPath,'struct_conversion','orderRavenFields.csv'));
+    fid = fopen(fullfile(ravenPath,'conversion','orderRavenFields.csv'));
     fields = textscan(fid,'%s','Delimiter',',','HeaderLines',0);
     fields = fields{1};
     fclose(fid);
 else % If model is COBRA
-    fid = fopen(fullfile(ravenPath,'struct_conversion','COBRA_structure_fields.csv')); % Taken from https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/definitions/COBRA_structure_fields.csv
+    fid = fopen(fullfile(ravenPath,'conversion','COBRA_structure_fields.csv')); % Taken from https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/definitions/COBRA_structure_fields.csv
     fields = textscan(fid,repmat('%s',1,15),'Delimiter','\t','HeaderLines',1);
     fields = fields{1};
     fclose(fid);

diff --git a/core/curateModelFromTables.m → curation/curateModelFromTables.m b/core/curateModelFromTables.m → curation/curateModelFromTables.m
diff --git a/core/canConsume.m → gapfilling/canConsume.m b/core/canConsume.m → gapfilling/canConsume.m
diff --git a/core/canProduce.m → gapfilling/canProduce.m b/core/canProduce.m → gapfilling/canProduce.m
diff --git a/core/checkProduction.m → gapfilling/checkProduction.m b/core/checkProduction.m → gapfilling/checkProduction.m
diff --git a/core/checkRxn.m → gapfilling/checkRxn.m b/core/checkRxn.m → gapfilling/checkRxn.m
diff --git a/core/consumeSomething.m → gapfilling/consumeSomething.m b/core/consumeSomething.m → gapfilling/consumeSomething.m
diff --git a/core/fillGaps.m → gapfilling/fillGaps.m b/core/fillGaps.m → gapfilling/fillGaps.m
diff --git a/core/fitTasks.m → gapfilling/fitTasks.m b/core/fitTasks.m → gapfilling/fitTasks.m
diff --git a/core/gapReport.m → gapfilling/gapReport.m b/core/gapReport.m → gapfilling/gapReport.m
diff --git a/core/makeSomething.m → gapfilling/makeSomething.m b/core/makeSomething.m → gapfilling/makeSomething.m
diff --git a/core/findRAVENroot.m → installation/findRAVENroot.m b/core/findRAVENroot.m → installation/findRAVENroot.m
diff --git a/installation/removeRavenFromPath.m b/installation/removeRavenFromPath.m
@@ -27,7 +27,7 @@ function removeRavenFromPath()
     end
 end
 
-ravenPath = unique(regexprep(currPath(ravenPath),'(\\|\/)((external)|(struct_conversion)|(solver))',''));
+ravenPath = unique(regexprep(currPath(ravenPath),'(\\|\/)((reconstruction)|(conversion)|(solver))',''));
 addOnDir = contains(ravenPath,'MATLAB Add-Ons');
 if any(addOnDir)
     warning(['RAVEN is installed as MATLAB Add-On at the following directory, but MATLAB '...

diff --git a/external/updateDocumentation.m → installation/updateDocumentation.m b/external/updateDocumentation.m → installation/updateDocumentation.m
@@ -20,8 +20,8 @@ function updateDocumentation()
 ravenDirs(startsWith(ravenDirs,strcat(ravenDir,filesep,'legacy',filesep,'software')))=[];
 
 %Remove keggModel.mat if it exists
-if exist(fullfile(ravenDir,'external','kegg','keggModel.mat'), 'file') == 2
-    delete(fullfile(ravenDir,'external','kegg','keggModel.mat'));
+if exist(fullfile(ravenDir,'reconstruction','kegg','keggModel.mat'), 'file') == 2
+    delete(fullfile(ravenDir,'reconstruction','kegg','keggModel.mat'));
 end
 
 %Remove existing "doc" directory from RAVEN

diff --git a/core/getExpressionStructure.m → localization/getExpressionStructure.m b/core/getExpressionStructure.m → localization/getExpressionStructure.m
diff --git a/external/getWoLFScores.m → localization/getWoLFScores.m b/external/getWoLFScores.m → localization/getWoLFScores.m
diff --git a/core/mapCompartments.m → localization/mapCompartments.m b/core/mapCompartments.m → localization/mapCompartments.m
diff --git a/external/parseScores.m → localization/parseScores.m b/external/parseScores.m → localization/parseScores.m
diff --git a/core/predictLocalization.m → localization/predictLocalization.m b/core/predictLocalization.m → localization/predictLocalization.m
diff --git a/core/addExchangeRxns.m → manipulation/addExchangeRxns.m b/core/addExchangeRxns.m → manipulation/addExchangeRxns.m
diff --git a/core/addGenesRaven.m → manipulation/addGenesRaven.m b/core/addGenesRaven.m → manipulation/addGenesRaven.m
diff --git a/core/addMets.m → manipulation/addMets.m b/core/addMets.m → manipulation/addMets.m
diff --git a/core/addRxns.m → manipulation/addRxns.m b/core/addRxns.m → manipulation/addRxns.m
diff --git a/core/addRxnsGenesMets.m → manipulation/addRxnsGenesMets.m b/core/addRxnsGenesMets.m → manipulation/addRxnsGenesMets.m
diff --git a/core/addTransport.m → manipulation/addTransport.m b/core/addTransport.m → manipulation/addTransport.m
diff --git a/core/changeGrRules.m → manipulation/changeGrRules.m b/core/changeGrRules.m → manipulation/changeGrRules.m
diff --git a/core/changeRxns.m → manipulation/changeRxns.m b/core/changeRxns.m → manipulation/changeRxns.m
diff --git a/io/closeModel.m → manipulation/closeModel.m b/io/closeModel.m → manipulation/closeModel.m
diff --git a/core/contractModel.m → manipulation/contractModel.m b/core/contractModel.m → manipulation/contractModel.m
diff --git a/core/convertToIrrev.m → manipulation/convertToIrrev.m b/core/convertToIrrev.m → manipulation/convertToIrrev.m
diff --git a/core/copyToComps.m → manipulation/copyToComps.m b/core/copyToComps.m → manipulation/copyToComps.m
diff --git a/core/deleteUnusedGenes.m → manipulation/deleteUnusedGenes.m b/core/deleteUnusedGenes.m → manipulation/deleteUnusedGenes.m
diff --git a/core/expandModel.m → manipulation/expandModel.m b/core/expandModel.m → manipulation/expandModel.m
diff --git a/core/findDuplicateRxns.m → manipulation/findDuplicateRxns.m b/core/findDuplicateRxns.m → manipulation/findDuplicateRxns.m
diff --git a/core/generateNewIds.m → manipulation/generateNewIds.m b/core/generateNewIds.m → manipulation/generateNewIds.m
diff --git a/core/mergeCompartments.m → manipulation/mergeCompartments.m b/core/mergeCompartments.m → manipulation/mergeCompartments.m
diff --git a/core/mergeModels.m → manipulation/mergeModels.m b/core/mergeModels.m → manipulation/mergeModels.m
diff --git a/core/permuteModel.m → manipulation/permuteModel.m b/core/permuteModel.m → manipulation/permuteModel.m
diff --git a/core/removeBadRxns.m → manipulation/removeBadRxns.m b/core/removeBadRxns.m → manipulation/removeBadRxns.m
diff --git a/core/removeGenes.m → manipulation/removeGenes.m b/core/removeGenes.m → manipulation/removeGenes.m
diff --git a/core/removeMets.m → manipulation/removeMets.m b/core/removeMets.m → manipulation/removeMets.m
diff --git a/core/removeReactions.m → manipulation/removeReactions.m b/core/removeReactions.m → manipulation/removeReactions.m
diff --git a/core/replaceMets.m → manipulation/replaceMets.m b/core/replaceMets.m → manipulation/replaceMets.m
diff --git a/core/setExchangeBounds.m → manipulation/setExchangeBounds.m b/core/setExchangeBounds.m → manipulation/setExchangeBounds.m
diff --git a/core/setParam.m → manipulation/setParam.m b/core/setParam.m → manipulation/setParam.m
diff --git a/core/simplifyModel.m → manipulation/simplifyModel.m b/core/simplifyModel.m → manipulation/simplifyModel.m
diff --git a/io/sortIdentifiers.m → manipulation/sortIdentifiers.m b/io/sortIdentifiers.m → manipulation/sortIdentifiers.m
diff --git a/core/sortModel.m → manipulation/sortModel.m b/core/sortModel.m → manipulation/sortModel.m
diff --git a/core/standardizeGrRules.m → manipulation/standardizeGrRules.m b/core/standardizeGrRules.m → manipulation/standardizeGrRules.m
diff --git a/hpa/parseHPA.m → omics/parseHPA.m b/hpa/parseHPA.m → omics/parseHPA.m
diff --git a/hpa/parseHPArna.m → omics/parseHPArna.m b/hpa/parseHPArna.m → omics/parseHPArna.m
diff --git a/hpa/scoreModel.m → omics/scoreModel.m b/hpa/scoreModel.m → omics/scoreModel.m
diff --git a/core/buildEquation.m → queries/buildEquation.m b/core/buildEquation.m → queries/buildEquation.m
diff --git a/core/checkModelStruct.m → queries/checkModelStruct.m b/core/checkModelStruct.m → queries/checkModelStruct.m
diff --git a/core/constructEquations.m → queries/constructEquations.m b/core/constructEquations.m → queries/constructEquations.m
diff --git a/core/constructS.m → queries/constructS.m b/core/constructS.m → queries/constructS.m
diff --git a/core/getAllRxnsFromGenes.m → queries/getAllRxnsFromGenes.m b/core/getAllRxnsFromGenes.m → queries/getAllRxnsFromGenes.m
diff --git a/core/getElementalBalance.m → queries/getElementalBalance.m b/core/getElementalBalance.m → queries/getElementalBalance.m
diff --git a/core/getExchangeRxns.m → queries/getExchangeRxns.m b/core/getExchangeRxns.m → queries/getExchangeRxns.m
diff --git a/core/getGenesFromGrRules.m → queries/getGenesFromGrRules.m b/core/getGenesFromGrRules.m → queries/getGenesFromGrRules.m
diff --git a/core/getIndexes.m → queries/getIndexes.m b/core/getIndexes.m → queries/getIndexes.m
diff --git a/core/getMetsInComp.m → queries/getMetsInComp.m b/core/getMetsInComp.m → queries/getMetsInComp.m
diff --git a/core/getRxnsInComp.m → queries/getRxnsInComp.m b/core/getRxnsInComp.m → queries/getRxnsInComp.m
diff --git a/core/getTransportRxns.m → queries/getTransportRxns.m b/core/getTransportRxns.m → queries/getTransportRxns.m
diff --git a/core/parseFormulas.m → queries/parseFormulas.m b/core/parseFormulas.m → queries/parseFormulas.m
diff --git a/core/parseRxnEqu.m → queries/parseRxnEqu.m b/core/parseRxnEqu.m → queries/parseRxnEqu.m
diff --git a/core/printFluxes.m → queries/printFluxes.m b/core/printFluxes.m → queries/printFluxes.m
diff --git a/core/printModel.m → queries/printModel.m b/core/printModel.m → queries/printModel.m
diff --git a/core/printModelStats.m → queries/printModelStats.m b/core/printModelStats.m → queries/printModelStats.m
diff --git a/external/combineMetaCycKEGGModels.m → reconstruction/combineMetaCycKEGGModels.m b/external/combineMetaCycKEGGModels.m → reconstruction/combineMetaCycKEGGModels.m
diff --git a/core/guessComposition.m → reconstruction/guessComposition.m b/core/guessComposition.m → reconstruction/guessComposition.m
diff --git a/external/getBlast.m → reconstruction/homology/getBlast.m b/external/getBlast.m → reconstruction/homology/getBlast.m
diff --git a/external/getBlastFromExcel.m → reconstruction/homology/getBlastFromExcel.m b/external/getBlastFromExcel.m → reconstruction/homology/getBlastFromExcel.m
diff --git a/external/getDiamond.m → reconstruction/homology/getDiamond.m b/external/getDiamond.m → reconstruction/homology/getDiamond.m
diff --git a/core/getModelFromHomology.m → ...struction/homology/getModelFromHomology.m b/core/getModelFromHomology.m → ...struction/homology/getModelFromHomology.m
diff --git a/external/makeFakeBlastStructure.m → ...ruction/homology/makeFakeBlastStructure.m b/external/makeFakeBlastStructure.m → ...ruction/homology/makeFakeBlastStructure.m
diff --git a/external/kegg/constructMultiFasta.m → reconstruction/kegg/constructMultiFasta.m b/external/kegg/constructMultiFasta.m → reconstruction/kegg/constructMultiFasta.m
diff --git a/external/kegg/getGenesFromKEGG.m → reconstruction/kegg/getGenesFromKEGG.m b/external/kegg/getGenesFromKEGG.m → reconstruction/kegg/getGenesFromKEGG.m
@@ -70,7 +70,7 @@
 end
 
 ravenPath=findRAVENroot();
-genesFile=fullfile(ravenPath,'external','kegg','keggGenes.mat');
+genesFile=fullfile(ravenPath,'reconstruction','kegg','keggGenes.mat');
 if ~exist(genesFile, 'file')
     try
         downloadKEGGgenes();
@@ -284,7 +284,7 @@
 
 %First check if the reactions have already been parsed
 ravenPath=findRAVENroot;
-rxnsFile=fullfile(ravenPath,'external','kegg','keggRxns.mat');
+rxnsFile=fullfile(ravenPath,'reconstruction','kegg','keggRxns.mat');
 if exist(rxnsFile, 'file')
     fprintf(['NOTE: Importing KEGG ORTHOLOGY list from ' strrep(rxnsFile,'\','/') '.\n']);
     load(rxnsFile,'model');
@@ -367,7 +367,7 @@ function downloadKEGGgenes()
 releaseTag = 'v2.11.1';
 
 archiveName = 'keggGenes.zip';
-targetDir   = fullfile(findRAVENroot(),'external','kegg');
+targetDir   = fullfile(findRAVENroot(),'reconstruction','kegg');
 targetFile  = fullfile(targetDir,'keggGenes.mat');
 url         = ['https://github.com/SysBioChalmers/RAVEN/releases/download/',...
                releaseTag,'/',archiveName];

diff --git a/external/kegg/getKEGGModelForOrganism.m → ...nstruction/kegg/getKEGGModelForOrganism.m b/external/kegg/getKEGGModelForOrganism.m → ...nstruction/kegg/getKEGGModelForOrganism.m
@@ -440,7 +440,7 @@
 %First remove all reactions without genes
 if keepSpontaneous==true
     fprintf('Removing non-spontaneous reactions without GPR rules... ');
-    load(fullfile(ravenPath,'external','kegg','keggRxns.mat'),'isSpontaneous');
+    load(fullfile(ravenPath,'reconstruction','kegg','keggRxns.mat'),'isSpontaneous');
     I=~any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous);
     spontRxnsWithGenes=model.rxns(any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous));
 else

diff --git a/external/kegg/getMetsFromKEGG.m → reconstruction/kegg/getMetsFromKEGG.m b/external/kegg/getMetsFromKEGG.m → reconstruction/kegg/getMetsFromKEGG.m
@@ -69,7 +69,7 @@
 end
 
 ravenPath=findRAVENroot();
-metsFile=fullfile(ravenPath,'external','kegg','keggMets.mat');
+metsFile=fullfile(ravenPath,'reconstruction','kegg','keggMets.mat');
 if exist(metsFile, 'file')
     fprintf(['Importing KEGG metabolites from ' strrep(metsFile,'\','/') '... ']);
     load(metsFile);

diff --git a/external/kegg/getModelFromKEGG.m → reconstruction/kegg/getModelFromKEGG.m b/external/kegg/getModelFromKEGG.m → reconstruction/kegg/getModelFromKEGG.m
@@ -47,7 +47,7 @@
 ravenPath=findRAVENroot();
 
 if nargin<1
-    keggPath=fullfile(ravenPath,'external','kegg');
+    keggPath=fullfile(ravenPath,'reconstruction','kegg');
 else
     keggPath=char(keggPath);
 end
@@ -64,7 +64,7 @@
     keepGeneral=false;
 end
 
-modelFile=fullfile(ravenPath,'external','kegg','keggModel.mat');
+modelFile=fullfile(ravenPath,'reconstruction','kegg','keggModel.mat');
 if exist(modelFile, 'file') && isNewestFile(ravenPath)
     fprintf(['Importing the global KEGG model from ' strrep(modelFile,'\','/') '... ']);
     load(modelFile);
@@ -267,10 +267,10 @@
 function output = isNewestFile(ravenPath)
 %The ad hoc function, which checks whether keggModel.mat is the more
 %recently modified than keggRxns.mat, keggGenes.mat and keggRxns.mat
-modelFile=fullfile(ravenPath,'external','kegg','keggModel.mat');
-rxnsFile=fullfile(ravenPath,'external','kegg','keggRxns.mat');
-genesFile=fullfile(ravenPath,'external','kegg','keggGenes.mat');
-metsFile=fullfile(ravenPath,'external','kegg','keggMets.mat');
+modelFile=fullfile(ravenPath,'reconstruction','kegg','keggModel.mat');
+rxnsFile=fullfile(ravenPath,'reconstruction','kegg','keggRxns.mat');
+genesFile=fullfile(ravenPath,'reconstruction','kegg','keggGenes.mat');
+metsFile=fullfile(ravenPath,'reconstruction','kegg','keggMets.mat');
 if (getFileTime(modelFile)>getFileTime(rxnsFile))&&...
         (getFileTime(modelFile)>getFileTime(genesFile))&&...
         (getFileTime(modelFile)>getFileTime(metsFile))

diff --git a/external/kegg/getPhylDist.m → reconstruction/kegg/getPhylDist.m b/external/kegg/getPhylDist.m → reconstruction/kegg/getPhylDist.m
@@ -32,7 +32,7 @@
 %Check if the reactions have been parsed before and saved. If so, load the
 %model
 ravenPath=findRAVENroot();
-distFile=fullfile(ravenPath,'external','kegg','keggPhylDist.mat');
+distFile=fullfile(ravenPath,'reconstruction','kegg','keggPhylDist.mat');
 if exist(distFile, 'file')
     fprintf(['Importing the KEGG phylogenetic distance matrix from ' strrep(distFile,'\','/') '... ']);
     load(distFile);

diff --git a/external/kegg/getRxnsFromKEGG.m → reconstruction/kegg/getRxnsFromKEGG.m b/external/kegg/getRxnsFromKEGG.m → reconstruction/kegg/getRxnsFromKEGG.m
@@ -71,14 +71,14 @@
 ravenPath=findRAVENroot();
 
 if nargin<1
-    keggPath=fullfile(ravenPath,'external','kegg');
+    keggPath=fullfile(ravenPath,'reconstruction','kegg');
 else
     keggPath=char(keggPath);
 end
 
 %Check if the reactions have been parsed before and saved. If so, load the
 %model
-rxnsFile=fullfile(ravenPath,'external','kegg','keggRxns.mat');
+rxnsFile=fullfile(ravenPath,'reconstruction','kegg','keggRxns.mat');
 if exist(rxnsFile, 'file')
     fprintf(['Importing KEGG reactions from ' strrep(rxnsFile,'\','/') '... ']);
     load(rxnsFile);

diff --git a/external/kegg/getWSLpath.m → reconstruction/kegg/getWSLpath.m b/external/kegg/getWSLpath.m → reconstruction/kegg/getWSLpath.m
diff --git a/external/kegg/keggMets.mat → reconstruction/kegg/keggMets.mat b/external/kegg/keggMets.mat → reconstruction/kegg/keggMets.mat
diff --git a/external/kegg/keggPhylDist.mat → reconstruction/kegg/keggPhylDist.mat b/external/kegg/keggPhylDist.mat → reconstruction/kegg/keggPhylDist.mat
diff --git a/external/kegg/keggRxns.mat → reconstruction/kegg/keggRxns.mat b/external/kegg/keggRxns.mat → reconstruction/kegg/keggRxns.mat
diff --git a/external/metacyc/addSpontaneousRxns.m → reconstruction/metacyc/addSpontaneousRxns.m b/external/metacyc/addSpontaneousRxns.m → reconstruction/metacyc/addSpontaneousRxns.m
diff --git a/external/metacyc/getEnzymesFromMetaCyc.m → ...struction/metacyc/getEnzymesFromMetaCyc.m b/external/metacyc/getEnzymesFromMetaCyc.m → ...struction/metacyc/getEnzymesFromMetaCyc.m
@@ -60,7 +60,7 @@
 
 if nargin<1
     ravenPath=findRAVENroot();
-    metacycPath=fullfile(ravenPath,'external','metacyc');
+    metacycPath=fullfile(ravenPath,'reconstruction','metacyc');
 else
     metacycPath=char(metacycPath);
 end

diff --git a/...rnal/metacyc/getMetaCycModelForOrganism.m → ...tion/metacyc/getMetaCycModelForOrganism.m b/...rnal/metacyc/getMetaCycModelForOrganism.m → ...tion/metacyc/getMetaCycModelForOrganism.m
@@ -100,9 +100,9 @@
 %Generate blast strcture by either DIAMOND or BLASTP
 if isempty(metacycBlastStruct)
     if useDiamond
-        blastStruc=getDiamond(organismID,fastaFile,{'MetaCyc'},fullfile(ravenPath,'external','metacyc','protseq.fsa'));
+        blastStruc=getDiamond(organismID,fastaFile,{'MetaCyc'},fullfile(ravenPath,'reconstruction','metacyc','protseq.fsa'));
     else
-        blastStruc=getBlast(organismID,fastaFile,{'MetaCyc'},fullfile(ravenPath,'external','metacyc','protseq.fsa'));
+        blastStruc=getBlast(organismID,fastaFile,{'MetaCyc'},fullfile(ravenPath,'reconstruction','metacyc','protseq.fsa'));
     end
     %Only look the query
     blastStructure=blastStruc(2);

diff --git a/external/metacyc/getMetsFromMetaCyc.m → reconstruction/metacyc/getMetsFromMetaCyc.m b/external/metacyc/getMetsFromMetaCyc.m → reconstruction/metacyc/getMetsFromMetaCyc.m
@@ -59,7 +59,7 @@
 % the model.
 if nargin<1
     ravenPath=findRAVENroot();
-    metacycPath=fullfile(ravenPath,'external','metacyc');
+    metacycPath=fullfile(ravenPath,'reconstruction','metacyc');
 else
     metacycPath=char(metacycPath);
 end

diff --git a/external/metacyc/getModelFromMetaCyc.m → reconstruction/metacyc/getModelFromMetaCyc.m b/external/metacyc/getModelFromMetaCyc.m → reconstruction/metacyc/getModelFromMetaCyc.m
@@ -35,7 +35,7 @@
 
 if nargin<1
     ravenPath=findRAVENroot();
-    metacycPath=fullfile(ravenPath,'external','metacyc');
+    metacycPath=fullfile(ravenPath,'reconstruction','metacyc');
 else
     metacycPath=char(metacycPath);
 end

diff --git a/external/metacyc/getRxnsFromMetaCyc.m → reconstruction/metacyc/getRxnsFromMetaCyc.m b/external/metacyc/getRxnsFromMetaCyc.m → reconstruction/metacyc/getRxnsFromMetaCyc.m
@@ -70,7 +70,7 @@
 % A line that contains only '//' separates each object.
 if nargin<1
     ravenPath=findRAVENroot();
-    metacycPath=fullfile(ravenPath,'external','metacyc');
+    metacycPath=fullfile(ravenPath,'reconstruction','metacyc');
 else
     metacycPath=char(metacycPath);
 end

diff --git a/external/metacyc/linkMetaCycKEGGRxns.m → reconstruction/metacyc/linkMetaCycKEGGRxns.m b/external/metacyc/linkMetaCycKEGGRxns.m → reconstruction/metacyc/linkMetaCycKEGGRxns.m
@@ -99,7 +99,7 @@
 
 %Get the MetaCyc path and update the metaCycRxns.mat
 ravenPath=findRAVENroot();
-rxnsFile=fullfile(ravenPath,'external','metacyc','metaCycRxns.mat');
+rxnsFile=fullfile(ravenPath,'reconstruction','metacyc','metaCycRxns.mat');
 save(rxnsFile,'metaCycRxns','rxnLinks','TRANSPORT','UNBALANCED','UNDETERMINED','isSpontaneous');
 fprintf(['Reaction associations between MetaCyc and KEGG have been successfully updated!\n\n']);
 

diff --git a/external/metacyc/metaCycEnzymes.mat → reconstruction/metacyc/metaCycEnzymes.mat b/external/metacyc/metaCycEnzymes.mat → reconstruction/metacyc/metaCycEnzymes.mat
diff --git a/external/metacyc/metaCycMets.mat → reconstruction/metacyc/metaCycMets.mat b/external/metacyc/metaCycMets.mat → reconstruction/metacyc/metaCycMets.mat
diff --git a/external/metacyc/metaCycRxns.mat → reconstruction/metacyc/metaCycRxns.mat b/external/metacyc/metaCycRxns.mat → reconstruction/metacyc/metaCycRxns.mat
diff --git a/external/metacyc/protseq.fsa → reconstruction/metacyc/protseq.fsa b/external/metacyc/protseq.fsa → reconstruction/metacyc/protseq.fsa
diff --git a/core/checkTasks.m → tasks/checkTasks.m b/core/checkTasks.m → tasks/checkTasks.m
diff --git a/core/parseTaskList.m → tasks/parseTaskList.m b/core/parseTaskList.m → tasks/parseTaskList.m
diff --git a/core/convertCharArray.m → utils/convertCharArray.m b/core/convertCharArray.m → utils/convertCharArray.m
diff --git a/core/dispEM.m → utils/dispEM.m b/core/dispEM.m → utils/dispEM.m
diff --git a/core/parallelPoolRAVEN.m → utils/parallelPoolRAVEN.m b/core/parallelPoolRAVEN.m → utils/parallelPoolRAVEN.m
diff --git a/core/printOrange.m → utils/printOrange.m b/core/printOrange.m → utils/printOrange.m
diff --git a/pathway/colorPathway.m → visualization/colorPathway.m b/pathway/colorPathway.m → visualization/colorPathway.m
diff --git a/plotting/colorSubsystem.m → visualization/colorSubsystem.m b/plotting/colorSubsystem.m → visualization/colorSubsystem.m
diff --git a/plotting/drawMap.m → visualization/drawMap.m b/plotting/drawMap.m → visualization/drawMap.m
diff --git a/plotting/drawPathway.m → visualization/drawPathway.m b/plotting/drawPathway.m → visualization/drawPathway.m
diff --git a/plotting/getColorCodes.m → visualization/getColorCodes.m b/plotting/getColorCodes.m → visualization/getColorCodes.m
diff --git a/plotting/getObjectiveString.m → visualization/getObjectiveString.m b/plotting/getObjectiveString.m → visualization/getObjectiveString.m
diff --git a/pathway/getPathwayDimensions.m → visualization/getPathwayDimensions.m b/pathway/getPathwayDimensions.m → visualization/getPathwayDimensions.m
diff --git a/plotting/iMM904.xml → visualization/iMM904.xml b/plotting/iMM904.xml → visualization/iMM904.xml
diff --git a/pathway/mapPathwayRxnNames.m → visualization/mapPathwayRxnNames.m b/pathway/mapPathwayRxnNames.m → visualization/mapPathwayRxnNames.m
diff --git a/pathway/markPathwayWithExpression.m → visualization/markPathwayWithExpression.m b/pathway/markPathwayWithExpression.m → visualization/markPathwayWithExpression.m
diff --git a/pathway/markPathwayWithFluxes.m → visualization/markPathwayWithFluxes.m b/pathway/markPathwayWithFluxes.m → visualization/markPathwayWithFluxes.m
diff --git a/plotting/plotAdditionalInfo.m → visualization/plotAdditionalInfo.m b/plotting/plotAdditionalInfo.m → visualization/plotAdditionalInfo.m
diff --git a/plotting/plotLabels.m → visualization/plotLabels.m b/plotting/plotLabels.m → visualization/plotLabels.m
diff --git a/plotting/setColorToMapRxns.m → visualization/setColorToMapRxns.m b/plotting/setColorToMapRxns.m → visualization/setColorToMapRxns.m
diff --git a/plotting/setOmicDataToRxns.m → visualization/setOmicDataToRxns.m b/plotting/setOmicDataToRxns.m → visualization/setOmicDataToRxns.m
diff --git a/plotting/setTitle.m → visualization/setTitle.m b/plotting/setTitle.m → visualization/setTitle.m
diff --git a/pathway/trimPathway.m → visualization/trimPathway.m b/pathway/trimPathway.m → visualization/trimPathway.m
diff --git a/plotting/yeastMap1.0c.xml → visualization/yeastMap1.0c.xml b/plotting/yeastMap1.0c.xml → visualization/yeastMap1.0c.xml