chore: change folder names

following #232
SysBioChalmers · Jun 25, 2020 · 0afd1c2 · 0afd1c2
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diff --git a/ComplementaryScripts/__init__.py → code/__init__.py b/ComplementaryScripts/__init__.py → code/__init__.py
diff --git a/ComplementaryScripts/deprecated/README.md → code/deprecated/README.md b/ComplementaryScripts/deprecated/README.md → code/deprecated/README.md
diff --git a/...recated/modelCuration/addiSce926changes.m → ...recated/modelCuration/addiSce926changes.m b/...recated/modelCuration/addiSce926changes.m → ...recated/modelCuration/addiSce926changes.m
diff --git a/...deprecated/modelCuration/fixBiomassComp.m → ...deprecated/modelCuration/fixBiomassComp.m b/...deprecated/modelCuration/fixBiomassComp.m → ...deprecated/modelCuration/fixBiomassComp.m
diff --git a/...ted/modelCuration/makeFormulasCompliant.m → ...ted/modelCuration/makeFormulasCompliant.m b/...ted/modelCuration/makeFormulasCompliant.m → ...ted/modelCuration/makeFormulasCompliant.m
diff --git a/...precated/modelCuration/modelCorrections.m → ...precated/modelCuration/modelCorrections.m b/...precated/modelCuration/modelCorrections.m → ...precated/modelCuration/modelCorrections.m
diff --git a/...ecated/modelCuration/takeOutFromFormula.m → ...ecated/modelCuration/takeOutFromFormula.m b/...ecated/modelCuration/takeOutFromFormula.m → ...ecated/modelCuration/takeOutFromFormula.m
diff --git a/...d/modelCuration/updateMetaboliteFormula.m → ...d/modelCuration/updateMetaboliteFormula.m b/...d/modelCuration/updateMetaboliteFormula.m → ...d/modelCuration/updateMetaboliteFormula.m
diff --git a/...ts/deprecated/otherChanges/addSLIMErxns.m → code/deprecated/otherChanges/addSLIMErxns.m b/...ts/deprecated/otherChanges/addSLIMErxns.m → code/deprecated/otherChanges/addSLIMErxns.m
diff --git a/.../deprecated/otherChanges/clusterBiomass.m → .../deprecated/otherChanges/clusterBiomass.m b/.../deprecated/otherChanges/clusterBiomass.m → .../deprecated/otherChanges/clusterBiomass.m
diff --git a/...deprecated/otherChanges/convertYmn2FBC2.m → ...deprecated/otherChanges/convertYmn2FBC2.m b/...deprecated/otherChanges/convertYmn2FBC2.m → ...deprecated/otherChanges/convertYmn2FBC2.m
diff --git a/ComplementaryScripts/increaseVersion.m → code/increaseVersion.m b/ComplementaryScripts/increaseVersion.m → code/increaseVersion.m
diff --git a/ComplementaryScripts/io.py → code/io.py b/ComplementaryScripts/io.py → code/io.py
diff --git a/ComplementaryScripts/loadYeastModel.m → code/loadYeastModel.m b/ComplementaryScripts/loadYeastModel.m → code/loadYeastModel.m
diff --git a/...pts/missingFields/BiGGidsCompliance.ipynb → code/missingFields/BiGGidsCompliance.ipynb b/...pts/missingFields/BiGGidsCompliance.ipynb → code/missingFields/BiGGidsCompliance.ipynb
diff --git a/...lementaryScripts/missingFields/GetMNXID.m → code/missingFields/GetMNXID.m b/...lementaryScripts/missingFields/GetMNXID.m → code/missingFields/GetMNXID.m
diff --git a/ComplementaryScripts/missingFields/README.md → code/missingFields/README.md b/ComplementaryScripts/missingFields/README.md → code/missingFields/README.md
diff --git a/...cripts/missingFields/addBiGGidentifiers.m → code/missingFields/addBiGGidentifiers.m b/...cripts/missingFields/addBiGGidentifiers.m → code/missingFields/addBiGGidentifiers.m
diff --git a/...ripts/missingFields/addConfidenceScores.m → code/missingFields/addConfidenceScores.m b/...ripts/missingFields/addConfidenceScores.m → code/missingFields/addConfidenceScores.m
diff --git a/...ntaryScripts/missingFields/addGeneNames.m → code/missingFields/addGeneNames.m b/...ntaryScripts/missingFields/addGeneNames.m → code/missingFields/addGeneNames.m
diff --git a/...entaryScripts/missingFields/addSBOterms.m → code/missingFields/addSBOterms.m b/...entaryScripts/missingFields/addSBOterms.m → code/missingFields/addSBOterms.m
diff --git a/...entaryScripts/missingFields/changeRules.m → code/missingFields/changeRules.m b/...entaryScripts/missingFields/changeRules.m → code/missingFields/changeRules.m
diff --git a/...aryScripts/missingFields/deleteRepeated.m → code/missingFields/deleteRepeated.m b/...aryScripts/missingFields/deleteRepeated.m → code/missingFields/deleteRepeated.m
diff --git a/...lementaryScripts/missingFields/findInDB.m → code/missingFields/findInDB.m b/...lementaryScripts/missingFields/findInDB.m → code/missingFields/findInDB.m
diff --git a/...taryScripts/missingFields/findSubSystem.m → code/missingFields/findSubSystem.m b/...taryScripts/missingFields/findSubSystem.m → code/missingFields/findSubSystem.m
diff --git a/...mentaryScripts/missingFields/getAllPath.m → code/missingFields/getAllPath.m b/...mentaryScripts/missingFields/getAllPath.m → code/missingFields/getAllPath.m
diff --git a/...yScripts/missingFields/getMissingFields.m → code/missingFields/getMissingFields.m b/...yScripts/missingFields/getMissingFields.m → code/missingFields/getMissingFields.m
diff --git a/...ryScripts/missingFields/mapIDsViaMNXref.m → code/missingFields/mapIDsViaMNXref.m b/...ryScripts/missingFields/mapIDsViaMNXref.m → code/missingFields/mapIDsViaMNXref.m
diff --git a/...cripts/modelCuration/CheckBalanceforSce.m → code/modelCuration/CheckBalanceforSce.m b/...cripts/modelCuration/CheckBalanceforSce.m → code/modelCuration/CheckBalanceforSce.m
diff --git a/...pts/modelCuration/CheckEnergyProduction.m → code/modelCuration/CheckEnergyProduction.m b/...pts/modelCuration/CheckEnergyProduction.m → code/modelCuration/CheckEnergyProduction.m
diff --git a/...ripts/modelCuration/MissingTransDeadEnd.m → code/modelCuration/MissingTransDeadEnd.m b/...ripts/modelCuration/MissingTransDeadEnd.m → code/modelCuration/MissingTransDeadEnd.m
diff --git a/ComplementaryScripts/modelCuration/README.md → code/modelCuration/README.md b/ComplementaryScripts/modelCuration/README.md → code/modelCuration/README.md
diff --git a/...aryScripts/modelCuration/SubstrateUsage.m → code/modelCuration/SubstrateUsage.m b/...aryScripts/modelCuration/SubstrateUsage.m → code/modelCuration/SubstrateUsage.m
diff --git a/...aryScripts/modelCuration/UpdateDBnewRxn.m → code/modelCuration/UpdateDBnewRxn.m b/...aryScripts/modelCuration/UpdateDBnewRxn.m → code/modelCuration/UpdateDBnewRxn.m
diff --git a/...Scripts/modelCuration/addBiologRxnToGEM.m → code/modelCuration/addBiologRxnToGEM.m b/...Scripts/modelCuration/addBiologRxnToGEM.m → code/modelCuration/addBiologRxnToGEM.m
diff --git a/...yScripts/modelCuration/addBiomassUpdate.m → code/modelCuration/addBiomassUpdate.m b/...yScripts/modelCuration/addBiomassUpdate.m → code/modelCuration/addBiomassUpdate.m
diff --git a/...ts/modelCuration/addDBNewGeneAnnotation.m → code/modelCuration/addDBNewGeneAnnotation.m b/...ts/modelCuration/addDBNewGeneAnnotation.m → code/modelCuration/addDBNewGeneAnnotation.m
diff --git a/...entaryScripts/modelCuration/addDBnewRxn.m → code/modelCuration/addDBnewRxn.m b/...entaryScripts/modelCuration/addDBnewRxn.m → code/modelCuration/addDBnewRxn.m
diff --git a/...pts/modelCuration/addGapfillingRxnToGEM.m → code/modelCuration/addGapfillingRxnToGEM.m b/...pts/modelCuration/addGapfillingRxnToGEM.m → code/modelCuration/addGapfillingRxnToGEM.m
diff --git a/...s/modelCuration/addMetabolomicsRxnToGEM.m → code/modelCuration/addMetabolomicsRxnToGEM.m b/...s/modelCuration/addMetabolomicsRxnToGEM.m → code/modelCuration/addMetabolomicsRxnToGEM.m
diff --git a/...aryScripts/modelCuration/addTransNewGPR.m → code/modelCuration/addTransNewGPR.m b/...aryScripts/modelCuration/addTransNewGPR.m → code/modelCuration/addTransNewGPR.m
diff --git a/...ementaryScripts/modelCuration/changerxn.m → code/modelCuration/changerxn.m b/...ementaryScripts/modelCuration/changerxn.m → code/modelCuration/changerxn.m
diff --git a/...ryScripts/modelCuration/checkMetBalance.m → code/modelCuration/checkMetBalance.m b/...ryScripts/modelCuration/checkMetBalance.m → code/modelCuration/checkMetBalance.m
diff --git a/...ryScripts/modelCuration/checkRxnBalance.m → code/modelCuration/checkRxnBalance.m b/...ryScripts/modelCuration/checkRxnBalance.m → code/modelCuration/checkRxnBalance.m
diff --git a/...ryScripts/modelCuration/checkSmatrixMNX.m → code/modelCuration/checkSmatrixMNX.m b/...ryScripts/modelCuration/checkSmatrixMNX.m → code/modelCuration/checkSmatrixMNX.m
diff --git a/...cripts/modelCuration/display_rxnMetInfo.m → code/modelCuration/display_rxnMetInfo.m b/...cripts/modelCuration/display_rxnMetInfo.m → code/modelCuration/display_rxnMetInfo.m
diff --git a/...taryScripts/modelCuration/downloadMNXdb.m → code/modelCuration/downloadMNXdb.m b/...taryScripts/modelCuration/downloadMNXdb.m → code/modelCuration/downloadMNXdb.m
diff --git a/...ementaryScripts/modelCuration/mapKEGGID.m → code/modelCuration/mapKEGGID.m b/...ementaryScripts/modelCuration/mapKEGGID.m → code/modelCuration/mapKEGGID.m
diff --git a/...ementaryScripts/modelCuration/mapMNXMID.m → code/modelCuration/mapMNXMID.m b/...ementaryScripts/modelCuration/mapMNXMID.m → code/modelCuration/mapMNXMID.m
diff --git a/...mentaryScripts/modelCuration/minimal_Y6.m → code/modelCuration/minimal_Y6.m b/...mentaryScripts/modelCuration/minimal_Y6.m → code/modelCuration/minimal_Y6.m
diff --git a/...Scripts/modelCuration/modMetsandSmatrix.m → code/modelCuration/modMetsandSmatrix.m b/...Scripts/modelCuration/modMetsandSmatrix.m → code/modelCuration/modMetsandSmatrix.m
diff --git a/...lementaryScripts/modelCuration/modifyID.m → code/modelCuration/modifyID.m b/...lementaryScripts/modelCuration/modifyID.m → code/modelCuration/modifyID.m
diff --git a/...odelCuration/updateMetaboliteAnnotation.m → ...odelCuration/updateMetaboliteAnnotation.m b/...odelCuration/updateMetaboliteAnnotation.m → ...odelCuration/updateMetaboliteAnnotation.m
diff --git a/ComplementaryScripts/modelTests/README.md → code/modelTests/README.md b/ComplementaryScripts/modelTests/README.md → code/modelTests/README.md
diff --git a/...ripts/modelTests/cobrapy-compliance.ipynb → code/modelTests/cobrapy-compliance.ipynb b/...ripts/modelTests/cobrapy-compliance.ipynb → code/modelTests/cobrapy-compliance.ipynb
diff --git a/...entaryScripts/modelTests/essentialGenes.m → code/modelTests/essentialGenes.m b/...entaryScripts/modelTests/essentialGenes.m → code/modelTests/essentialGenes.m
diff --git a/...ryScripts/modelTests/findDuplicatedRxns.m → code/modelTests/findDuplicatedRxns.m b/...ryScripts/modelTests/findDuplicatedRxns.m → code/modelTests/findDuplicatedRxns.m
diff --git a/ComplementaryScripts/modelTests/growth.m → code/modelTests/growth.m b/ComplementaryScripts/modelTests/growth.m → code/modelTests/growth.m
diff --git a/ComplementaryScripts/otherChanges/README.md → code/otherChanges/README.md b/ComplementaryScripts/otherChanges/README.md → code/otherChanges/README.md
diff --git a/...taryScripts/otherChanges/anaerobicModel.m → code/otherChanges/anaerobicModel.m b/...taryScripts/otherChanges/anaerobicModel.m → code/otherChanges/anaerobicModel.m
diff --git a/ComplementaryScripts/otherChanges/fitGAM.m → code/otherChanges/fitGAM.m b/ComplementaryScripts/otherChanges/fitGAM.m → code/otherChanges/fitGAM.m
diff --git a/...mentaryScripts/otherChanges/getNewIndex.m → code/otherChanges/getNewIndex.m b/...mentaryScripts/otherChanges/getNewIndex.m → code/otherChanges/getNewIndex.m
diff --git a/...ipts/otherChanges/rescalePseudoReaction.m → code/otherChanges/rescalePseudoReaction.m b/...ipts/otherChanges/rescalePseudoReaction.m → code/otherChanges/rescalePseudoReaction.m
diff --git a/...entaryScripts/otherChanges/scaleBioMass.m → code/otherChanges/scaleBioMass.m b/...entaryScripts/otherChanges/scaleBioMass.m → code/otherChanges/scaleBioMass.m
diff --git a/...ementaryScripts/otherChanges/sumBioMass.m → code/otherChanges/sumBioMass.m b/...ementaryScripts/otherChanges/sumBioMass.m → code/otherChanges/sumBioMass.m
diff --git a/ComplementaryScripts/saveYeastModel.m → code/saveYeastModel.m b/ComplementaryScripts/saveYeastModel.m → code/saveYeastModel.m
diff --git a/...ntaryData/databases/BiGGmetDictionary.csv → data/databases/BiGGmetDictionary.csv b/...ntaryData/databases/BiGGmetDictionary.csv → data/databases/BiGGmetDictionary.csv
diff --git a/...ta/databases/BiGGmetDictionary_newIDs.csv → data/databases/BiGGmetDictionary_newIDs.csv b/...ta/databases/BiGGmetDictionary_newIDs.csv → data/databases/BiGGmetDictionary_newIDs.csv
diff --git a/...ntaryData/databases/BiGGrxnDictionary.csv → data/databases/BiGGrxnDictionary.csv b/...ntaryData/databases/BiGGrxnDictionary.csv → data/databases/BiGGrxnDictionary.csv
diff --git a/...ta/databases/BiGGrxnDictionary_newIDs.csv → data/databases/BiGGrxnDictionary_newIDs.csv b/...ta/databases/BiGGrxnDictionary_newIDs.csv → data/databases/BiGGrxnDictionary_newIDs.csv
diff --git a/...aryData/databases/DBnewGeneAnnotation.tsv → data/databases/DBnewGeneAnnotation.tsv b/...aryData/databases/DBnewGeneAnnotation.tsv → data/databases/DBnewGeneAnnotation.tsv
diff --git a/ComplementaryData/databases/README.md → data/databases/README.md b/ComplementaryData/databases/README.md → data/databases/README.md
diff --git a/ComplementaryData/databases/SGDgeneNames.tsv → data/databases/SGDgeneNames.tsv b/ComplementaryData/databases/SGDgeneNames.tsv → data/databases/SGDgeneNames.tsv
diff --git a/...Data/databases/TransRxnGeneAnnotation.tsv → data/databases/TransRxnGeneAnnotation.tsv b/...Data/databases/TransRxnGeneAnnotation.tsv → data/databases/TransRxnGeneAnnotation.tsv
diff --git a/...a/databases/Yeast7.6MNXMetMappingList.tsv → data/databases/Yeast7.6MNXMetMappingList.tsv b/...a/databases/Yeast7.6MNXMetMappingList.tsv → data/databases/Yeast7.6MNXMetMappingList.tsv
diff --git a/...a/databases/Yeast7.6MNXRxnMappingList.tsv → data/databases/Yeast7.6MNXRxnMappingList.tsv b/...a/databases/Yeast7.6MNXRxnMappingList.tsv → data/databases/Yeast7.6MNXRxnMappingList.tsv
diff --git a/ComplementaryData/databases/kegg.tsv → data/databases/kegg.tsv b/ComplementaryData/databases/kegg.tsv → data/databases/kegg.tsv
diff --git a/...taryData/databases/lipidAbbreviations.csv → data/databases/lipidAbbreviations.csv b/...taryData/databases/lipidAbbreviations.csv → data/databases/lipidAbbreviations.csv
diff --git a/ComplementaryData/databases/swissprot.tsv → data/databases/swissprot.tsv b/ComplementaryData/databases/swissprot.tsv → data/databases/swissprot.tsv
diff --git a/...ata/modelCuration/Biolog_newRxnMatrix.tsv → data/modelCuration/Biolog_newRxnMatrix.tsv b/...ata/modelCuration/Biolog_newRxnMatrix.tsv → data/modelCuration/Biolog_newRxnMatrix.tsv
diff --git a/...elCuration/Biolog_newRxnMetAnnotation.tsv → ...elCuration/Biolog_newRxnMetAnnotation.tsv b/...elCuration/Biolog_newRxnMetAnnotation.tsv → ...elCuration/Biolog_newRxnMetAnnotation.tsv
diff --git a/...yData/modelCuration/Biolog_newRxnProp.tsv → data/modelCuration/Biolog_newRxnProp.tsv b/...yData/modelCuration/Biolog_newRxnProp.tsv → data/modelCuration/Biolog_newRxnProp.tsv
diff --git a/...ta/modelCuration/Biomass_newRxnMatrix.tsv → data/modelCuration/Biomass_newRxnMatrix.tsv b/...ta/modelCuration/Biomass_newRxnMatrix.tsv → data/modelCuration/Biomass_newRxnMatrix.tsv
diff --git a/...yData/modelCuration/Biomass_newRxnMet.tsv → data/modelCuration/Biomass_newRxnMet.tsv b/...yData/modelCuration/Biomass_newRxnMet.tsv → data/modelCuration/Biomass_newRxnMet.tsv
diff --git a/...Data/modelCuration/Biomass_newRxnProp.tsv → data/modelCuration/Biomass_newRxnProp.tsv b/...Data/modelCuration/Biomass_newRxnProp.tsv → data/modelCuration/Biomass_newRxnProp.tsv
diff --git a/...a/modelCuration/DBnewRxnIDmappinglist.tsv → data/modelCuration/DBnewRxnIDmappinglist.tsv b/...a/modelCuration/DBnewRxnIDmappinglist.tsv → data/modelCuration/DBnewRxnIDmappinglist.tsv
diff --git a/...a/modelCuration/DBnewRxnMetAnnotation.tsv → data/modelCuration/DBnewRxnMetAnnotation.tsv b/...a/modelCuration/DBnewRxnMetAnnotation.tsv → data/modelCuration/DBnewRxnMetAnnotation.tsv
diff --git a/...entaryData/modelCuration/DBnewRxnProp.tsv → data/modelCuration/DBnewRxnProp.tsv b/...entaryData/modelCuration/DBnewRxnProp.tsv → data/modelCuration/DBnewRxnProp.tsv
diff --git a/...aryData/modelCuration/DBnewrRxnMatrix.tsv → data/modelCuration/DBnewrRxnMatrix.tsv b/...aryData/modelCuration/DBnewrRxnMatrix.tsv → data/modelCuration/DBnewrRxnMatrix.tsv
diff --git a/.../modelCuration/GapfillingnewRxnMatrix.tsv → .../modelCuration/GapfillingnewRxnMatrix.tsv b/.../modelCuration/GapfillingnewRxnMatrix.tsv → .../modelCuration/GapfillingnewRxnMatrix.tsv
diff --git a/...ta/modelCuration/GapfillingnewRxnProp.tsv → data/modelCuration/GapfillingnewRxnProp.tsv b/...ta/modelCuration/GapfillingnewRxnProp.tsv → data/modelCuration/GapfillingnewRxnProp.tsv
diff --git a/...delCuration/Metabolomics_newRxnMatrix.tsv → ...delCuration/Metabolomics_newRxnMatrix.tsv b/...delCuration/Metabolomics_newRxnMatrix.tsv → ...delCuration/Metabolomics_newRxnMatrix.tsv
diff --git a/...tion/Metabolomics_newRxnMetAnnotation.tsv → ...tion/Metabolomics_newRxnMetAnnotation.tsv b/...tion/Metabolomics_newRxnMetAnnotation.tsv → ...tion/Metabolomics_newRxnMetAnnotation.tsv
diff --git a/...modelCuration/Metabolomics_newRxnProp.tsv → ...modelCuration/Metabolomics_newRxnProp.tsv b/...modelCuration/Metabolomics_newRxnProp.tsv → ...modelCuration/Metabolomics_newRxnProp.tsv
diff --git a/...delCuration/Missingmetaboliteformulas.tsv → ...delCuration/Missingmetaboliteformulas.tsv b/...delCuration/Missingmetaboliteformulas.tsv → ...delCuration/Missingmetaboliteformulas.tsv
diff --git a/ComplementaryData/modelCuration/README.md → data/modelCuration/README.md b/ComplementaryData/modelCuration/README.md → data/modelCuration/README.md
diff --git a/...taryData/modelCuration/TransRxnNewGPR.tsv → data/modelCuration/TransRxnNewGPR.tsv b/...taryData/modelCuration/TransRxnNewGPR.tsv → data/modelCuration/TransRxnNewGPR.tsv
diff --git a/...taryData/modelCuration/databasenewGPR.tsv → data/modelCuration/databasenewGPR.tsv b/...taryData/modelCuration/databasenewGPR.tsv → data/modelCuration/databasenewGPR.tsv
diff --git a/...modelCuration/iSce926curatedGeneRules.tsv → ...modelCuration/iSce926curatedGeneRules.tsv b/...modelCuration/iSce926curatedGeneRules.tsv → ...modelCuration/iSce926curatedGeneRules.tsv
diff --git a/...aryData/modelCuration/iSce926newGenes.tsv → data/modelCuration/iSce926newGenes.tsv b/...aryData/modelCuration/iSce926newGenes.tsv → data/modelCuration/iSce926newGenes.tsv
diff --git a/...elCuration/metabolite_manual_curation.tsv → ...elCuration/metabolite_manual_curation.tsv b/...elCuration/metabolite_manual_curation.tsv → ...elCuration/metabolite_manual_curation.tsv
diff --git a/...yData/modelCuration/modMetsandSmatrix.tsv → data/modelCuration/modMetsandSmatrix.tsv b/...yData/modelCuration/modMetsandSmatrix.tsv → data/modelCuration/modMetsandSmatrix.tsv
diff --git a/ComplementaryData/modelCuration/modifyID.tsv → data/modelCuration/modifyID.tsv b/ComplementaryData/modelCuration/modifyID.tsv → data/modelCuration/modifyID.tsv
diff --git a/...ntaryData/physiology/Biolog_Substrate.tsv → data/physiology/Biolog_Substrate.tsv b/...ntaryData/physiology/Biolog_Substrate.tsv → data/physiology/Biolog_Substrate.tsv
diff --git a/ComplementaryData/physiology/README.md → data/physiology/README.md b/ComplementaryData/physiology/README.md → data/physiology/README.md
diff --git a/...ology/biomassComposition_Cofactor_Ion.tsv → ...ology/biomassComposition_Cofactor_Ion.tsv b/...ology/biomassComposition_Cofactor_Ion.tsv → ...ology/biomassComposition_Cofactor_Ion.tsv
diff --git a/...iology/biomassComposition_Forster2003.tsv → ...iology/biomassComposition_Forster2003.tsv b/...iology/biomassComposition_Forster2003.tsv → ...iology/biomassComposition_Forster2003.tsv
diff --git a/...iology/biomassComposition_Lahtvee2017.tsv → ...iology/biomassComposition_Lahtvee2017.tsv b/...iology/biomassComposition_Lahtvee2017.tsv → ...iology/biomassComposition_Lahtvee2017.tsv
diff --git a/...a/physiology/chemostatData_Tobias2013.tsv → data/physiology/chemostatData_Tobias2013.tsv b/...a/physiology/chemostatData_Tobias2013.tsv → data/physiology/chemostatData_Tobias2013.tsv
diff --git a/.../physiology/chemostatData_VanHoek1998.tsv → .../physiology/chemostatData_VanHoek1998.tsv b/.../physiology/chemostatData_VanHoek1998.tsv → .../physiology/chemostatData_VanHoek1998.tsv
diff --git a/ModelFiles/boundaryMets.txt → model/boundaryMets.txt b/ModelFiles/boundaryMets.txt → model/boundaryMets.txt
diff --git a/ModelFiles/dependencies.txt → model/dependencies.txt b/ModelFiles/dependencies.txt → model/dependencies.txt
diff --git a/ModelFiles/txt/yeastGEM.txt → model/txt/yeastGEM.txt b/ModelFiles/txt/yeastGEM.txt → model/txt/yeastGEM.txt
diff --git a/ModelFiles/xml/yeastGEM.xml → model/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml → model/xml/yeastGEM.xml
diff --git a/ModelFiles/yml/yeastGEM.yml → model/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml → model/yml/yeastGEM.yml