diff --git a/code/DepMapGeneEss/PrepDepMapData.m b/code/DepMapGeneEss/PrepDepMapData.m
index 36777950..62831a35 100644
--- a/code/DepMapGeneEss/PrepDepMapData.m
+++ b/code/DepMapGeneEss/PrepDepMapData.m
@@ -37,7 +37,7 @@
 save('data/arrayDataDepMap.mat','arrayDataDepMap');
 
 %Generate ftINIT prepData - only needs to be done once. Can take up to an hour to run
-model = importYaml('../../model/Human-GEM.yml');
+model = readYAMLmodel('../../model/Human-GEM.yml');
 [model.grRules, skipped] = simplifyGrRules(model.grRules, true);%takes a few minutes to run
 prepData = prepHumanModelForftINIT(model, true, '../../data/metabolicTasks/metabolicTasks_Essential.txt', '../../model/reactions.tsv');
 save('data/prepDataGeneSymbols.mat', 'prepData')
diff --git a/code/io/readYAMLmodel_HumanGEM.m b/code/io/readYAMLmodel_HumanGEM.m
deleted file mode 100644
index 27129f6f..00000000
--- a/code/io/readYAMLmodel_HumanGEM.m
+++ /dev/null
@@ -1,679 +0,0 @@
-function model=readYAMLmodel(fileName, verbose)
-% readYAMLmodel
-%   Reads a yaml file matching (roughly) the cobrapy yaml structure
-%
-%   Input:
-%   fileName    a model file in yaml file format. A dialog window will open
-%               if no file name is specified.
-%   verbose     set as true to monitor progress (optional, default false)
-%
-%   Output:
-%   model       a model structure
-%
-% Usage: model = readYAMLmodel(fileName, verbose)
-if nargin<1 || isempty(fileName)
-    [fileName, pathName] = uigetfile({'*.yml;*.yaml'}, 'Please select the model file');
-    if fileName == 0
-        error('You should select a model file')
-    else
-        fileName = fullfile(pathName,fileName);
-    end
-end
-if nargin < 2
-    verbose = false;
-end
-
-if ~isfile(fileName)
-    error('Yaml file %s cannot be found', string(fileName));
-end
-
-if verLessThan('matlab','9.9') %readlines introduced 2020b
-    fid=fopen(fileName);
-    line_raw=cell(1000000,1);
-    i=1;
-    while ~feof(fid)
-        line_raw{i}=fgetl(fid);
-        i=i+1;
-    end
-    line_raw(i:end)=[];
-    line_raw=string(line_raw);
-    fclose(fid);
-else
-    line_raw=readlines(fileName);
-end
-% If entry is broken of multiple lines, concatenate. Assumes at least 6
-% leading spaces to avoid metaData to be concatenated.
-newLine=regexp(line_raw,'^ {6,}([\w\(\)].*)','tokenExtents');
-brokenLine=find(~cellfun('isempty',newLine));
-for i=1:numel(brokenLine)
-    extraLine = char(line_raw(brokenLine(i)));
-    extraLine = extraLine(newLine{brokenLine(i)}{1}(1):end);
-    line_raw{brokenLine(i)-1} = strjoin({line_raw{brokenLine(i)-1},extraLine},' ');
-end
-line_raw(brokenLine)=[];
-
-line_key = regexprep(line_raw,'^ *-? ([^:]+)(:)($| .*)','$1');
-line_key = regexprep(line_key,'(.*!!omap)|(---)|( {4,}.*)','');
-
-line_value = regexprep(line_raw, '.*:$','');
-line_value = regexprep(line_value, '[^":]+: "?(.+)"?$','$1');
-line_value = regexprep(line_value, '(")|(^ {4,}- )','');
-
-modelFields =   {'id',char();...
-               'name',char();...
-        'description',char();...
-            'version',char();...
-               'date',char();...
-         'annotation',struct();...
-               'rxns',{};...
-           'rxnNames',{};...
-               'mets',{};...
-           'metNames',{};...
-                  'S',sparse([]);...
-                 'lb',{};... %Changed to double in the end.
-                 'ub',{};... %Changed to double in the end.
-                'rev',{};... %Changed to double in the end.
-                  'c',[];...
-                  'b',cell(0,0);... %Changed to double in the end.
-              'genes',cell(0,0);...
-            'grRules',cell(0,0);...
-         'rxnGeneMat',sparse([]);...
-           'rxnComps',cell(0,0);... %Changed to double in the end.
-         'subSystems',cell(0,0);...
-            'eccodes',cell(0,0);...
-         'rxnMiriams',cell(0,0);...
-          'rxnDeltaG',{};... %Changed to double in the end.
-           'rxnNotes',cell(0,0);...
-      'rxnReferences',cell(0,0);...
-'rxnConfidenceScores',cell(0,0);...
-           'metComps',cell(0,0);... %Changed to double in the end.
-             'inchis',cell(0,0);...
-          'metSmiles',cell(0,0);...
-        'metFormulas',cell(0,0);...
-         'metMiriams',cell(0,0);...
-          'metDeltaG',{};... %Changed to double in the end.
-         'metCharges',cell(0,0);... %Changed to double in the end.
-           'metNotes',cell(0,0);...
-              'comps',cell(0,0);...
-          'compNames',cell(0,0);...
-        'compOutside',cell(0,0);...
-          'geneComps',cell(0,0);... %Changed to double in the end.
-        'geneMiriams',cell(0,0);...
-     'geneShortNames',cell(0,0);...
-       'proteins',cell(0,0);...
-      'unconstrained',cell(0,0);... %Changed to double in the end.
-            'metFrom',cell(0,0);...
-            'rxnFrom',cell(0,0)};
-for i=1:size(modelFields,1)
-    model.(modelFields{i,1})=modelFields{i,2};
-end
-
-% If GECKO model
-if any(contains(line_key,'geckoLight'))
-    isGECKO=true;
-    ecFields = {'geckoLight', false;...
-                      'rxns', {};...
-                      'kcat', {};...
-                    'source', cell(0,0);...
-                     'notes', cell(0,0);...
-                   'eccodes', cell(0,0);...
-                     'genes', cell(0,0);...
-                   'enzymes', cell(0,0);...
-                        'mw', cell(0,0);...
-                  'sequence', cell(0,0);...
-                     'concs', cell(0,0);...
-                 'rxnEnzMat', []};
-    for i=1:size(ecFields,1)
-        model.ec.(ecFields{i,1})=ecFields{i,2};
-    end
-    ecGecko=cell(25000,2);      ecGeckoNo=1;
-    enzStoich=cell(100000,3);   enzStoichNo=1;
-else
-    isGECKO=false;
-end
-
-section = 0;
-metMiriams=cell(100000,3);   metMirNo=1;
-rxnMiriams=cell(100000,3);   rxnMirNo=1;
-geneMiriams=cell(100000,3);  genMirNo=1;
-subSystems=cell(100000,2);   subSysNo=1;
-eccodes=cell(100000,2);      ecCodeNo=1;
-equations=cell(100000,3);   equatiNo=1;
-
-for i=1:numel(line_key)
-    tline_raw = line_raw{i};
-    tline_key = line_key{i};
-    tline_value = line_value{i};
-    % import different sections
-    switch tline_raw
-        case '- metaData:'
-            section = 1;
-            if verbose
-                fprintf('\t%d\n', section);
-            end
-            continue % Go to next line
-        case '- metabolites:'
-            section = 2;
-            if verbose
-                fprintf('\t%d\n', section);
-            end
-            pos=0;
-            continue
-        case '- reactions:'
-            section = 3;
-            if verbose
-                fprintf('\t%d\n', section);
-            end
-            pos=0;
-            continue
-        case '- genes:'
-            section = 4;
-            if verbose
-                fprintf('\t%d\n', section);
-            end
-            pos=0;
-            continue
-        case '- compartments: !!omap'
-            section = 5;
-            if verbose
-                fprintf('\t%d\n', section);
-            end
-            pos=0;
-            continue
-        case '- ec-rxns:'
-            section = 6;
-            if verbose
-                fprintf('\t%d\n', section);
-            end
-            pos=0;
-            continue
-        case '- ec-enzymes:'
-            section = 7;
-            if verbose
-                fprintf('\t%d\n', section);
-            end
-            pos=0;
-            continue
-    end
-
-    % skip over empty keys
-    if isempty(tline_raw) || (isempty(tline_key) && contains(tline_raw,'!!omap'))
-        continue;
-    end
-    
-    % import metaData
-    if section == 1
-        switch tline_key
-            case {'short_name','id'} %short_name used by human-GEM
-                model.id = tline_value;
-            case 'name'
-                model.name = tline_value;                
-            case 'full_name' %used by human-GEM
-                model.description = tline_value;
-            case 'version'
-                model.version = tline_value;
-            case 'date'
-                model.date = tline_value;                
-            case 'taxonomy'
-                model.annotation.taxonomy = tline_value;
-            case {'description','note'} %description used by human-GEM
-                model.annotation.note = tline_value;
-            case 'github'
-                model.annotation.sourceUrl = tline_value;
-            case 'sourceUrl'
-                model.annotation.sourceUrl = tline_value;                
-            case 'givenName'
-                model.annotation.givenName = tline_value;
-            case 'familyName'
-                model.annotation.familyName = tline_value;
-            case 'authors'
-                model.annotation.authorList = tline_value;
-            case 'email'
-                model.annotation.email = tline_value;
-            case 'organization'
-                model.annotation.organization = tline_value;
-            case 'geckoLight'
-                if strcmp(tline_value,'true')
-                    model.ec.geckoLight = true;
-                end
-        end; continue
-    end
-
-    % import metabolites:
-    if section == 2
-        switch tline_key
-            case 'id'
-                pos = pos + 1;
-                model = readFieldValue(model, 'mets', tline_value,pos);
-                readList=''; miriamKey='';
-            case 'name'
-                model = readFieldValue(model, 'metNames', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'compartment'
-                model = readFieldValue(model, 'metComps', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'formula'
-                model = readFieldValue(model, 'metFormulas', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'charge'
-                model = readFieldValue(model, 'metCharges', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'notes'
-                model = readFieldValue(model, 'metNotes', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'inchis'
-                model = readFieldValue(model, 'inchis', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'smiles'
-                model = readFieldValue(model, 'metSmiles', tline_value, pos);
-                readList=''; miriamKey='';    
-            case 'deltaG'
-                model = readFieldValue(model, 'metDeltaG', tline_value, pos);
-                readList=''; miriamKey='';                                
-            case 'metFrom'
-                model = readFieldValue(model, 'metFrom', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'annotation'
-                readList = 'annotation';
-            otherwise
-                switch readList
-                    case 'annotation'
-                        [metMiriams, miriamKey, metMirNo] = gatherAnnotation(pos,metMiriams,tline_key,tline_value,miriamKey,metMirNo);
-                    otherwise
-                        error(['Unknown entry in yaml file: ' tline_raw])
-                end
-        end; continue
-    end
-
-    % import reactions:
-    if section == 3
-        switch tline_key
-            case 'id'
-                pos = pos + 1;
-                model = readFieldValue(model, 'rxns', tline_value,pos);
-                readList=''; miriamKey='';
-            case 'name'
-                model = readFieldValue(model, 'rxnNames', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'lower_bound'
-                model.lb(pos,1) = {tline_value};
-                readList=''; miriamKey='';
-            case 'upper_bound'
-                model.ub(pos,1) = {tline_value};
-                readList=''; miriamKey='';
-            case 'rev'
-                model.rev(pos,1) = {tline_value};
-                readList=''; miriamKey='';
-            case 'gene_reaction_rule'
-                model = readFieldValue(model, 'grRules', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'rxnNotes'
-                model = readFieldValue(model, 'rxnNotes', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'rxnFrom'
-                model = readFieldValue(model, 'rxnFrom', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'deltaG'
-                model = readFieldValue(model, 'rxnDeltaG', tline_value, pos);
-                readList=''; miriamKey='';                
-            case 'objective_coefficient'
-                model.c(pos,1) = 1;
-                readList=''; miriamKey='';
-            case 'references'
-                model = readFieldValue(model, 'rxnReferences', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'confidence_score'
-                model = readFieldValue(model, 'rxnConfidenceScores', tline_value, pos);
-                readList=''; miriamKey='';
-            case 'eccodes'
-                if isempty(tline_value)
-                    readList = 'eccodes';
-                else
-                    eccodes(ecCodeNo,1:2)={pos,tline_value};
-                    ecCodeNo=ecCodeNo+1;
-                end
-            case 'subsystem'
-                if isempty(tline_value)
-                    readList = 'subsystem';
-                else
-                    subSystems(subSysNo,1:2)={pos,tline_value};
-                    subSysNo=subSysNo+1;
-                end
-            case 'metabolites'
-                readList = 'equation';
-            case 'annotation'
-                readList = 'annotation';
-                
-            otherwise
-                switch readList
-                    case 'eccodes'
-                        eccodes(ecCodeNo,1:2)={pos,regexprep(tline_value,'^ +- "?(.*)"?$','$1')};
-                        ecCodeNo=ecCodeNo+1;
-                    case 'subsystem'
-                        subSystems(subSysNo,1:2)={pos,regexprep(tline_value,'^ +- "?(.*)"?$','$1')};
-                        subSysNo=subSysNo+1;
-                    case 'annotation'
-                        [rxnMiriams, miriamKey,rxnMirNo] = gatherAnnotation(pos,rxnMiriams,tline_key,tline_value,miriamKey,rxnMirNo);
-                    case 'equation'
-                        coeff = sscanf(tline_value,'%f');
-                        equations(equatiNo,1:3)={pos,tline_key,coeff};
-                        equatiNo=equatiNo+1;
-                    otherwise
-                        error(['Unknown entry in yaml file: ' tline_raw])
-                end                
-        end; continue
-    end
-
-    % import genes:
-    if section == 4
-        switch tline_key
-            case 'id'
-                pos = pos + 1;
-                model = readFieldValue(model, 'genes', tline_value, pos);
-                readList = '';
-                miriamKey = '';
-            case 'name'
-                model = readFieldValue(model, 'geneShortNames', tline_value, pos);
-            case 'protein'
-                model = readFieldValue(model, 'proteins', tline_value, pos);
-            case 'annotation'
-                readList = 'annotation';
-            otherwise
-                switch readList
-                    case 'annotation'
-                        [geneMiriams, miriamKey,genMirNo] = gatherAnnotation(pos,geneMiriams,tline_key,tline_value,miriamKey,genMirNo);
-                    otherwise
-                        error(['Unknown entry in yaml file: ' tline_raw])
-                end
-        end; continue
-    end
-
-    % import compartments:
-    if section == 5
-        model.comps(end+1,1) = {tline_key};
-        model.compNames(end+1,1) = {tline_value};
-    end
-
-    % import ec reaction info
-    if section == 6
-        switch tline_key
-            case 'id'
-                pos = pos + 1;
-                model.ec = readFieldValue(model.ec, 'rxns', tline_value, pos);
-                readList='';
-            case 'kcat'
-                model.ec = readFieldValue(model.ec, 'kcat', tline_value, pos);
-                readList='';
-            case 'source'
-                model.ec = readFieldValue(model.ec, 'source', tline_value, pos);
-                readList='';
-            case 'notes'
-                model.ec = readFieldValue(model.ec, 'notes', tline_value, pos);
-                readList='';
-            case 'eccodes'
-                if isempty(tline_value)
-                    readList = 'eccodes';
-                else
-                    ecGecko(ecGeckoNo,1:2)={pos,tline_value};
-                    ecGeckoNo=ecGeckoNo+1;
-                end
-            case 'enzymes'
-                readList = 'enzStoich';
-            otherwise
-                switch readList
-                    case 'eccodes'
-                        ecGecko(ecGeckoNo,1:2)={pos,regexprep(tline_value,'^ +- "?(.*)"?$','$1')};
-                        ecGeckoNo=ecGeckoNo+1;
-                    case 'enzStoich'
-                        coeff = sscanf(tline_value,'%f');
-                        enzStoich(enzStoichNo,1:3)={pos,tline_key,coeff};
-                        enzStoichNo=enzStoichNo+1;
-                    otherwise
-                        error(['Unknown entry in yaml file: ' tline_raw])
-                end
-        end; continue
-    end
-
-    % import ec enzyme info
-    if section == 7
-        switch tline_key
-            case 'genes'
-                pos = pos + 1;
-                model.ec = readFieldValue(model.ec, 'genes', tline_value, pos);
-            case 'enzymes'
-                model.ec = readFieldValue(model.ec, 'enzymes', tline_value, pos);
-            case 'mw'
-                model.ec = readFieldValue(model.ec, 'mw', tline_value, pos);
-            case 'sequence'
-                model.ec = readFieldValue(model.ec, 'sequence', tline_value, pos);
-            case 'concs'
-                model.ec = readFieldValue(model.ec, 'concs', tline_value, pos);
-            otherwise
-                error(['Unknown entry in yaml file: ' tline_raw])
-        end; continue
-    end
-end
-
-%Parse annotations
-if ~isempty(metMiriams)
-    locs = cell2mat(metMiriams(:,1));
-    for i=unique(locs)'
-        model.metMiriams{i,1}.name=metMiriams(locs==i,2);
-        model.metMiriams{i,1}.value=metMiriams(locs==i,3);
-    end
-end
-if ~isempty(rxnMiriams)
-    locs = cell2mat(rxnMiriams(:,1));
-    for i=unique(locs)'
-        model.rxnMiriams{i,1}.name=rxnMiriams(locs==i,2);
-        model.rxnMiriams{i,1}.value=rxnMiriams(locs==i,3);
-    end
-end
-if ~isempty(geneMiriams)
-    locs = cell2mat(geneMiriams(:,1));
-    for i=unique(locs)'
-        model.geneMiriams{i,1}.name=geneMiriams(locs==i,2);
-        model.geneMiriams{i,1}.value=geneMiriams(locs==i,3);
-    end
-end
-
-%Parse subSystems
-if ~isempty(subSystems)
-    locs = cell2mat(subSystems(:,1));
-    for i=unique(locs)'
-        model.subSystems{i,1}=subSystems(locs==i,2);
-    end
-end
-
-%Parse ec-codes
-if ~isempty(eccodes)
-    locs = cell2mat(eccodes(:,1));
-    for i=unique(locs)'
-        eccodesCat=strjoin(eccodes(locs==i,2),';');
-        model.eccodes{i,1}=eccodesCat;
-    end
-    emptyEc=cellfun('isempty',model.eccodes);
-    model.eccodes(emptyEc)={''};
-end
-
-% follow-up data processing
-if verbose
-    fprintf('\nimporting completed\nfollow-up processing...');
-end
-[~, model.metComps] = ismember(model.metComps, model.comps);
-[~, model.geneComps] = ismember(model.geneComps, model.comps);
-[~, model.rxnComps] = ismember(model.rxnComps, model.comps);
-
-% Fill S-matrix
-rxnIdx = cellfun('isempty', equations(:,1));
-equations(rxnIdx,:) = '';
-rxnIdx = cell2mat(equations(:,1));
-[~,metIdx] = ismember(equations(:,2),model.mets);
-coeffs = cell2mat(equations(:,3));
-model.S=sparse(max(metIdx),max(rxnIdx));
-linearIndices = sub2ind([max(metIdx), max(rxnIdx)],metIdx,rxnIdx);
-model.S(linearIndices) = coeffs;
-
-% Convert strings to numeric
-model.metCharges = str2double(model.metCharges);
-model.lb = str2double(model.lb);
-model.ub = str2double(model.ub);
-model.rxnConfidenceScores = str2double(model.rxnConfidenceScores);
-model.b = zeros(length(model.mets),1);
-model.metDeltaG = str2double(model.metDeltaG);
-model.rxnDeltaG = str2double(model.rxnDeltaG);
-
-% Fill some other fields
-model.annotation.defaultLB = min(model.lb);
-model.annotation.defaultUB = max(model.ub);
-if numel(model.lb)<numel(model.rxns) %No LB reported = min
-    model.lb(end+1:numel(model.rxns)-numel(model.lb),1) = double(model.annotation.defaultLB);
-end
-if numel(model.ub)<numel(model.rxns) %No UB reported = max
-    model.ub(end+1:numel(model.rxns)-numel(model.ub),1) = double(model.annotation.defaultUB);
-end
-if ~all(cellfun('isempty',model.rev))
-    model.rev = str2double(model.rev);
-else
-    model.rev = [];
-end
-if numel(model.rev)<numel(model.rxns) %No rev reported, assume from LB and UB
-    model.rev(end+1:numel(model.rxns)-numel(model.rev),1) = double(model.lb<0 & model.ub>0);
-end
-
-% Remove empty fields, otherwise fill to correct length
-% Reactions
-for i={'rxnNames','grRules','eccodes','rxnNotes','rxnReferences',...
-       'rxnFrom','subSystems','rxnMiriams'} % Empty strings
-   model = emptyOrFill(model,i{1},{''},'rxns');
-end
-for i={'c'} % Zeros
-   model = emptyOrFill(model,i{1},0,'rxns',true);
-end
-for i={'rxnConfidenceScores','rxnDeltaG'} % NaNs
-   model = emptyOrFill(model,i{1},NaN,'rxns');
-end
-for i={'rxnComps'} % Ones, assume first compartment
-   model = emptyOrFill(model,i{1},1,'rxns');
-end
-% Metabolites
-for i={'metNames','inchis','metFormulas','metMiriams','metFrom','metSmiles','metNotes'} % Empty strings
-   model = emptyOrFill(model,i{1},{''},'mets');
-end
-for i={'metCharges','unconstrained'} % Zeros
-   model = emptyOrFill(model,i{1},0,'mets');
-end
-for i={'metDeltaG'} % % NaNs
-    model = emptyOrFill(model,i{1},NaN,'mets');
- end
-for i={'metComps'} % Ones, assume first compartment
-   model = emptyOrFill(model,i{1},1,'mets');
-end
-% Genes
-for i={'geneMiriams','geneShortNames','proteins'} % Empty strings
-   model = emptyOrFill(model,i{1},{''},'genes');
-end
-for i={'geneComps'} % Ones, assume first compartment
-   model = emptyOrFill(model,i{1},1,'genes');
-end
-% Comps
-for i={'compNames'} % Empty strings
-   model = emptyOrFill(model,i{1},{''},'comps');
-end
-for i={'compOutside'} % First comp
-   model = emptyOrFill(model,i{1},model.comps{1},'comps');
-end
-% Single fields are kept, even if empty
-% for i={'description','name','version','date','annotation'}
-%     if isempty(model.(i{1}))
-%         model = rmfield(model,i{1});
-%     end
-% end
-
-% Make rxnGeneMat fields and map to the existing model.genes field
-[genes, rxnGeneMat] = getGenesFromGrRules(model.grRules);
-model.rxnGeneMat = sparse(numel(model.rxns),numel(model.genes));
-[~,geneOrder] = ismember(genes,model.genes);
-if any(geneOrder == 0)
-    error(['The grRules includes the following gene(s), that are not in '...
-           'the list of model genes: ', genes{~geneOrder}])
-end
-model.rxnGeneMat(:,geneOrder) = rxnGeneMat;
-
-% Finalize GECKO model
-if isGECKO
-    % Fill in empty fields and empty entries
-    for i={'kcat','source','notes','eccodes'} % Even keep empty
-        model.ec = emptyOrFill(model.ec,i{1},{''},'rxns',true);
-    end
-    for i={'enzymes','mw','sequence'}
-        model.ec = emptyOrFill(model.ec,i{1},{''},'genes',true);
-    end
-    model.ec = emptyOrFill(model.ec,'concs',{'NaN'},'genes',true);
-    model.ec = emptyOrFill(model.ec,'kcat',{'0'},'genes',true);
-    % Change string to double
-    for i={'kcat','mw','concs'}
-        if isfield(model.ec,i{1})
-            model.ec.(i{1}) = str2double(model.ec.(i{1}));
-        end
-    end
-    % Fill rxnEnzMat
-    rxnIdx              = cellfun('isempty', enzStoich(:,1));
-    enzStoich(rxnIdx,:) = '';
-    rxnIdx              = cell2mat(enzStoich(:,1));
-    [~,enzIdx]          = ismember(enzStoich(:,2),model.ec.enzymes);
-    coeffs              = cell2mat(enzStoich(:,3));
-    model.ec.rxnEnzMat  = zeros(numel(model.ec.rxns), numel(model.ec.genes));
-    linearIndices       = sub2ind([numel(model.ec.rxns), numel(model.ec.genes)], rxnIdx, enzIdx);
-    model.ec.rxnEnzMat(linearIndices) = coeffs;
-    %Parse ec-codes
-    if ~isempty(ecGecko)
-        locs = cell2mat(ecGecko(:,1));
-        for i=unique(locs)'
-            ecGeckoCat=strjoin(ecGecko(locs==i,2),';');
-            model.ec.eccodes{i,1}=ecGeckoCat;
-        end
-        emptyEc=cellfun('isempty',model.ec.eccodes);
-        model.ec.eccodes(emptyEc)={''};
-    end
-end
-
-if verbose
-    fprintf(' Done!\n');
-end
-end
-
-function model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)
-if nargin<5
-    keepEmpty=false;
-end
-if isnumeric(emptyEntry)
-    emptyCells=isempty(model.(field));
-else
-    emptyCells=cellfun('isempty',model.(field));
-end
-if all(emptyCells) && ~keepEmpty
-    model = rmfield(model, field);
-elseif numel(model.(field))<numel(model.(type))
-    model.(field)(end+1:numel(model.(type)),1)=emptyEntry;
-end
-end
-
-function model = readFieldValue(model, fieldName, value, pos)
-if numel(model.(fieldName))<pos-1
-    model.(fieldName)(end+1:pos,1) = {''};
-end
-model.(fieldName)(pos,1) = {value};
-end
-
-function [miriams,miriamKey,entryNumber] = gatherAnnotation(pos,miriams,key,value,miriamKey,entryNumber)
-if isempty(key)
-    key=miriamKey;
-else
-    miriamKey=key;
-end
-if ~isempty(value)
-    miriams(entryNumber,1:3) = {pos, key, strip(value)};
-    entryNumber = entryNumber + 1;
-end
-end
diff --git a/code/io/writeYAMLmodel_HumanGEM.m b/code/io/writeYAMLmodel_HumanGEM.m
deleted file mode 100644
index b40bf18e..00000000
--- a/code/io/writeYAMLmodel_HumanGEM.m
+++ /dev/null
@@ -1,378 +0,0 @@
-function writeYAMLmodel(model,fileName,preserveQuotes,sortIds)
-% writeYAMLmodel
-%   Writes a yaml file matching (roughly) the cobrapy yaml structure
-%
-%   model           a model structure
-%   fileName        name that the file will have.  A dialog window will 
-%                   open if no file name is specified.
-%   preserveQuotes  if quotes should be preserved for strings
-%                   (logical, default=true)
-%   sortIds         if metabolites, reactions, genes and compartments
-%                   should be sorted alphabetically by their identifier,
-%                   otherwise they are kept in their original order
-%                   (logical, default=false)   
-%
-% Usage: writeYAMLmodel(model,fileName,preserveQuotes,sortIds)
-if nargin<2|| isempty(fileName)
-    [fileName, pathName] = uiputfile({'*.yml;*.yaml'}, 'Select file for model export',[model.id '.yml']);
-    if fileName == 0
-        error('You should provide a file location')
-    else
-        fileName = fullfile(pathName,fileName);
-    end
-end
-fileName=char(fileName);
-
-if nargin < 3
-    preserveQuotes = true;
-end
-if nargin < 4
-    sortIds = false;
-end
-if ~endsWith(fileName,{'.yml','.yaml'})
-    fileName = strcat(fileName,'.yml');
-end
-
-%Check that model is in RAVEN format:
-if isfield(model,'rules')
-    model = ravenCobraWrapper(model);
-end
-
-%Sort identifiers alphabetically
-if sortIds == true
-    model = sortIdentifiers(model);
-end
-
-%Simplify Miriam fields:
-if isfield(model,'metMiriams')
-    [model.newMetMiriams,model.newMetMiriamNames]   = extractMiriam(model.metMiriams);
-end
-if isfield(model,'rxnMiriams')
-    [model.newRxnMiriams,model.newRxnMiriamNames]   = extractMiriam(model.rxnMiriams);
-end
-if isfield(model,'geneMiriams')
-    [model.newGeneMiriams,model.newGeneMiriamNames] = extractMiriam(model.geneMiriams);
-end
-if isfield(model,'compMiriams')
-    [model.newCompMiriams,model.newCompMiriamNames] = extractMiriam(model.compMiriams);
-end
-
-%Open file:
-fid = fopen(fileName,'wt');
-if fid == -1
-    error(['Cannot write to ' fileName ', does the directory exist?'])
-end
-fprintf(fid,'---\n!!omap\n');
-
-%Insert file header (metadata)
-writeMetadata(model,fid);
-
-%Metabolites:
-fprintf(fid,'- metabolites:\n');
-for i = 1:length(model.mets)
-    fprintf(fid,'    - !!omap\n');
-    writeField(model, fid, 'mets',        'txt', i, '  - id',          preserveQuotes)
-    writeField(model, fid, 'metNames',    'txt', i, '  - name',        preserveQuotes)
-    writeField(model, fid, 'metComps',    'txt', i, '  - compartment', preserveQuotes)
-    writeField(model, fid, 'metFormulas', 'txt', i, '  - formula',     preserveQuotes)
-    writeField(model, fid, 'metCharges',  'num', i, '  - charge',      preserveQuotes)
-    writeField(model, fid, 'inchis',      'txt', i, '  - inchis',      preserveQuotes)
-    writeField(model, fid, 'metSmiles',   'txt', i, '  - smiles',      preserveQuotes)
-    writeField(model, fid, 'metMiriams',  'txt', i, '  - annotation',  preserveQuotes)
-    writeField(model, fid, 'metDeltaG',   'num', i, '  - deltaG',      preserveQuotes)
-    writeField(model, fid, 'metNotes',    'txt', i, '  - notes',       preserveQuotes)
-    writeField(model, fid, 'metFrom',     'txt', i, '  - metFrom',     preserveQuotes)
-end
-
-%Reactions:
-fprintf(fid,'- reactions:\n');
-for i = 1:length(model.rxns)
-    fprintf(fid,'    - !!omap\n');
-    writeField(model, fid, 'rxns',                 'txt', i, '  - id',                    preserveQuotes)
-    writeField(model, fid, 'rxnNames',             'txt', i, '  - name',                  preserveQuotes)
-    writeField(model, fid, 'S',                    'txt', i, '  - metabolites',           preserveQuotes)
-    writeField(model, fid, 'lb',                   'num', i, '  - lower_bound',           preserveQuotes)
-    writeField(model, fid, 'ub',                   'num', i, '  - upper_bound',           preserveQuotes)
-    writeField(model, fid, 'grRules',              'txt', i, '  - gene_reaction_rule',    preserveQuotes)
-    writeField(model, fid, 'rxnFrom',              'txt', i, '  - rxnFrom',               preserveQuotes)
-    if model.c(i)~=0
-        writeField(model, fid, 'c',                    'num', i, '  - objective_coefficient', preserveQuotes)    
-    end
-    writeField(model, fid, 'eccodes',              'txt', i, '  - eccodes',               preserveQuotes)
-    writeField(model, fid, 'rxnReferences',        'txt', i, '  - references',            preserveQuotes)
-    writeField(model, fid, 'subSystems',           'txt', i, '  - subsystem',             preserveQuotes)
-    writeField(model, fid, 'rxnMiriams',           'txt', i, '  - annotation',            preserveQuotes)
-    writeField(model, fid, 'rxnDeltaG',            'num', i, '  - deltaG',                preserveQuotes)
-    writeField(model, fid, 'rxnConfidenceScores',  'num', i, '  - confidence_score',      preserveQuotes)
-    writeField(model, fid, 'rxnNotes',             'txt', i, '  - rxnNotes',              preserveQuotes)
-end
-
-%Genes:
-fprintf(fid,'- genes:\n');
-for i = 1:length(model.genes)
-    fprintf(fid,'    - !!omap\n');
-    writeField(model, fid, 'genes',          'txt', i, '  - id',         preserveQuotes)
-    writeField(model, fid, 'geneShortNames', 'txt', i, '  - name',       preserveQuotes)
-    writeField(model, fid, 'proteins',   'txt', i, '  - protein',    preserveQuotes)
-    writeField(model, fid, 'geneMiriams',    'txt', i, '  - annotation', preserveQuotes)
-end
-
-%Compartments:
-fprintf(fid,'- compartments: !!omap\n');
-for i = 1:length(model.comps)
-    writeField(model, fid, 'compNames',   'txt', i, ['- ' model.comps{i}], preserveQuotes)
-    writeField(model, fid, 'compMiriams', 'txt', i, '- annotation',             preserveQuotes)
-end
-
-
-%EC-model:
-if isfield(model,'ec')
-    fprintf(fid,'- ec-rxns:\n');
-    for i = 1:length(model.ec.rxns)
-        fprintf(fid,'  - !!omap\n');
-        writeField(model.ec, fid, 'rxns',      'txt', i, '- id',      preserveQuotes)
-        writeField(model.ec, fid, 'kcat',      'num', i, '- kcat',    preserveQuotes)
-        writeField(model.ec, fid, 'source',    'txt', i, '- source',  preserveQuotes)
-        writeField(model.ec, fid, 'notes',     'txt', i, '- notes',   preserveQuotes)
-        writeField(model.ec, fid, 'eccodes',   'txt', i, '- eccodes', preserveQuotes)
-        writeField(model.ec, fid, 'rxnEnzMat', 'txt', i, '- enzymes', preserveQuotes)
-    end
-
-    fprintf(fid,'- ec-enzymes:\n');
-    for i = 1:length(model.ec.genes)
-        fprintf(fid,'  - !!omap\n');
-        writeField(model.ec, fid, 'genes',    'txt', i, '- genes',    preserveQuotes)
-        writeField(model.ec, fid, 'enzymes',  'txt', i, '- enzymes',  preserveQuotes)
-        writeField(model.ec, fid, 'mw',       'num', i, '- mw',       preserveQuotes)
-        writeField(model.ec, fid, 'sequence', 'txt', i, '- sequence', preserveQuotes)
-        writeField(model.ec, fid, 'concs',    'num', i, '- concs',    preserveQuotes)
-    end
-end
-
-%Close file:
-fclose(fid);
-
-end
-
-function writeField(model,fid,fieldName,type,pos,name,preserveQuotes)
-%Writes a new line in the yaml file if the field exists and the field is
-%not empty at the correspoinding position. It's recursive for some fields
-%(metMiriams, rxnMiriams, and S)
-
-if isfield(model,fieldName)
-    if strcmp(fieldName,'metComps')
-        %metComps: write full name
-        fieldName = 'comps';
-        pos       = model.metComps(pos);
-    end
-    
-    field = model.(fieldName);
-    
-    if strcmp(fieldName,'metMiriams')
-        if ~isempty(model.metMiriams{pos})
-            fprintf(fid,'    %s: !!omap\n',name);
-            for i=1:size(model.newMetMiriams,2)
-                %'i' represents the different miriam names, e.g.
-                %kegg.compound or chebi
-                if ~isempty(model.newMetMiriams{pos,i})
-                    %As during the following writeField call the value of
-                    %'i' would be lost, it is temporarily concatenated to
-                    %'name' parameter, which will be edited later
-                    writeField(model, fid, 'newMetMiriams', 'txt', pos, ['      - ' model.newMetMiriamNames{i} '_' sprintf('%d',i)], preserveQuotes)
-                end
-            end
-        end
-        
-    elseif strcmp(fieldName,'rxnMiriams')
-        if ~isempty(model.rxnMiriams{pos})
-            fprintf(fid,'    %s: !!omap\n',name);
-            for i=1:size(model.newRxnMiriams,2)
-                if ~isempty(model.newRxnMiriams{pos,i})
-                    writeField(model, fid, 'newRxnMiriams', 'txt', pos, ['      - ' model.newRxnMiriamNames{i} '_' sprintf('%d',i)], preserveQuotes)
-                end
-            end
-        end
-        
-    elseif strcmp(fieldName,'geneMiriams')
-        if ~isempty(model.geneMiriams{pos})
-            fprintf(fid,'    %s: !!omap\n',name);
-            for i=1:size(model.newGeneMiriams,2)
-                if ~isempty(model.newGeneMiriams{pos,i})
-                    writeField(model, fid, 'newGeneMiriams', 'txt', pos, ['      - ' model.newGeneMiriamNames{i} '_' sprintf('%d',i)], preserveQuotes)
-                end
-            end
-        end
-        
-    elseif strcmp(fieldName,'compMiriams')
-        if ~isempty(model.compMiriams{pos})
-            fprintf(fid,'    %s: !!omap\n',name);
-            for i=1:size(model.newCompMiriams,2)
-                if ~isempty(model.newCompMiriams{pos,i})
-                    writeField(model, fid, 'newCompMiriams', 'txt', pos, ['      - ' model.newCompMiriamNames{i} '_' sprintf('%d',i)], preserveQuotes)
-                end
-            end
-        end
-        
-    elseif strcmp(fieldName,'S')
-        %S: create header & write each metabolite in a new line
-        fprintf(fid,'    %s: !!omap\n',name);
-        if sum(field(:,pos) ~= 0) > 0
-            model.mets   = model.mets(field(:,pos) ~= 0);
-            model.coeffs = field(field(:,pos) ~= 0,pos);
-            %Sort metabolites:
-            [model.mets,order] = sort(model.mets);
-            model.coeffs       = model.coeffs(order);
-            for i = 1:length(model.mets)
-                writeField(model, fid, 'coeffs',  'num', i, ['      - ' model.mets{i}], preserveQuotes)
-            end
-        end
-
-    elseif strcmp(fieldName,'rxnEnzMat')
-        %S: create header & write each enzyme in a new line
-        fprintf(fid,'    %s: !!omap\n',name);
-        if sum(field(pos,:) ~= 0) > 0
-            model.enzymes = model.enzymes(field(pos,:) ~= 0);
-            model.coeffs  = field(pos,field(pos,:) ~= 0);
-            %Sort metabolites:
-            [model.enzymes,order] = sort(model.enzymes);
-            model.coeffs          = model.coeffs(order);
-            for i = 1:length(model.enzymes)
-                writeField(model, fid, 'coeffs',  'num', i, ['    - ' model.enzymes{i}], preserveQuotes)
-            end
-        end        
-
-    elseif sum(strcmp({'subSystems','newMetMiriams','newRxnMiriams','newGeneMiriams','newCompMiriams','eccodes'},fieldName)) > 0
-        %eccodes/rxnNotes: if 1 write in 1 line, if more create header and list
-        if strcmp(fieldName,'subSystems')
-            list = field{pos};  %subSystems already comes in a cell array
-            if isempty(list)
-                return
-            end
-        elseif strcmp(fieldName,'newMetMiriams')
-            index = str2double(regexprep(name,'^.+_',''));
-            name  = regexprep(name,'_\d+$','');
-            list = strsplit(model.newMetMiriams{pos,index},'; ');
-        elseif strcmp(fieldName,'newRxnMiriams')
-            index = str2double(regexprep(name,'^.+_',''));
-            name  = regexprep(name,'_\d+$','');
-            list = strsplit(model.newRxnMiriams{pos,index},'; ');
-        elseif strcmp(fieldName,'newGeneMiriams')
-            index = str2double(regexprep(name,'^.+_',''));
-            name  = regexprep(name,'_\d+$','');
-            list = strsplit(model.newGeneMiriams{pos,index},'; ');
-        elseif strcmp(fieldName,'newCompMiriams')
-            index = str2double(regexprep(name,'^.+_',''));
-            name  = regexprep(name,'_\d+$','');
-            list = strsplit(model.newCompMiriams{pos,index},'; ');
-        elseif ~isempty(field{pos})
-            list = strrep(field{pos},' ','');
-            list = strsplit(list,';');
-        else
-            return % empty, needs no line in file
-        end
-        list=strip(list);
-
-        if length(list) == 1 && ~strcmp(list{1},'') && ~strcmp(fieldName,'subSystems')
-            if preserveQuotes
-                list = ['"' list{1} '"'];
-            end
-            fprintf(fid,'    %s: %s\n',name,list);
-        elseif ischar(list) && strcmp(fieldName,'subSystems')
-            if preserveQuotes
-                list = ['"' list '"'];
-            end
-            fprintf(fid,'    %s: %s\n',name,list);            
-        elseif length(list) > 1 || strcmp(fieldName,'subSystems')
-            if preserveQuotes
-                for j=1:numel(list)
-                    list{j} = ['"' list{j} '"'];
-                end
-            end
-            fprintf(fid,'    %s:\n',name);
-            for i = 1:length(list)
-                fprintf(fid,'%s        - %s\n',regexprep(name,'(^\s*).*','$1'),list{i});
-            end
-        end
-        
-    elseif sum(pos) > 0
-        %All other fields:
-        if strcmp(type,'txt')
-            value = field{pos};
-            if preserveQuotes && ~isempty(value)
-                value = ['"',value,'"'];
-            end
-        elseif strcmp(type,'num')
-            if isnan(field(pos))
-                value = [];
-            else
-                value = sprintf('%.15g',full(field(pos)));
-            end
-        end
-        if ~isempty(value)
-            fprintf(fid,'    %s: %s\n',name,value);
-        end
-    end
-end
-end
-
-function writeMetadata(model,fid)
-% Writes model metadata to the yaml file. This information will eventually
-% be extracted entirely from the model, but for now, many of the entries
-% are hard-coded defaults for HumanGEM.
-
-fprintf(fid, '- metaData:\n');
-if isfield(model,'id')
-    fprintf(fid, '    id: "%s"\n',  model.id);
-else
-    fprintf(fid, '    id: "blankID"\n');
-end
-if isfield(model,'name')
-    fprintf(fid, '    name: "%s"\n',model.name);
-else
-    fprintf(fid, '    name: "blankName"\n');
-end
-if isfield(model,'version')
-    fprintf(fid, '    version: "%s"\n',model.version);
-end
-fprintf(fid, '    date: "%s"\n',datestr(now,29));  % 29=YYYY-MM-DD
-if isfield(model,'annotation')
-    if isfield(model.annotation,'defaultLB')
-        fprintf(fid, '    defaultLB: "%g"\n',   model.annotation.defaultLB);
-    end
-    if isfield(model.annotation,'defaultUB')
-        fprintf(fid, '    defaultUB: "%g"\n',   model.annotation.defaultUB);
-    end
-    if isfield(model.annotation,'givenName')
-        fprintf(fid, '    givenName: "%s"\n',   model.annotation.givenName);
-    end
-    if isfield(model.annotation,'familyName')
-        fprintf(fid, '    familyName: "%s"\n',  model.annotation.familyName);
-    end
-    if isfield(model.annotation,'authors')
-        fprintf(fid, '    authors: "%s"\n',     model.annotation.authors);
-    end
-    if isfield(model.annotation,'email')
-        fprintf(fid, '    email: "%s"\n',       model.annotation.email);
-    end
-    if isfield(model.annotation,'organization')
-        fprintf(fid, '    organization: "%s"\n',model.annotation.organization);
-    end
-    if isfield(model.annotation,'taxonomy')
-        fprintf(fid, '    taxonomy: "%s"\n',    model.annotation.taxonomy);
-    end
-    if isfield(model.annotation,'note')
-        fprintf(fid, '    note: "%s"\n',        model.annotation.note);
-    end
-    if isfield(model.annotation,'sourceUrl')
-        fprintf(fid, '    sourceUrl: "%s"\n',   model.annotation.sourceUrl);
-    end
-end
-if isfield(model,'ec')
-    if model.ec.geckoLight
-        geckoLight = 'true';
-    else
-        geckoLight = 'false';
-    end
-    fprintf(fid,'    geckoLight: "%s"\n',geckoLight);
-end
-end
diff --git a/code/modelCuration/GlycolysisCuration.m b/code/modelCuration/GlycolysisCuration.m
index 2dbaab27..f7037223 100644
--- a/code/modelCuration/GlycolysisCuration.m
+++ b/code/modelCuration/GlycolysisCuration.m
@@ -2,7 +2,7 @@
 rxnStruct = importTsvFile('../../data/modelCuration/addRxnGly_20230414.tsv');
 MetStruct = importTsvFile('../../data/modelCuration/addMetGly_20230414.tsv');
 
-model = importYaml('Human-GEM.yml');
+model = readYAMLmodel('Human-GEM.yml');
 
 rxnsToAdd.rxns = rxnStruct.rxnID;
 rxnsToAdd.eccodes = rxnStruct.ECNumber;
diff --git a/code/modelCuration/addAAnewRxn20230518.m b/code/modelCuration/addAAnewRxn20230518.m
index 38a5f702..2f4b69a4 100644
--- a/code/modelCuration/addAAnewRxn20230518.m
+++ b/code/modelCuration/addAAnewRxn20230518.m
@@ -2,7 +2,7 @@
 rxnStruct = importTsvFile('../../data/modelCuration/addRxnAA_20230518.tsv');
 MetStruct = importTsvFile('../../data/modelCuration/addMetAA_20230518.tsv');
 
-model = importYaml('Human-GEM.yml');
+model = readYAMLmodel('Human-GEM.yml');
 
 rxnsToAdd.rxns = rxnStruct.rxnID;
 rxnsToAdd.eccodes = rxnStruct.ECNumber;
@@ -91,4 +91,4 @@
 structure.rxnRetired = [structure.rxnRetired;rxnStruct.emptyID(idx,1) ];
 
 exportTsvFile(structure, '../../model/reactions.tsv')
-exportYaml(newModel, 'Human-GEM.yml');
+writeYAMLmodel(newModel, 'Human-GEM.yml');
diff --git a/code/modelCuration/addRxnACOD1_20221102.m b/code/modelCuration/addRxnACOD1_20221102.m
index 2c4f38e7..7bd1f27e 100644
--- a/code/modelCuration/addRxnACOD1_20221102.m
+++ b/code/modelCuration/addRxnACOD1_20221102.m
@@ -1,5 +1,5 @@
 % load model and new reaction info
-ihuman = importYaml('../../model/Human-GEM.yml');
+ihuman = readYAMLmodel('../../model/Human-GEM.yml');
 rxnsToAdd = importTsvFile('../../data/modelCuration/addRxnACOD1_20221102.tsv');
 
 % add new genes to Human-GEM
@@ -28,6 +28,6 @@
 end
 
 % update yaml model and reaction association file
-exportYaml(newGEM, '../../model/Human-GEM.yml');
+writeYAMLmodel(newGEM, '../../model/Human-GEM.yml');
 exportTsvFile(rxnAssoc,'../../model/reactions.tsv');
 
diff --git a/code/modelCuration/changeCompAbbrevs.m b/code/modelCuration/changeCompAbbrevs.m
index 544dfac6..c1fc35d2 100644
--- a/code/modelCuration/changeCompAbbrevs.m
+++ b/code/modelCuration/changeCompAbbrevs.m
@@ -7,7 +7,7 @@
 modelname = 'Human-GEM';
 
 % load model and other data files
-model = importYaml(fullfile('..', '..', 'model', [modelname '.yml']));
+model = readYAMLmodel(fullfile('..', '..', 'model', [modelname '.yml']));
 metAssoc = importTsvFile(fullfile('..', '..', 'model', 'metabolites.tsv'));
 metAssoc_table = struct2table(metAssoc);
 metsDep = importTsvFile(fullfile('..', '..', 'data', 'deprecatedIdentifiers', 'deprecatedMetabolites.tsv'));
@@ -30,7 +30,7 @@
 metAssoc.mets = regexprep(metAssoc.mets, 'p$', 'x');
 
 % export the new model and files
-exportYaml(model, fullfile('..', '..', 'model', [modelname '.yml']));
+writeYAMLmodel(model, fullfile('..', '..', 'model', [modelname '.yml']));
 exportTsvFile(metAssoc, fullfile('..', '..', 'model', 'metabolites.tsv'));
 exportTsvFile(metsDep_table, fullfile('..', '..', 'data', 'deprecatedIdentifiers', 'deprecatedMetabolites.tsv'));
 
diff --git a/code/modelCuration/removeDuplicateRxns_issue345.m b/code/modelCuration/removeDuplicateRxns_issue345.m
index 0b8e82db..3146c7b1 100644
--- a/code/modelCuration/removeDuplicateRxns_issue345.m
+++ b/code/modelCuration/removeDuplicateRxns_issue345.m
@@ -1,7 +1,7 @@
 
 
 % load Human-GEM
-model = importYaml('../../model/Human-GEM.yml');
+model = readYAMLmodel('../../model/Human-GEM.yml');
 
 
 % specify pairs of duplicate reactions, where reactions in first column are
@@ -107,7 +107,7 @@
 
 % delete reactions from model and annotation file
 model = removeReactions(model, rxns(:,2));
-exportYaml(model, '../../model/Human-GEM.yml');
+writeYAMLmodel(model, '../../model/Human-GEM.yml');
 rxnAssocTable(rxn_indx(:,2), :) = [];
 exportTsvFile(rxnAssocTable, rxnAssocFile);
 
diff --git a/code/test/testMetabolicTasks.m b/code/test/testMetabolicTasks.m
index e8288809..917d0a2f 100644
--- a/code/test/testMetabolicTasks.m
+++ b/code/test/testMetabolicTasks.m
@@ -20,7 +20,7 @@
 
 % Import yaml model
 ymlFile=fullfile(modelPath,'model','Human-GEM.yml');
-ihuman = importYaml(ymlFile, true);
+ihuman = readYAMLmodel(ymlFile);
 
 % parse metabolic tasks
 model = addBoundaryMets(ihuman);
diff --git a/code/updateAnimalGEM.m b/code/updateAnimalGEM.m
index 5ce90e94..fb62b78a 100644
--- a/code/updateAnimalGEM.m
+++ b/code/updateAnimalGEM.m
@@ -58,7 +58,7 @@
     load(matFile);
 elseif isfile(ymlFile)
     % Load Human-GEM Yaml file
-    ihuman = importYaml(ymlFile);
+    ihuman = readYAMLmodel(ymlFile);
 else
     error('ERROR: No model file is found!');
 end
diff --git a/data/testResults/README.md b/data/testResults/README.md
index 7d79c2be..95c98d79 100644
--- a/data/testResults/README.md
+++ b/data/testResults/README.md
@@ -4,7 +4,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/
 
 The test results shown here were obtained by the GitHub Actions run in:
 
-- **PR #939** (MACAW)
+- **PR #942** (MACAW)
 - **PR #883** (gene essentiality)
 
 The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request.