VisualisationandmapmanipulationinCellDesigner(PART1)Authors:

JenniferModamio,AnnaDanielsdottir,SystemsBiochemistrygroup,UniversityofLuxembourg.

NicolasSompairac,BioinformaticsandComputationalSystemsBiologyofCancer,InstitutCurie.

Reviewer(s):RonanFleming,InnaKupersteinandAndreiZinovyev.INTRODUCTIONVisualisationofdataontopofbiochemicalpathwaysisanimportanttoolforinterpretingtheresultsofconstrained-basedmodeling.Itcanbeaninvaluableaidfordevelopinganunderstandingofthebiologicalmeaningimpliedbyaprediction.Biochemicalnetworkmapspermitthevisualintegrationofmodelpredictionswiththeunderlyingbiochemicalcontext.Patternsthatareverydifficulttoappreciateinavectorcanoftenbemuchbetterappreciatedbystudyingagenericmapcontextualisedwithmodelpredictions.Genome-scalebiochemicalnetworkvisualisationisparticularlydemanding.Nocurrentlyavailablesoftwaresatisfiesalloftherequirementsthatmightbedesiredforvisualisationofpredictionsfromgenome-scalemodels.

HerewepresentatoolforthevisualisationofcomputationalpredictionsfromTheConstraint-basedReconstructionandAnalysisToolbox(COBRAToolbox)[1]toavailablemetabolicmapsdevelopedinCellDesigner[2].

Severalmapsareusedinthistutorialforillustration:(i)acomprehensivemitochondrialmetabolicmapcompassing1263metabolicreactionsextractedfromthelatestversionofthehumancellularmetabolism,Recon3D[3].(ii)SmallmapcontaningGlycolisisandTCAforfastertestingandmanipulation.(iii)Amitochondriamapcombiningmetabolicpathwayswithprotein-proteininteractions(PPI).ProteinsandcomplexesimplicatedinmitochondrialreactionshavebeenextractedfromtheParkinsonDiseasemap(PDMap)[4].

Inthistutorial,manipulationofCellDesgnermapsinCOBRAtoolboxandvisualisingmodelpredictionsisexplained.Themaincoveredtopicsare:

LoadingmetabolicmodelsandmodelscontainingbothmetabolicandregulatorynetworksconstructedinCellDesignerDetectionandcorrectionofdiscrepanciesbetweenmapandmodelsBasicmapmanipulation(changecolorandsizeofnodesandreactions,directionalityofreactions,reactiontypes...)Basicmodelanalysisvisualisation(visualisationofFluxBalanceAnalysis)

EQUIPMENTSETUPTovisualisethemetabolicmapsitisnecessarytoobtaintheversion4.4ofCellDesigner.Thissoftwarecanbefreelydownloadedfrom:

http://www.celldesigner.org/download.html

InitialiseTheCobraToolboxandsetthesolver.Ifneeded,initialisethecobratoolbox.

initCobraToolbox(false)%don'tupdatethetoolbox

Thepresenttutorialcanrunwithglpkpackage,whichdoesnotrequireadditionalinstallationandconfiguration.Although,fortheanalysisoflargemodelsitisrecommendedtousetheGUROBIpackage.

ifchangeCobraSolver('gurobi','LP',0)changeCobraSolver('gurobi6','all')end

Modelsetup.Inthistutorial,weprovidedtwoexclusivemetabolicmodels.AmitochondrialmodelandasmallmetabolicmodelspecificforGlycolysisandCitricacidcycle.Bothmodelswereextractedfromthelatestversionofthedatabaseofthehumancellularmetabolism,Recon3D[3].Forextrainformationaboutmetabolitesstructuresandreactions,andtodownloadthelatestCOBRAmodelreleases,visittheVirtualMetabolicHumandatabase(VMH,https://vmh.life).

Beforeproceedingwiththesimulations,loadthemodelintotheworkspace:

modelFileName='Recon2.0model.mat';modelDirectory=getDistributedModelFolder(modelFileName);modelFileName=[modelDirectoryfilesepmodelFileName];model=readCbModel(modelFileName);

PROCEDUREAforementioned,twokindofmapswillbeusedalongthetutorial.Dependingonthenatureofthespeciesinthemap(metabolitesorproteins),differentfunctionswillbeusedtoimporttheXMLfileproducedinCellDesignerintoMATLAB.

1.ImportaCellDesignerXMLfiletoMATLABenvironment

A)ParseaMetabolicmapThetransformXML2MapfunctionparsesanXMLfilefromCellDesigner(CD)intoaMatlabstructure.ThisstructureisorganisedsimilarlytothestructurefoundintheCOnstraint-BaseandReconstructionAnalysis(COBRA)models.

Loadtwotypesofmetabolicmaps:

1. Asmallmetabolicmodelrepresentativeofglycolysisandcitricacidcycle.2. Abiggermetabolicmaprepresentativeofthemitochondrialmetabolism.

[xmlGly,mapGly]=transformXML2Map('glycolysisAndTCA.xml');[xmlMitoMetab,mapMitoMetab]=...transformXML2Map('metabolicMitochondria.xml');

Thisfunctioninternallycallsthefunctionxml2structwhichparsestheXMLfiletoageneralMatlabstructure.Afterwards,thisgeneralstructureisreorganised.Duetothisinternalfunction,therearetwooutputs:"xml"isthegeneralMatlabstructureobtainfromxml2structfunction,whereas"map"isthedesiredfinalstructurethatcouldbelatermanipulated.

B)ParseaMetabolicmapcombinedwithProtein-Protein-Interactions(PPI)ThetransformFullXML2MapfunctionparsesanXMLfilefromCellDesigner(CD)intoaMatlabstructure.Theresultantstructurecontainsalltheinformationcommonlystoredinametabolicmap,plusextrainformationcorrespondingtoproteinsandcomplexes.

[xmlPPI,mapPPI]=transformFullXML2Map('metabolicPPIMitochondria.xml');

NOTE!TheXMLfiletobeparsedmustbeinthecurrentfolderinMATLABwhenexecutingthefunction.TIMING

ThetimetoparseaCellDesignermapfromaXMLfiletoaMATLABstructureorvice-versadependsonthesizeofthemap,andcanvaryfromsecondstominutes.

TROUBLESHOOTING(Controlerrorcheck)Inordertoproperlyvisualisethemodelingobtainedduringmodelanalysis,themapusedforthevisualisationmustmatchwiththemodelunderstudy.Errorsinreactionormetabolitenamesarehighlycommon,leadingtomismatchesandthereforewrongrepresentationofdata.

Inordertoensureapropervisualisationoftheoutputscomingfrommodelanalysis,acontrolerrorcheckishighlyrecommended.

ThefunctioncheckCDerrorsgivesfouroutputssummarisingallpossiblediscrepanciesbetweenmodelandmap.

[diffReactions,diffMetabolites,diffReversibility,diffFormula]=...checkCDerrors(mapGly,model);

Fouroutputsareobtainedfromthisfunction:

"diffReactions"summarisespresentandabsentreactionsbetweenmodelandmap.

"diffMetabolites"summarisespresentandabsentmetabolites.

NOTE!NotethathavingmoremetabolitesandreactionsintheCOBRAmodelisnormalsincethemodelcancontainmoreelementsthanthemap.Fromtheotherhand,themapshouldonlycontainelementspresentinthemodel."diffReversibility"summarisesdiscrepanciesindefiningthereversibilityofreactions.

Thelastoutput"diffFormula"summarisesdiscrepanciesinreactionsformulae(kineticrates)andalsolistsduplicatedreactions.

SomefunctionshavebeendevelopedtomodifyattributesinthemapautomaticallyfromMATLAB:

ErrorsinreactionnamescanbemanuallycorrectedintheMatlabstructurewiththefunctioncorrectRxnNameCD.Intheexampleoneofthemostcommonerrorsisshown:spacesinnamesareidentifiedaserrors.

correctRxns=diffReactions.extraRxnModel;mapGlyCorrected=correctRxnNameCD(mapGly,...diffReactions,correctRxns);

ErrorsinmetabolitescanbecorrectedmanuallyorautomaticallybythefunctioncorrectErrorMetsbygivingalistofcorrectmetabolitenames.Intheexample,"diffMetabolites.extraMetsModel"correspondtothecorrectnameofwrongmetabolitesin"diffMetabolites.extraMetsMap".

correctMets=diffMetabolites.extraMetsModel;mapGlyCorrected=correctMetNameCD(mapGlyCorrected,...diffMetabolites,correctMets);

Twofunctionscanbeusedtosolveerrorsindefiningthereactionreversibility.ThefunctionstransformToReversibleMapandtransformToIrreversibleMap,modifythereversibilityofreactionsinthemap.Reactionlistsobtainedfrom"diffReversibility"canbeusedasaninputofthenextfunctions.

Tocorrectareversiblereactioninthemap,irreversibleinthemodel.

mapGlyCorrected=transformToIrreversibleMap(mapGlyCorrected,...diffReversibility.wrongReversibleRxnsMap);

Tocorrectairreversiblereactioninthemap,reversibleinthemodel.

mapGlyCorrected=transformToReversibleMap(mapGlyCorrected,...diffReversibility.wrongIrreversibleRxnsMap);

NOTE!ReversibilityerrorsduetobasedirectionofthearrowcanonlybemanuallyfixedinCelldesigner.Whencreatinga"reversible"reactioninCellDesigner,firsta"irreverisble"reactioniscreatedandhasaparticulardirection.This"base"directioncanbeinterpretedasanerrorasitdictateswhatmetabolitesarereactantsorproducts.Inordertocheckthereactionreversibility,reactionformulaecanbeprintedfromthemapandmodelusingdifferentfunctions.

wrongFormula=mapFormula(mapGly,...diffReversibility.wrongIrreversibleRxnsMap);

Printthesameformulainthemodeltoseethecorrectedformula:

rightFormula=printRxnFormula(model,...diffReversibility.wrongIrreversibleRxnsMap);

PrintreactionformulafromthecorrectedfilemapGlyCorrected:

correctedFormula=mapFormula(mapGlyCorrected,...diffReversibility.wrongIrreversibleRxnsMap);

Anticipatedresults

Beforecorrectingformula'serrors,runthecontrolcheckagain.Probablyseveralerrorsintheoutput"diffFormula"havealreadybeentakencareofwhencorrectingpreviousoutputs.

[diffReactions,diffMetabolites,diffReversibility,diffFormula]=...checkCDerrors(mapGlyCorrected,model);

NOTE!FormulaerrorscanonlybemanuallycorrectedfromtheXMLfileinCelldesigner.

2.ExportthemodifiedMATLABstructuretoCellDesignerXMLfileInordertosavethecorrectionspreviouslymadeintoanXMLfile,twofunctionsareavailabledependingontheMATLABstructureused.

A)ParseametabolicMATLABstructureThe"transformMap2XML"functionparsedaMATLABstructure(fromasimplemetabolicmap)intoaXMLfile.Inordertosavethepreviouscorrectionsmade.

transformMap2XML(xmlGly,...mapGlyCorrected,'GlycolysisAndTCACorrected.xml');

B)ParseametabolicMATLABstructurecombinedwithPPIAsintheparsingfromXMLtoaMATLABstructure,adifferentfunctionwillbeusedwhenproteinsandcomplexesarepresentinthemap"transformFullMap2XML".

VisualisationofMetabolicnetworksEQUIPMENTSETUP

CellDesignerusestheHTML-basedcolourformat.ThisinformationifusedtomodifycolorsofpathwaysofinterestsuchasFluxes.ThefunctioncreateColorsMapcontainsallreferencesfordifferentcoloursHTMLcodetobedirectlyrecognisedinCellDesignerandassociatedtoaspecificname.Therefore,userswontneedtogiveacodebutacolournameincapitals(143colorsarerecognized).

%CheckthelistofavailablecolourstouseinCelldesigner(retrieve143colors)%opencreateColorsMap.m

PROCEDURESeveralmodificationcanbedoneinthemaps.AllattributescanbeeasilyreachedintheCOBRAtypeMATLABstructureandmodified.Thecolour,name,typeandsizeofnodescanbeeasilymodifiedfromMATLABinsteadofdoingitmanuallyinCellDesigner.Furthermore,otherattributessuchasreactiontypeorreversibility(previouslymentioned)canalsobemodified.

1.ChangereactioncolourandwidthThefunctionchangeRxnColorAndWidthmodifiesthewidthandcolourofreactionsprovidedintheformofalistofnames.

Anticipatedresults

Allreactionspresentinthemapcanbecolouredifthelistgivenisextractedfromthemapandnotfromthemodel.Seethenextexample:

Intheexample,allreactionsinthemapwillbecolouredasLight-salmonandhaveawidthof10(width=1bydefault).Furthermore,thenewlygeneratedmapwillbetransformedtobeopenedinCD.

mapGlyColoured=changeRxnColorAndWidth(mapGlyCorrected,...mapGlyCorrected.rxnName,'LIGHTSALMON',10);transformMap2XML(xmlGly,mapGlyColoured,'mapGlyRxnColoured.xml');

NOTE!inthisexampleallreactionspresentinthemaparebeinggivenasinputlist.However,thislistcancontainasetofreactionsgivenbytheuser.

2.AddcolourtometabolitesThefunctionaddColourNodeaddscolourtoallnodeslinkedtoaspecificlistofreactions.TakingasanexamplethepreviouslistwecanmodifythecolourofallthosenodesinthemapinLight-steel-blue.Furthermore,thenewlygeneratedmapwillbetransformedintoaXMLfile.

mapGlyColouredNodes=addColourNode(mapGlyColoured,...mapGlyColoured.rxnName,'LIGHTSTEELBLUE');transformMap2XML(xmlGly,...mapGlyColouredNodes,'mapGlyMetColoured.xml');

3.ChangingthecolourofindividualmetaboliteItispossibletochangethecolourofspecificmetabolitesinthemapgivenalistofmetabolitenames.HereforexamplewewanttovisualisewhereATPandADPappearinordertogiveaglobalvisualimageofwhereenergyisbeingproducedandconsumed.

First,foraneasiervisualisationallmetabolitespresentinthemapwillbecolouredinwhite.Afterwards,selectedmetabolites"mitochondrialATPandADP"willbecolouredinRed.Finally,thenewlygeneratedmapwillbetransformedintoaXMLfile.

mapATPADP=changeMetColor(mapGly,...mapGly.specName,'WHITE');%ChangethecolourofallnodesinthemaptowhitemapATPADP=changeMetColor(mapATPADP,...{'atp[m]'},'RED');%ChangespecificallythecolourofATPandADPmapATPADP=changeMetColor(mapATPADP,{'adp[m]'},'RED');

transformMap2XML(xmlGly,mapATPADP,'mapATPADPColoured.xml');

Furthermore,wecanalsocolorreactionslinkedtospecificmetabolitesbycombiningfunctionsfortheCOBRAmodelsandVisualisation.ThefunctionfindRxnsFromMetsidentifyallreactionscontainingspecificmetabolites.Herewewanttofindreactionscontaining"mitochondrialATPandADP",andcolourthesereactionsin"aquamarine".Moreover,thenewlygeneratedmapwillbetransformedintoaXMLfile.

rxnsATPADP=findRxnsFromMets(model,{'atp[m]';'adp[m]'});mapATPADPRxns=changeRxnColorAndWidth(mapATPADP,...rxnsATPADP,'AQUAMARINE',10);

transformMap2XML(xmlGly,mapATPADPRxns,'mapATPADPRxnsColoured.xml');

NOTE!ThisfuntioncolorsalistofspecificmetaboliteswhereasthefunctionaddColourNodecolorallnodeslinkedtoaspecificlistofreactions.ThiscombinationofspecificmetabolitesandreactionscanbealsodirectlydoneusingthefunctionmodifyReactionsMetabolitesmentionedbefore.However,usingthefunctionsdescribedinthissection,onecancolourmetabolitesassociatedtothesamereactionandchosecoloursindifferentways.

(ThistutorialcontinuesinPART2)*

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