fanmod-manual

FANMODfastnetworkmotifdetection–manual–FlorianRascheandSebastianWernickeInstitutf¨urInformatik,Friedrich-Schiller-Universit¨atJena,Ernst-Abbe-Platz2,D-07743Jena,Germany{m3rafl,wernicke}@minet.uni-jena.de.June12,20061Introductionfanmod[6]isatoolforfindingso-callednetworksmotifsinanetwork,thatis,itfindssmallvertex-inducedsubgraphsthatoccursignificantlymoreoftenthaninrandomnetworks.Forageneralintroductiontotheconceptofnetworkmotifs,see[3,2].fanmodisabletosearchfornetworkmotifsofsizebetweenthreeandeightvertices.Itcanalsoanalyzecolorednetworks,allowingtheusertobringmoreinformationintothenetworkratherthanjustconnectivities.fanmoddetectsmotifsbyusingtheso-calledrand-esualgorithmwhichmakesitfasterthansimilarprogramsbasedonotheralgorithms,especiallyforlargermotifs.Moredetailsontherand-esualgorithmcanbefoundin[5].fanmodfeaturesagraphicalinterfaceforeasysetupofalgorithmparameters;theresultscanbeexportedtohtml.Eventhoughthismanualhasbecomequitelongbycoveringallthedetails,theuseoffanmodshouldbequiteintuitive.Wehavepaidattentiontogivingallparameterssounddefaultvalues,soifyouwishtostartdetectingmotifsrightawaytheshortintroductioninSection3shouldbeallyouneed.Wheneveryouwanttotunetheparameters,findoutmoreaboutsomedetailsoftheprogram,orifanythingelseremainsunclear,pleaseconsultthemoredetailedsections:–Section4dealswiththealgorithmparametersyoucansetbeforerunningthemainalgorithm.–Section5detailswhathappenswhenthealgorithmisrunningandhowitcanbeinfluenced.–Section6providesdetailsonhowtoviewandprocesstheresultsthatareoutputbythemainalgorithm.–Section7providesthenecessarydetailsonworkingwithcolorednetworks.Happymotifdetecting!2Fig.1.Thethreeareasofthemaininterfacewindowoffanmod.Theycorrespondtothethreeworkingstepswhenusingthetool—settingupthealgorithm,runningthealgorithm,andprocessingtheresults.2LicenseYoumayusefanmodforallofyourresearchpurposesaslongasyoudothefollowing:–Youacknowledgeitsuseinanypublishedworkthatfullyorinpartderivesitsresultsfromitsusage.(Ifyouwishtomakeabibliographicalreference,pleaseconsiderciting[5]forthatpurpose.)–Youdonotsellanythingthatisbasedonorderivedfromyouruseoffanmod.Absolutelynoguaranteesorwarrantiesaremadeconcerningthesuitability,cor-rectness,oranyotheraspectofthedistributedfiles.Anyuseisatyourownrisk.Notethatfanmodusesthenautyprogramversion2.2byBrendanMcKay[1];hencenauty’slicenserestrictionsalsoapplytoyouruseoffanmod.13QuickStartThissectiondescribesthebasicstepsofamotifsearchwithoutgoingtoomuchintodetail;wehavetriedtogivealloptionsinfanmodsounddefaultvalues.Hence,thissectionisperfectforsomefirststepswithfanmod—andforthosewhosimplycannotwaittofindtheirfirstmotifs;-).1Morespecifically,thismeansthatyoumaynotdetectmotifsforanyapplicationwithnontrivialmilitarysignificanceasnauty’slicenseforbidsthat.3Fig.2.Theframesandbuttonsofthemainwindow,namedastheyarereferencedinthetext.Figure1showsthemainwindowthatappearswhenyoustartfanmod.Theinterfacefollowsatop-downlogic,i.e.,theupperhalfisforsettingthealgorithmparametersandthelowerhalfforrunningthealgorithmandviewing/processingitsresults.AmoredetailedsubdivisionoftheseareasintoframesisshowninFigure2.3.1SelectinganInputGraphThefirststepistochooseaninputfilethatdescribesthenetworkyouwouldliketoanalyze.Youcanselectthisfilewithintheinputgraphframe.Also,youcanselectwhetherthenetworkisdirectedandwhethertheverticesand/oredgesarecolored.Inthisquickstartsection,wewillonlydealwithuncolorednetworksforthesakeofsimplicity.Ifyouwishtoanalyzecolorednetworks,pleasereadSection7.Theinputfileshouldcontainonelineforeachedgeinyournetwork,eachlinemustcontainatleasttwointegers.Itmaycontainuptofiveintegers,butthatisonlyimportantforcolorednetworks.Hence,alineintheinputfilelookslikethis:int1int2[int3][int4][int5]Ifthenetworkisundirected,thelineisinterpretedasanedgebetweentheverticeslabelledint1andint2;ifthenetworkisdirected,itisinterpretedasadirectededgefromvertexint1tovertexint2.ThisinterpretationisillustratedinFigure3.Notethatitisrecommendedthattheverticesinthenetworkare4012301230103022331011003203213undirecteddirectedFig.3.Interpretationoftheinputfileforundirected(left)anddirectednetworks(right).labelledwithconsecutiveintegers,thelowestintegerbeingzero(seeSection4.1fordetails).3.2SettingtheOptionsThemostimportantoptionsofthemotifsearchareinthealgorithmoptionsframe.Hereyoucanchoosethesubgraphsize(thatis,thesizeofthemotifstobedetected)andwhethertoperformafullenumerationofsubgraphsorjustsamplesomeoftheminthenetwork.Forinformationonsamplingandtheappropriateparameters,pleaserefertoSection4.2.Asmotifsaredetectedbycomparingtheirfrequencyofoccurrenceintheoriginalnetworktotheirfrequencyofoccurrenceinanumberofsimilar,yetrandomizednetworks,youhavetostatehowmanyrandomnetworksshouldbelookedatandhowtheyshouldbecreated.Thenumberofrandomizednetworkscanbesetinthenumberofnetworksboxontherightoftherandomnetworksframe.AnexplanationoftheotheravailableoptionsisdeferredtoSection4.3.Intheoutputframeyoucansetthefilewheretheoutputistobewrittentoandselectwhichfileformatistobeused.Asadefault,anoutputfilenameisderivedfromtheinputfile.3