How to write a thesis and which software tools to use.docx
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Howtowriteathesisandwhichsoftwaretoolstouse
Howtowriteathesis(Bachelor,Master,orPhD)andwhichsoftwaretoolstouse
HowtowriteaPhDthesis?
Thisisnotatrivialtask.Relatedliteratureneedstobefound,notesneedtobetakenandfinallythethesishastobedraftedandwrittenincludingthecreationofthebibliography.DozensofbooksexistabouthowtodoaliteraturesurveyandhowtowriteaPhDandscholarlyliteratureingeneral(e.g.[1-9]).However,softwaretoolsthatmighthelpindoingaliteraturesurveyorwritingathesisarehardlycoveredbythesebooks,ifatall.ThisissurprisingasmanysoftwaretoolsexistfacilitatingthedailyworkofaPhDstudent.
InthistutorialwepresentanewmethodtoreviewingscholarlyliteratureanddraftingaPhDthesiswithmindmappingsoftware,PDFreadersandreferencemanagers. ThistutorialfocusesonPhDstudents.However,BachelorandMasterstudentscanusetheherepresentedmethodsaswelltoplanandwritetheirthesis.Whatmakesthistutorialspecialisthefactthateverything–PDFfiles,thecontentofPDFs(bookmarks)andreferencesareintegratedwithmindmappingandwordprocessingsoftware.
TomakethetutorialbetterunderstandableweprovidemanyexamplesforwhichweassumethatyouwanttowriteaPhDthesisaboutacademicsearchengines.
Pleasenotethat
∙Alltoolspresentedinthistutorialarefreeandopensource(exceptMicrosoftWord)
∙AlltoolspresentedinthistutorialarebasedonJavaandrunonWindows,LinuxandMacOS(again,exceptMicrosoftWord)
∙Alltoolsusedinthistutorialmaybesubstituted:
oSciPloreMindmappingmaybesubstitutedwithFreeMind,MindManager,XMINDandmostothermindmappingtoolsallowingtolinkPDFfiles
oFoxitReadermaybesubstitutedwithAdobeAcrobat
oJabRefmaybesubstitutedwithanyotherreferencemanagersupportingBibTeX(e.g.BibDesk,ReferencerandMendeley)
oMicrosoftWordmaybesubstitutedwithOpenOfficeorLaTeXoranyotherwordprocessorthatBibTeXsupport/pluginsexistfor
YouwillspendthenextcoupleofyearsdoingyourPhD(ormonthsifyouaredoingaMasterorBachelor).WehighlyrecommendtoreadthisandothertutorialstofindoutthewaythatisbestforyoutomanageyourliteratureandreferencesandwriteyourPhD.Spendingafewhoursnowwillsaveyoudaysifnotevenweekslater.Thistutorialwillbeupdatedfromtimetotimetoconsiderthelatestfeaturesofthetoolspresentedhere.Lastupdateofthistutorial:
Mai2010
Beforestarting,wepresentsomeuserfeedbackthatwegotbyemailforoursoftwareandthistutorial.Wehopeitmotivatesyoutoreadthecompletetutorial
.
Thistutorialisdividedintothreeparts.thefirstpartcovershowtomanageliterature.ThesecondpartcovershowtodraftaPhDthesis.ThefinalpartcovershowtowriteaPhDthesisandhowtomanagereferences.
HowtoWriteaPhDThesis(PartI):
LiteratureManagement
TowriteagoodPhDthesisitiskeytokeeptrackofrelatedworkinyourfield.Thatincludesthatyouknowalltherelevantstudies,results,facts,ideasandsooninyourfield.Keepinmind,bytheendofyourliteraturereviewyouwillhavereadoratleastskippedthroughhundredsofbooksandpapers.Youmustbeageniustoremembereveryinterestingfactandideayouhavereadinapaperwithoutanytools.Beforethecomputer-age,academicscouldonlyrelyonindexcards,(postit)notes,highlightingpens,indices,etc.Withcomputers,andespeciallymindmappingsoftware,newpossibilitiesevolved.
Inthispartofthetutorialweexplainhowtosearchforliteraturewithacademicsearchengines.ThenweshowhowyoucreatesummariesofyourPDFswithbookmarksandkeeponoverviewofallimportantinformationinourmindmap.Bytheend,yourmindmapwillcontainliterallyallinformationthatyouhaveconsideredtobeimportant.Wheneveryouwanttoknowsomething,youcanlookitupinyourmindmap,andreadinmoredetailaboutitbyclickingonthelinktothePDF.
Searchingfor(Electronic)Literature
AprerequisiteforagoodPhDthesisistoknowwhatothershavedoneinyourfieldofresearch.Buthowtofindthisrelatedwork?
Duetocomputersandtheinternet,searchingforliteraturehaschangeddramaticallyoverthelastyears.Insteadofusingcataloguesinlibraries,studentscanusefulltextsearchofferedbyacademicsearchenginesanddatabasessuchasGoogleScholar,SciPloreandACMDigitalLibrary.Inaddition,academicsearchenginesusuallyoffersophisticatedrankingalgorithmswhichhelpinfindingthemostrelevantdocuments[10-12].
Dozensofacademicsearchenginesexist.Somearefocusingonspecificdisciplinessuchascomputerscienceandsomearetryingtocoverseveralorevenalldisciplines.Forthefieldofcomputerscience,popularacademicdatabasesareSpringerlink,ACMDigitalLibraryandIEEEXploreaswellasScienceDirectandtosometimesEmeraldInsight(Wikipediaprovidesyouwithanextensivelistofavailableresources).Allthesedatabasesrequireasubscriptiontoaccesstheircontent.Ifyouarelucky,youruniversityhasanagreementwiththesedatabasessoyoucanaccessalltheirarticlesforfree.Askyoursupervisororinyourlibrarywhichdatabasesyouhaveaccessto.FreealternativesareCiteSeerandSciPlorewhichprovideyoufreeaccesstomanyacademicarticles.GoogleScholarisaspecialcase:
Oftenyoucandownloadthelinkedcontentforfreebutnotalways.
Inthistutorialwewillfocussolelyonthemanagementofelectronicliterature.
StoringFilesinFolderStructures
MostacademicsearchenginesanddatabasesoffertodownloadscholarlyliteratureinPDFformat.Theprobablysimplestwaytostore(andretrieve)thesePDFsisareasonablestructuredfoldersystem.EachPDFcanbestoredinonefolderwhichislabeledwithanappropriatedescriptor.ItisusuallyhelpfultogiveameaningfulfilenametothePDFsuchasthearticle’stitle.Incasethatonedocumentfitsintotwoormorecategories,mostoperatingsystemsallowcreatingashortcutoraliasforafile(seepicure).Somefeelthisapproachasbeingtoostructuredandprefertagging.
Possibility:
SavePDFsforyourPhDindifferentfolders
Tagging
Taggingallowsassigningmultiplekeywords(tags)toafileindependentlyofwherethefileisstored.Basedonthesetags,userscanretrievethefilesfromtheirharddrive.PopulartaggingtoolsforthedesktopareTag2Find,iTag,andPunakea.TherearealsoservicesallowingtotagandstoreacademicarticlesonlinesuchasConnotea,CiteULikeorBibsonomy.
However,fortheapproachwepresentinthistutorialwewillfocusondesktoptoolsand,moreimportantly,neitherfolderstructuresnortagsareimportantfortheapproachwepresent.Ofcourse,agoodfolderstructureneverharmsbutyoudonotreallyneedit.
StartingtoSearchandStoringFilesinOneflatFolder
InthebeginningofyourPhDyoushouldjustsearchforthemostrelevantkeywordsinacademicsearchenginesandstorewhateverpaperyougetonyourharddrive.IfyouwantedtodoaPhDaboutacademicsearchengines,itmightmakesensetostartdoingsomeresearchaboutGoogleScholar,oneoftheleadingacademicsearchengines.Let’sassumeyouhavefoundahandfullofinterestingPDFsandstoredtheminc:
\myliterature\(don’tspendtoomuchtimewithjudgingtherelevanceofaPDF.Ifthetitleorabstractsoundinteresting,storeit).
YourfirstPDFsforwritingaPhDthesis
MemorizingaPDF’simportantinformation
Whatyoureallyneedtoknowasaresearcheris:
WherehaveIreadwhichinformation?
Foryourthesisitisworthlesstoknowsomethingbutnotwheretheinformationisfrom.Eventuallyyouwillhavetoreferencetheorigin(ideallywithpagenumber).Asafirststept,PDFreadersareperfecttokeeptrackofaPDF’smostimportantinformation.YouneedaPDFreaderthatcancreatebookmarksandideallyhighlightpassagesandcreateannotations.IfyouhaveaccesstoAdobeAcrobatthat’sgreat(thefreeAcrobatReaderisnotsufficient).OtherwisewewouldrecommendthefreeversionofFoxitReader.
Now,wheneveryoureadaninterestingPDFyoucreateabookmarkforeverystatementthatmightbeinterestingforyourPhDthesis.Wewouldalsosuggesthighlightingtheinterestingtextdirectlyinthedocument.Havealookatthepicture.
HighlightingimportantinformationforyourPhDthesis
ThisisthePDFofanarticletitled“AcademicSearchEngineOptimization(ASEO):
OptimizingScholarlyLiteratureforGoogleScholarandCo.”.ItisabouthowtogetyourpapersindexedandwellrankedbyacademicsearchenginessuchasGoogleScholar.IfyouwriteyourPhDaboutacademicsearchenginesitmightbeinterestingtokeepinmindthatthispaperistheveryfirstpaperaboutacademicsearchengineoptimization.Andalsothedefinitionof“academicsearchengineoptimization”mightberelevantlaterforyourPhDthesis.Thereforeyoucreateabookmarkforeachofthisinformation(seethepicture).
Itisuptoyouhowdetailedyoumakethebookmarkstructure.Intheverybeginningitmightbeappropriatetocreatejustonebookmarkthatbrieflydescribesthepaper(e.g.“firstpaperaboutacademicsearchengineoptimization”).Ifyouneedmoreinformationyoucouldcomebacktothispaperlater.Itiseasytogetlostwithalltheinformationyouread.So,forthebeginning,really,createbookmarksonlyfortheveryimportantinformation.WhenfinishingreadingthefirstPDFyouproceedwiththeotherPDFsinthesameway.
ManaginginformationfromvariousPDFs
Inthelongrun,itisnotveryhelpfultohavetheinformationonlyinthePDFs.Hereiswheremindmappingjoinsthegame.Mindmapswere‘invented’byTonyBuzaninthe1970s[13].Am