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BestPrac*cesforDataManagementWhenUsingInstrumenta*on
Atutorialoneffec*vedatacollec*on,saving,andprocessingmethods
CreatedbytheOfficeofResearchComplianceandTrainingAspartoftheResearchandDataIntegrity(ReaDI)Program
SupportedbyColumbiaUniversityStandingCommiIeeontheConductofResearch
Columbia University | ReaDI Program Research and Data Integrity
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WhyManagementofDataisCrucial
• Gooddatamanagementprac*ceskeepyouorganized– Datafilesareeasiertolocate– Less*mespentrepea*ngexperimentsbecauseadatafileisunabletobelocated
– Reduced*mesearchingfordatafileswhenwri*ngpublica*onsorthesis
• Somefederallyfundedgrantsandmanypublica*onsrequiredatabemadepublicallyaccessible– Wellmanageddatawitheasilyiden*fiablefilenamesaidinthedistribu*onofdata
• Maintainingaccuraterecordsprovidesintegritytoresearchresults,defendsagainstaccusa*onsoffraud,andsuppliesproofofintellectualproperty
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Outline
I. Bestprac*cesforLabelingtheLaboratoryNotebookandNamingDataFiles
II. PlanningAheadIII. Organiza*onandCollec*onofDataIV. Addi*onalConsidera*onsUsing
Instrumenta*onandProcessingDataV. Summary
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I.BestPrac*cesforLabelingtheLaboratoryNotebookandNamingDataFiles
• Thissec*onwillintroduce:– Theimportanceofusingalaboratorynotebook– Notebooklabelingprac*ces– Datafilenamingprac*ces
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ImportanceoftheLaboratoryNotebook• Alaboratorynotebookisanimportanttoolbecause:
– ItisawriIenrecordofprocedures,reagents,data,calcula*ons,thoughts,explana*ons,andresultsofexperiments
– Itisalegaldocumentusedtodefendintellectualpropertyandaccusa*onsoffraud
– Itisknowledgeforfutureresearchers– Itisthefounda*onofathesisandotherpublica*ons
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LaboratoryNotebook:AResearcher’sToolforDataOrganiza*on
• BeforegeXngstartedwithdatacollec*onitisimportanttochoosealabelingsystemforyournotebook,anddocumentit
• Anotebooklabelingsystemwillbeatoolusedtoreferencedatacollectedtoapar*cularentrybytheresearcheroranybodywan*ngtoviewresearcher’sresults
• Formoreinforma*onaboutgoodlaboratorynotebookprac*cesrefertotheGoodLaboratoryNotebookPrac0cesTutorial
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LabelingYourLaboratoryNotebook• CheckwithyourPIorlabmanager
forestablishedconven*onsforyourresearchgroup
• Onthecoverofyourlabnotebookinclude,asappropriate:– Yourname– Yourposi*on– YourPI’sname– The*tleoftheprojectorstudy– Datesthenotebookused– Volumenumber
• Labelthespineifusingaboundnotebook
IndicatesthenotebookbelongstoSciN.Tistandthatitisthe4thnotebookusedbySci
Ini*alsofSciN.Tistandnotebooknumber
SNTIV
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LabelingYourLaboratoryNotebook
• Includethesameinforma*ononthefirstpageofthenotebook,alongwith:– Youremail– Yourphonenumber– Yourlaband/orofficeaddress– Theabbreviatednamebywhichthisnotebookwillbeindicatedinfilenamesorotherreferences
Thisnotebookbelongsto:Sci N. Tist
Contactinforma*on:[email protected]
Office #: 212-555-555 Smith Hall
1000 First St. Room 300 NY, NY 01001Datesused:
Feb 2010-Jan 2011Notebook#:
IVNotebookabbrevia*on:
SNT_IV
i
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BestPrac*cesforDataFileNaming• Checkiftherearestandardsthatarerequiredbyyourresearchgroup
and/ordiscipline• Filesnamesshouldinclude:
– Dateofdatacollec*on(ordatafilecreated),lis*ngyearfirstsortsfileschronologically
– Notebookandpagenumberthatitrefersto– Ifmul*plefilesarebeingcreatedonthesamedateandreferringtothe
samesample,notebook,andpagenumberuseanumbering(orleIering)codetodis*nguishbetweendatafiles
– Addi*onally,filenamesmayincludetheprojectiden*fica*onorabriefdescrip*on
Iden*fier: DateNotebook/Page#
Sample/SpecialNotes
Series
Interpreta*on: SciN.TistNotebookIVPage285
Sample&detectorused
Differentfilesofsamesampleindicatedby
con*nua*onofleGering
DateTaken:Dec17th2010
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• Writedownthenameofthedatafileinthecorrespondingnotebooktomaintainarecordofthedatafilebeingcreated
• Considercrea*ngatextfile,tobesavedinthesamefolder,thatdefinesthefilenamingconven*on
• Someconven*onssuggestaninstrumentiden*fica*on• Beconsistentanddocumentthenamingconven*onthatischosen• Specialconsidera*onneedstobegivenwhennamingfileswithPII
(PersonallyIden*fiableInforma*on)orPHI(PersonalHealthInforma*on).RefertoRASCALtrainingsTC0019orTC0087forregula*onsoutlinedbyHIPAAandhumansubjectsresearch
BestPrac*cesforDataFileNaming,Con*nued
20101217_SNT_IV_285_Fe2O3_inLens_a.*f
101217_SNT_IV285_Fe2O3_inLens_a.*f101217_SNT4_285_Fe2O3inLens_a.*f
Allofthefollowingwouldbeconsideredequivalentfilenames:
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• LeIersfromAtoZandnumbers0to9• Useunderscoresratherthanspaces• Usebriefnames(<30characters)• Avoidusingspecialcharacters– Ex:\`’•=/<>^:;|#*().?%,“@!+{}~-[]
• The3-leIerfileextensionshouldbereservedforapplica*on-specificcodes,e.g.,.wrl,.mov,.*f
• Differen*atefilenamepartsusingmixedcasesorunderscores• Whencrea*ngasequen*allynumberedseriesoffiles,useleading
zeroessothattheysortproperlye.g.,file001.txt,file002.txt,file003.txt…file042.txt
TipsforNamingDataFiles
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I.Summary
• CheckwithyourPIorlabmanageriftherearestandardsfornotebookanddatafilenaming.Adheretotheexpecta*onsofyourPIandresearchdiscipline
• Laboratorynotebooksshouldbelabeledsothatitiden*fiestheresearcheranddatesused,andifapplicable,theresearchproject
• Documentyourlaboratorynotebooklabelingconven*onandbeconsistent
• Filenamesofcollecteddatashouldincludethedateofcollec*on,notebookandpagenumberiden*fier,andashortdescrip*on
• Onceadatafilenamingformatischosen,writeitdownandbeconsistent
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II.PlanningAhead
• Thissec*onwilladdress– Importantdetailstoconsiderbeforeexperimenta*on– Notebookprepara*on– Tipsforcrea*ngdatatables– Informa*onthatneedstobeincludedinthelaboratorynotebook
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ImportantDetailstoConsiderBeforeExperimenta*on
• Beforebeginningdatacollec*on,itisessen*altoknowhowtheinstrumentsavesandexportsdata
• Unsurehowtheinstrumentsavesandexportsdata?– Askafellowgroupmember(graduatestudent,post-doc,staffscien*st,etc.)
– Askthepersonwhomaintainstheinstrument– Prac*cewithanunimportantsample(blank)
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Ques*onsRelatedtoInstrumenta*on
• Whatfileformatshoulddatabeexportedas?– Knowwhichfileformatsarecompa*blewithotheropera*ngsystems,analysesprograms,anddataarchiving
– Avoidusingfileextensionsthatareuniquetoapar*cularso�wareusedfordatacollec*on.Ifdataareavailableonlyinclosedorproprietaryformats,arethereprogramsavailableforfilemigra*ontoamoreusefulformat?
– Mostcompa*bleformatsinclude:• ASCII,PDF,.csv,FLAC,TIFF,JPEG2000,MPEG-4,XML,RDF,.txt,.r
• Whatdescriptorsshouldbeadded?Whatinforma*onwillyouneedtofind,iden*fy,orunderstandthefileinthefuture?– Unitsandotherrelevantinforma*on– Independent&dependentvariablecolumnheaders– Theabilitytoaddnotesordescriptors
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NotebookPrepara*on• Priortorunningsamplesorstar*ngtheexperiment,makesureyou
knowtheanswerstothefollowing,andthattheanswerscanbefoundintheexperimentdocumenta*on– Howmanysampleswillbelookedat?– Howiseachsampledifferent?– Whatdescriptorswillyouusetodis*nguisheachsample?– Ifthesamesampleisbeingprobedmul*ple*mes,whatarethevarying
parameters?– Whatistheminimumamountofinforma*onthatmustberecordedto
reproducetheexperiment?• Createatableinyournotebookwithdescrip*veheaders
– Createatemplate(canuseWordorExcel)thatcanbere-usedeach*methatpar*cularinstrumenta*onisbeingused
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GeneralTipsforCrea*ngATable• Usedescrip*velabels,includingunits,inheaderrow,foreachcolumn• Thecolumnfurthesttothele�shouldbetheindependentvariable(the
itemthatischanging,i.e.yoursample)• Dependentvariablesshouldfollowinthenextcolumns• Anyderivedvariables(fromcalcula*ons)followthedependentvariables.
Calcula*onsandformulasneedtobedocumented• Deriveddatashouldreflectthesamenumberofsignificantfiguresasthe
measuredvalues• Ifcrea*ngatemplate,theuseofformaXng(ex:color,boldface,or
italicizedfonts)canhelpvisuallyorganizedata
hIp://www.sedl.org/a�erschool/toolkits/science/pdf/ast_sci_data_tables_guidelines.pdf
Sample pH(Trial1) pH(Trial2) pH(Trial3) AveragepH
Unfunc*onalizedWO3nanopar*clesinH2O
3.58 3.62 3.64 3.61
Citricacidmodified-TiO2nanopar*clesinH2O
5.38 5.44 5.45 5.42
IndependentVariable DerivedVariableDependentVariables
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RelevantInforma*ontobeIncludedinNotebook• AnyparametersthatareREQUIREDtoreproducetheexperiment
needtoberecorded– E.g.:Substrates,energyoutput/input,solu*onsused,backgroundsamples,etc.
• Anyobserva*onsregardingtheinstrumenta*onprocessthatwouldbeconsidered“unusual”– E.g.:noisebackgroundduetoconstruc*on,elevatedtemperaturesduetobrokenAC,etc.
• Anyso�warethatisuniquetothatinstrumentoracodethathasbeenwriIenforpar*culartypesofexperiments– E.g.:LabVIEWprogramspecificallydesignedforexperiment
• Ini*alobserva*onswhiledataisbeingcollected• Duringdatacollec*on,anypre-plannedtablesshouldbefilledin
a�ereachfileiscreated
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ExampleNotebookEntry
2010December17ScanningElectronMicroscopy(SEM)imagesof
285 286
Fe2O3nanopar*cles.Synthesized2010December15asreferredtoonpage282ofthisnotebook
InstrumentParameters:Accelera*ngvoltage:2.0kVUsedbothIn-LensandSE2detectorsSubstrateused:Si-wafer<0.001Ω
Specialnotes:construc*ononfloorcreatedsomeminordifficultywithfocusingimages
ImageFileName Detector Scale
20101217_SNT_IV_285InLens 1um
_Fe2O3_InLens_b
_Fe2O3_InLens_c
20101217_SNT_IV_285
Used Bar
_Fe2O3_InLens_a
20101217_SNT_IV_285
20101217_SNT_IV_285
_Fe2O3_SE2_d
200nm
200nm
2um
InLens
InLens
SE2
Datafileloca*oninResearchGroupArchive:SciNTist_ResearchàInstrumenta*onàSEMà20101217_SNT_IV_285
ü
ü
ü
ü
ü
üü Thoroughdescrip*onofsampleü Instrumentparametersusedü Specialnotesü Tablethatorganizesdatacollectedü Descrip*vefilenamewith
referencetonotebookloca*onü Wheresaveddatafilesarelocated
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II.Summary
• Bepreparedpriortodatacollec*on• Createatableinnotebooktoaidinorganiza*onofthe
experimentanddatacollec*on• Thenotebookneedstocontainallthenecessaryinforma*on
sothattheexperimentcouldberepeatedbyyourselforotherresearchers
• Includethedatafilenameinthenotebookentryalongwiththefileloca*on
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III.Organiza*onofCollectedData
• Thissec*onwillevaluatetheimportanceof:– Archivingdata– Anelectronicfilingsystem– Useoffoldersandsub-folders– Useofsharedcomputersandportablestoragedevices– Transferringdatafromaportablestoragedevicetodataarchive
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ArchivingData
• Itisessen*althatamethodforarchivingdataisestablishedpriortoanydatacollec*on
• ItistheresponsibilityofthePItomaintainarchiveddata;checkwithyourPIontheproceduresforstoringandsavingdata
• ArchiveddatashouldbesecuredasrequiredbyUniversitypoliciesandprocedures,andstate,and/orfederalregula*ons
• Archiveddatashouldbeinoneloca*onthatisaccessiblebyallgroupmembersand/orcollaborators(e.g.:researchgroupdrive,onlinerepository,etc.)withatleasttwoback-ups– Inaddi*ontothefileonthelocalmachine,thereshouldbeonecopy
backeduponaseparatelocalsystem,andonecopyheldatageographicallydistantloca*on
• Formoreinforma*onregardingdatamanagementandstorage,pleasevisit(InsertRDMtutoriallinkbyJoelandAmy)
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ElectronicFilingSystemforDataOrganiza*on
• Beforedatacollec*on,itisimportanttodetermineanelectronicfilingsystemthatbestsuitsyourresearchproject
• Theuseofafilingsystemhelpsorganizecollecteddata
• Withinthearchive,itmaybeusefultocreatean“Instruments”folder;ataminimum,afileforEACHtypeofinstrumentusedtocollectdatashouldbecreated
• Ifmorethanoneofthesametypeofinstrumentisused,butinadifferentfacility,withdifferentcapabili*es,etc.,useunderscorestohelpiden*fyeachone– Itisextremelyimportanttodocumentwhere
eachdatasetoriginates,forreproducibilityofexperiments
ArchivedData
Instrumenta*on
XRDSEMNMR_Apollo
NMR_Hermes
TwodifferentNMRinstrumentswithdifferentfeaturese.g.strengthofthemagnet
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OrganizingSub-folders• Withineachinstrumentfolder,createanewfolderinwhichallthe
datacollectedcanbeorganized• Useofsub-foldershelpskeepdataorganizedforeasierreferral• Namesub-foldersusingdate,descrip*ons,notebookiden*fiers,etc.
– Remainconsistentwiththenamesofsub-folders WithintheNMR_Hermesfolder,sub-
foldershavebeencreated
Foldersarelabeledwithdate,notebookreference,andbriefsampledescrip*on Eachfoldercontains
datarelatedtothispar*cularsample,e.g.:1H-NMR,13C-NMR,COSY,etc.
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Collec*ngDataUsingPortableDataStorage• Manyinstrumentsareconnectedtoacomputerthatissharedwith
manyotherresearchersfromdifferentgroupsanddisciplines• Ifprivilegesareallowed,createafolderonthesharedcomputer
withyournametouseastemporarystoragewhilecollec*ngdata• Donotusesharedcomputersforpermanent(long-term)data
storage• Wheneverpossible,savedatatoasecureserverthatemploys
regularbackupprotocols,withqualitycontrolcheck• Aportableflashdrivecanbeusedtoremovedatafromshared
computerstoapermanentstorageloca*on• Usesamefolderandsub-folderorganiza*ononportableflashdrive• Usepasswordprotectedflashdriveifsavingsensi*vedata
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TransferringDatatoaPermanentLoca*on• Flashdrivesshouldneverbeusedaspermanentstorage• Usingthesamefolderandsub-folderorganiza*onfacilitatestransferof
data– Clickanddrag(orcopyandpaste)datafilesintocorrectfoldersondataarchive
• Neverdeletedatafromportabledeviceun*ldatahasbeentransferredandcanbeconfirmedbyeitheropeningdatafileand/orusingachecksumalgorithm Samesub-folder
iden*fica*on
CopyandPaste
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III.Summary
• Adataarchivesystemwithmul*pledataback-upsshouldbeestablishedbythePIoftheresearchgroup
• Crea*onoffoldersfordifferenttypesofinstrumenta*onkeepsdatafilesorganized
• Useofsub-foldersallowsforeasierreferraltocollecteddatafiles• Portableflashdrivesarenotmeantforpermanentdatastorage• Datacollectedonportabledevicesshouldbetransferredtoadata
archiveASAP• Specialrequirementsgoverntheproperhandlingofhumansubjects
data
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IV.Addi*onalConsidera*onsUsingInstrumenta*onandProcessingData
• Thissec*onwillproviderecommenda*onsforthefollowingscenarios:– Useofinstrumenta*onwithusermodifiedso�wareand/orprogramming
– Useofinstrumentsthathavelimitedabilitydescribingdatabeingcollected
– Processingmul*pledatasets– Instrumenta*onethics
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InstrumentsThatAllowAddi*onalRemarks
• Someinstrumentshavemul*plewaysofallowingaddi*onalcommentswithintheprogram
• Ifyouchoosetou*lizetheseop*ons,then:– Beawarethatthesecomments
areo�ennotexportabletoanotherfileformat,andthattheoriginalproprietaryprogrammayberequiredtoviewthesecomments
– BesuretorecordALLcommentsaboutthedatafileinyournotebookaswell
– Donotusethisop*ontoreplacedescrip*vecommentsinyournotebook
– Donotusethisop*ontoreplacedescrip*vedatafilenames
• Theuserisabletoincludeanyiden*fiersaboutthesample
• The“DataView”op*oninthisprogramallowstheremarkstobeseen;usefulforquickanalysis
• Theremarksarenotexportedwiththedatafile
hIp://www.ecochemie.nl/Products/Echem/So�ware/Tutorials.html
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UniqueSo�wareandProgramming• Whenusingso�warelikeLabVIEWtowriteaspecificprogram,itis
importantto:– RecordinnotebooktheEXACTmethodsandcodesused,includinghand-drawingsand/orprinted-outimagesaffixedtolaboratorynotebookpage
– Describethedifferentelementsused,includingmodelnumbersifapplicable
– Savethefilesothatitcanbereferredtothenotebookentry20090207_SNT_III_45_Torque_Isokinetic_Contraction_BlockDiagram
ThisLabVIEWwascreatedonFeb.7,2009tomeasuretorqueparametersandcanbereferredtopage45inSciN.Tist’snotebook#3
hIp://www.nyu.edu/classes/mcdonough/m&eiii.htm
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Sample Excita*onwavelength
PulseEnergy(mJ)
SavedAs RenamedAs
10nmNiNanopar*clesSNT_V_32
400nm 0.100 Print_01
20nmNiNanopar*clesSNT_V_15
550nm 0.050 Print_02
75nmNiNanopar*clesSNT_V_40
600nm 0.100 Print_03
InstrumentsThatAssignDefaultFileNames• Someinstrumentsdonotallowuserstogivefilenames,butgenerate
adefaultname• Forthesetypesofinstruments,itisusefultoincludeanaddi*onal
columninyourtabletorecordthedefaultnamegiven,thenrenamefileslater
Defaultfilenamegiventoexporteddatafromtheinstrument
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RenamingDefaultFileNames• Defaultnamesgivenodescrip*onofthedatatheycontain• RenamedatafilesASAPusingnotebooktableasguidance
– Right-clickfileandselectrenameop*onorfilerenamingtoolsformul*plefiles
• Useafilenamethatisdescrip*ve,sothefilesareeasiertofindforlaterreferral
Sample Excita*onwavelength
PulseEnergy(mJ)
SavedAs RenamedAs
10nmNiNanopar*clesSNT_V_32
400nm 0.100 Print_01 20110914_SNT_V_32_10nmNiNPs_400nm
_Excite
Useofaddi*onalcolumnforrenamedfilename• maintainsorganiza*on• maintainsawriIenrecordinnotebookof
datafilebeingcreated• simplifiesreferencewhensearchingfor
electronicdatafiles
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ProcessingData• Somedatasetsrequirefurthermanipula*onsa�ercollec*on(e.g.,
baselinecorrec*on,backgroundsubtrac*on,etc.).Thesetransforma*onscannottaketheplaceofrawdata
• Neveraltertherawdataset– Indicatethatitistherawdatainthefilename– Saveeachdatamanipula*onwithitsownuniquefilename
• Ifworkingwithmul*pledatasetsinonespreadsheetordatabase,usedescrip*ve*tlesthatrefertotherawdatafile
A B C D E F1
Time(sec)
MeasuredPhotovoltageat350nmexcita*onfordiffentSnO2Samples,taken201004012 Voltage(mV)
3
DarkBackgroundNoiseSignal
20100401_SNT_IV_34100nmSnO2NanorodsSynthesized20100329
20100401_SNT_IV_34100nmSnO2Nanopar*clesSynthesized20100315
20100401_SNT_IV_34100nmSnO2NanorodsBackgroundSubt(C#-B#)
20100401_SNT_IV_34100nmSnO2Nanopar*clesBackgroundSubt(D#-B#)
4 0.00E+00 1.0547E-04 2.8320E-03 1.2793E-03 2.7266E-03 1.1738E-035 5.00E-10 1.4453E-04 2.9297E-03 1.4258E-03 2.7852E-03 1.2812E-036 1.00E-09 1.2109E-04 3.1250E-03 1.9531E-03 3.0039E-03 1.8320E-03
Filenameofdataandbriefdescrip*on ExplainshowdatawasmanipulatedDescribestheinstrument
parameters,date,anddependentvariablesIndependentvariableandinstrumentbackground
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Instrumenta*onBestPrac*ces• AwriIenrecord(eitherpaperordigital)shouldbeusedto
recordwhousedtheinstrumentandwhen.Besuretofilloutthelogaccurately
• Inthelogbook,recordanymalfunc*ons,maintenanceperformed,changedseXngs,etc.
• Mostinstrumentsareequippedwithsecuritycontrols,whichiden*fiespersonand*mestamp.TheseshouldNEVERbedisabled
• Eachuser/groupshouldhaveuniqueloginandpassword.NEVERshareyourpassword,especiallywithunauthorizedusers
• Loginandlogbookinforma*onprovides“audittrail”ofinstrumentusage
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SummaryofBestPrac*cesforDataManagementUsingInstrumenta*on
1. AlwayscheckwithyourPIaboutexpectedstandardstobefollowedbyallgroupmembers
2. Usedocumentednotebookanddatafilenamingconven*onstokeepdataorganized
3. Preparenotebookpriortothebeginningofexperimenta*on4. Useatabletoorganizedataasitiscollected5. Organizedatausingelectronicfilingsystemwithdescrip*vefolderand
sub-foldernames6. UseportablestorageonlyasTEMPORARYmeanstotransferdatatoa
permanentloca*on7. Understandthecapabili*esofinstrumentsregardingexpor*ngdatafiles8. Whenprocessingdata,neveralterrawdatasets9. Usecleardescriptorsifcombiningmul*pledatasetstoonespreadsheet10. Useinstrumentlogbooksanddonotsharelogininforma*on
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Addi*onalResourcesandFurtherReading:
• TutorialonGoodLaboratoryNotebookPrac0ces• TutorialonDataManagement• RASCALtrainingsTC0019and/orTC0087forPHI,PII• Laboratorynotebookanddatafilenamingbestprac*ces:– hIp://datalib.edina.ac.uk/mantra/libtraining/Session2GroupExercise1.pdf
– hIp://uresearch.miami.edu/?p=103&s=25– hIps://www.training.nih.gov/assets/Lab_Notebook_508_%28new%29.pdf
CreatedbyMichelleC.Benson,[email protected]
AIribu*onNon-CommercialInterna*onal4.0
