Recording science in the digital era: from paper to electronic notebooks and other digital tools

393 Pages·2019·19.321 MB·English

by  Willoughby, Cerys

Recording Science in the Digital Era
FromPapertoElectronicNotebooksandOtherDigitalTools
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Recording Science in the
Digital Era
From Paper to Electronic Notebooks and
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oi:1 Cerys Willoughby
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or Email:[email protected]
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10. PrintISBN:978-1-78801-420-5
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20 Apartfromfairdealingforthepurposesofresearchfornon-commercialpurposesorfor
uly privatestudy,criticismorreview,aspermittedundertheCopyright,DesignsandPatents
5 J Act1988andtheCopyrightandRelatedRightsRegulations2003,thispublicationmay
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on notbereproduced,storedortransmitted,inanyformorbyanymeans,withouttheprior
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P Preface
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0.1 Technologyhashadanenormousimpactonscience,providingnewwaysto
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oi: capture vast amounts of data in digital form, providing mechanisms to
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g | control instruments and automate research, facilitating complex calcu-
or lationsandsimulations,andofferingwaystoaskandanswernewquestions
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s.rs in science. Despite computers and software becoming essential day-to-day
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u tools for scientists, the majority are still capturing the records of their
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s:// research using paper notebooks. Electronic Laboratory Notebooks (ELNs)
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o Such digital tools can (and should) make life easier for researchers. For
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01 example, they can perform complex calculations, connect to instrumentsto
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y automatically collect data, connect to repositories to access previous
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5 J research, provide facilities that enable collaboration and witness approval,
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on provideaccesstocontentfromanylocation,andsoon.However,suchtools
d can also have drawbacks, for example, incompatibility between systems,
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blis legacy data formats, issues around data security, and concerns about intel-
u lectual property protection. Just as importantly, such tools are often very
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complex to use in comparison to a paper notebook – what could be easier
to use than pen and paper? The march of technology is inevitable and the
needforresearcherstoworkwithELNsandotherdigitalsystemsisincreas-
ingly likely, for example, to meet the requirements of organisations,
funders, and regulatory bodies; or to collaborate with partners around the
world. Members of the scientific community need to understand what
these tools can do and how they can make things better for their research,
but they also need to understand the issues that exist in this area and how
functionalitymaydevelopinthefuture.
Although there is a relatively long history of ELN development, the
marketplace is still very much open. There are a few dominant players,
RecordingScienceintheDigitalEra:FromPapertoElectronicNotebooksand
OtherDigitalTools
ByCerysWilloughby
©CerysWilloughby2019
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
v
View Online
vi Preface
particularly targeted at corporate laboratories, but the lack of adoption of
such tools outside of these environments meansthere is avast opportunity
for developers to create new tools with capabilities that would be of
immense value to researchers. A key aspect of developing digital tools is to
ensure their usability, but in order to do this, the needs and working prac-
05 tices of researchers must be understood. Many different groups are inter-
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3 ments for data management and sharing, but the realityappearsto be that
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1 many, particularly in academic environments, do not have a good under-
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8 standingofwhatthebenefitsofELNsareandthechoicesavailable.
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8 The aim of this book isto document this area of growing importance for
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9/ all those involved in science. The book aims to not only highlight the pros
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10 and cons of moving from paper to digital recording of scientific research,
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1 but also to consider how digital tools can be designed and improved to
doi: bettersupportusersofthesesystems.Animproveddesignandfunctionality
org | can not only encourage more participation, but also ensure that these
c. systems capture and enable access to high quality records that can best
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bs.r facilitate good science into the future. There are limited materials available
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s://p discussing ELNs and other tools for capturing and managing the scientific
p record. Existing materials typically describe the design or use of ELNs and
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9 tools on the quality and content of the scientific record. There is also a
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2 limited amount of discussion about how researchers record and organise
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ul their records, and how a ‘user-centred’ focus can improve the design of
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15 tools for scientific researchers, including ELNs. This book brings together
on research into the motivations for recording scientific research, how scienti-
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he fic researchers (and chemists in particular) record their experiments and
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bli other research, the current benefits and problems with ELNs and other
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digital tools, and additional needs in this digital world that can inform
both the functionality and interface design of tools to support researchers
into the future.The book provides examples ofdifferent kindsof electronic
notebooks and ELNs for both field and laboratory scientists, and provides
some practical advice on implementing an ELN and making the transition
frompapertodigitalrecord-keeping.
In order for high quality data to be effectively used and re-used by the
scientific community, it must be both discoverable and trustworthy. This
requires high quality context in the form of metadata to be available with
the data, and for good practices to be following in curation and manage-
mentofthedataandrecords.Thisbookalsoprovidesanoverviewofdigital
curation, data management, and preservation, as well as discussing some
existingtoolsandhowtoolssuchasELNscanbebetterdesignedtocapture
metadata ‘at source’. The book also looks at issues in Open Science and
how digital tools influence the dissemination of data and results, and how
they can help to improve data sharing and public engagement in science.
Thebookalsoconsidershownewtechnologiesmaychangehowthescienti-
fic record is used and captured in the future. Although a primary topic of
View Online
Preface vii
this book is Electronic Laboratory Notebooks, and many of the examples
are from chemistry, examples of digital tools and their applications within
science are provided from across numerous disciplines, including both
field-basedandlaboratory-basedsciences.Thesameissuesarefacedacross
alldisciplines,andalthoughthespecificdigitaltoolsusedtomitigatethem
05 may be different, in the majority of cases, they are attempting to solve the
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3 I have a long list of peoplewho I would like to thank for their help, both
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1 in the production of this book, and for the research behind the examples
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8 included in the book. First, I would like to express my thanksto Colin Bird
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8 for his very helpful comments and advice on the chapters, along with his
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9/ endless support and encouragement. I thank Jeremy Frey for his guidance
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10 during my research and for helping provide the opportunity to write this
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1 book. I would like to thank Sami Kanza for her helpful advice and com-
doi: mentsonthechaptersofthisbook.IwouldliketothankConnorSheppard
org | and Helen Armes from the Royal Society of Chemistry for their help
c. and advice with the book. I would like to thank Colin Bird, Tom Clabon,
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bs.r Laura Cowen, Jeremy Frey, Steve Hughes, Sami Kanza, Katja McLaughlin,
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p Phil Willoughby for generously allowing me to use their likenesses in
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9 Iwouldalsoliketothankthevariouspeoplewho havecontributedtomy
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2 studies and user research. From Southampton University, Thomas
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ul Logothetis, Colin Flowers, Simon Coles, and students and researchers from
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15 the School of Chemistry. I have been fortunate enough tovisit a numberof
on locations around theworld to engage in user research, and wherever I have
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he gone, I have received a great welcome and hospitality. Thanks in particular
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UNSW, Sydney; Mat Todd and his team, Paul Ylioja, Swapnil Anam, and
Murray Robertson at the University of Sydney; Karl Mueller and his team,
Kelly Murphy, Nikki LaFemina, and Eric Poweleit at Penn State University;
and Mark Rutland, his family, and colleagues from KTH. Apologies to
anyoneIhaveforgotten,mymemoryismorefalliblethanmost!
CerysWilloughby
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P Contents
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ed 2.2 EarlyRecord-keeping 14
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ScientificRecord 20
2.5 Conclusion 32
References 33
Chapter3 KeepingandManagingRecords 36
3.1 Introduction 36
3.2 TheRecord-keepingProcess 37
3.3 LearningtoKeepRecords 45
3.4 StructureandOrganisationoftheRecords 47
RecordingScienceintheDigitalEra:FromPapertoElectronicNotebooksand
OtherDigitalTools
ByCerysWilloughby
©CerysWilloughby2019
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
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x Contents
3.5 SearchingandRetrievingContent 49
3.6 LinkingtoDataandOtherRecords 52
3.7 ImagesinRecord-keeping 54
3.8 Record-keepingBehaviour 56
3.9 ThePrivateNatureofNotebooks 57
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sc. 4.5 ManagingtheLaboratory:LaboratoryInformation
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Chapter5 ManagingandPreservingDigitalResearchData 87
5.1 Introduction 87
5.2 ReproducingScience 89
5.3 ResearchDataManagementandDigitalCuration 92
5.4 MetadataforCuration 96
5.5 TypesofMetadata 99
5.6 ProvenanceandIdentification 104
5.7 PreservingtheRecord 107
5.8 Conclusion 111
References 112
Chapter6 AMoreIn-depthLookatElectronicLaboratoryNotebooks 115
6.1 Introduction 115
6.2 BenefitsofElectronicNotebooks 116
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Contents xi
6.3 ElectronicLaboratoryNotebookExamples 122
6.4 ExperienceswithElectronicLaboratory
Notebooks 127
6.5 BarrierstoAdoptionofElectronicLaboratory
Notebooks 130
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8.3 ConceptualModelsandMetaphors 165
8.4 ResearchRoles 167
8.4.1 Administrator 168
8.4.2 Supervisor/PrincipleInvestigator 168
8.4.3 Researcher 169
8.4.4 Collaborator 169
8.4.5 Observer 169
8.4.6 Teacher 170
8.4.7 Student 170
8.5 Personas 170
8.6 Scenarios 171
8.6.1 Scenario1:ClosedResearchIncluding
InteractionwithaFundingBody 171
8.6.2 Scenario2:FullyOpenResearchIncluding
InteractionwithGlobalScientific
Collaborators 174
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8.6.3 Scenario3:ClosedResearchinaLocal
ResearchGroup 174
8.6.4 Scenario4:UndergraduatePracticalCourse 178
8.7 Storyboards 180
8.8 NextStepsinDesigningDigitalTools 188
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References 231
Chapter10 CreatingContextfortheRecordUsingMetadata 233
10.1 Introduction 233
10.2 MetadataUseinScience 236
10.3 User-definedMetadatainScience 241
10.4 UseofUser-definedMetadatainLabTrove
andOtherPlatforms 242
10.5 MetadataFrictionandtheBurdenofCuration 247
10.6 AutomaticCreationofMetadataand
SmartAssistance 250
10.7 InvitationstoEncouragetheCreationof
User-definedMetadata 253
10.8 EncouragingCurationatSourcebyUsingCuesand
ChangingPerspectives 256