Developing an open source ELN to support open & interdisciplinary science

DEVELOPING AN OPEN
SOURCE ELN TO SUPPORT
OPEN & INTERDISCIPLINARY
SCIENCE
Jeremy G. Frey
University of Southampton
@profechem
13/01/2017Jeremy Frey LabTrove ELN
1

A Chemist’s Digital Aura
http://mosaically.com/PhotoMosaic/3289771f-0bf3-49bf-bc8a-
1810167096ff
2

3

The three Norns (Fates)
Past, Present and Future
Research Notetaking in the Digital Era
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This journal is c The Royal Society of Chemistry 2013 Chem. Soc. Rev., 2013, 42, 8157--8175 8157
Cite this: Chem. Soc. Rev.,2013,
42, 8157
Laboratory notebooks in the digital era: the role
of ELNs in record keeping for chemistry and
other sciences
Colin L. Bird, Cerys Willoughby and Jeremy G. Frey*
Egyptian evidence of scientific records dates back almost 50 centuries. In more recent times da Vinci
and Faraday provide role models for scrupulous recording of ideas, observations, and conclusions. Their
medium was paper, but despite the quality of their notebooks, we cannot turn the clock back. Our
primary purpose is to review the influences of the digital era on scientific record keeping. We examine
the foundations of the emerging opportunities for preserving and curating electronic records focussing
on electronic laboratory notebooks (ELNs), with an emphasis on their characteristics and usability.
Introduction
The origin of science itself is a subject for philosophical discus-
sion; so dating the first recording of a scientific endeavour
must almost inevitably also be a matter for speculation. How-
ever, we do know of an instance of recorded occupational
medicine that has been attributed to the Egyptian architect,
physician, and statesman Imhotep (27th century BCE), based
on a study of the Edwin Smith papyrus.1
The History of Science article in Wikipedia covers the
development of science and scientific methodology from the
ancient civilisations through to the modern era, and includes
several examples of the recording of information in a manner
that we could regard as scientific. Observations were repre-
sented numerically as well as in narrative form, for example
the recording of astronomical information in Mesopotamia.2
There is also historical evidence of the reuse and repurposing of
Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton,
Highfield, Southampton, SO17 1BJ, UK. E-mail: j.g.frey@soton.ac.uk
Colin L. Bird
Having obtained his BSc and PhD
in Chemistry at the University of
Southampton, Colin Bird joined
IBM UK Laboratories. After con-
tributing to IBM’s electrochromic
display technology, he transferred
to the IBM UK Scientific Centre to
develop advanced image and
visualisation applications. His
work on content-based image
retrieval led to a one-year
secondment in 1999 back to the
University of Southampton. On
returning to IBM, he was involved
in various aspects of information management, specialising in
classification and metadata, and became an information architect.
When he left IBM, he resumed his collaboration with Professor Jeremy
Frey on e-Research projects, which began in 2000 as an industrial
partner for the CombeChem project.
Cerys Willoughby
Cerys Willoughby obtained her
BSc in Geology from the
University of Wales, Aberystwyth
and her MSc in Environmental
Sciences from University of
Wales, Swansea. After spending
some time teaching teenagers
and adults, she joined IBM UK
Laboratories as a software
engineer. Working in a variety of
roles in the company she
specialised in usability and
information architecture. She
began collaborating with Professor
Jeremy Frey in 2007 as a guest lecturer on usability and accessibility
for an e-Research course and is currently undertaking a part time PhD
at the University of Southampton.
Received 30th March 2013
DOI: 10.1039/c3cs60122f
www.rsc.org/csr
Chem Soc Rev
REVIEW ARTICLE
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5
Jeremy Frey LabTrove ELN
Experiences with a researcher-centric ELN†
Katrina A. Badiola,a
Colin Bird,b
William S. Brocklesby,c
John Casson,d
Richard T. Chapman,e
Simon J. Coles,b
James R. Cronshaw,a
Adam Fisher,b
Jeremy G. Frey,*b
Danmar Gloria,f
Martin C. Grossel,b
D. Brynn Hibbert,f
Nicola Knight,b
Lucy K. Mapp,b
Luke Marazzi,b
Brian Matthews,d
Andy Milsted,bh
Russell S. Minns,b
Karl T. Mueller,g
Kelly Murphy,g
Tim Parkinson,h
Rosanne Quinnell,a
John S. Robinson,h
Murray N. Robertson,a
Michael Robins,a
Emma Springate,e
Graham Tizzard,b
Matthew H. Todd,a
Alice E. Williamson,a
Cerys Willoughby,b
Erica Yangd
and Paul M. Yliojaa
Electronic Laboratory Notebooks (ELNs) are progressively replacing traditional paper books in both
commercial research establishments and academic institutions. University researchers require specific
features from ELNs, given the need to promote cross-institutional collaborative working, to enable the
sharing of procedures and results, and to facilitate publication. The LabTrove ELN, which we use as our
exemplar, was designed to be researcher-centric (i.e., not only aimed at the individual researcher's basic
needs rather than to a specific institutional or subject or disciplinary agenda, but also able to be tailored
because it is open source). LabTrove is being used in a heterogeneous set of academic laboratories, for a
range of purposes, including analytical chemistry, X-ray studies, drug discovery and a biomaterials
project. Researchers use the ELN for recording experiments, preserving data collected, and for project
coordination. This perspective article describes the experiences of those researchers from several
viewpoints, demonstrating how a web-based open source electronic notebook can meet the diverse
needs of academic researchers.
1 Introduction
Electronic Laboratory Notebooks (ELNs) are progressively
replacing traditional paper books for keeping the experimental
record,1
especially in commercial research establishments.
Important drivers for this change are the need to comply with
regulatory requirements and the desire to protect and expand
intellectual property (IP); structured notebook systems should
provide the necessary audit trails.2
ELNs offer considerably
more to researchers and to research groups than do systems
that offer only content management and sharing facilities. ELNs
unite the objects that comprise the record of research and
preserve the provenance of each object and its contribution to
the overall narrative.
The 2013 review of laboratory notebooks in the digital era (by
three of the authors)1
not only explores the history and the
expanding use of electronic laboratory notebooks but also
presents the results of a comprehensive survey of the literature
relating to ELNs. It is clear from the survey and from consid-
erations of the scientic applications for which ELNs have been
deployed that digital notebooks come in a range of embodi-
ments. The distinction between commercial and academic
institutions is but one aspect; in many cases the designers of
ELNs have adapted both the input and output to match the
specic applications for which the ELNs are used. Most ELNs,
especially the major commercial offerings, are proprietary.
There is, however, increasing interest in open source imple-
mentations, as they enable individual laboratories or institu-
tions to tailor the operation and the data preservation to suit
their particular needs. The review also examines the social and
technical issues that combine to inuence moves from paper to
digital notebooks.
There are many concerns in the academic environment with
the adoption of digital notebooks. The obvious issues of cost are
signicant but more fundamental are the concerns with the
a
School of Chemistry, The University of Sydney, NSW 2006, Australia
b
Chemistry, University of Southampton, Southampton, SO17 1BJ, UK. E-mail: J.G.
Frey@soton.ac.uk
c
OptoElectronics Research Centre, University of Southampton, SO17 1BJ, UK
d
Scientic Computing Department, STFC Rutherford Appleton Laboratory, Chilton,
Didcot, Oxfordshire, OX11 0QX, UK
e
Central Laser Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot,
Oxfordshire, OX11 0QX, UK
f
School of Chemistry, UNSW Australia, Sydney, NSW 2052, Australia
g
Penn State University, Department of Chemistry, University Park, 104 Chemistry
Building, PA, USA
h
Electronics and Computer Science, University of Southampton, Southampton, SO17
1BJ, UK
† Electronic supplementary information (ESI) available. See DOI:
10.1039/c4sc02128b
Cite this: Chem. Sci., 2015, 6, 1614
Received 17th July 2014
Accepted 20th October 2014
DOI: 10.1039/c4sc02128b
www.rsc.org/chemicalscience
1614 | Chem. Sci., 2015, 6, 1614–1629 This journal is © The Royal Society of Chemistry 2015
Chemical
Science
PERSPECTIVE
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http://commons.wikimedia.org/wiki/File:ISS-30_Ice_floes_along_the_Kamchatka_coastline.jpg
Reducing and
Managing
Uncertainty
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Intelligent Open Access to Data
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StructureGate

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13/01/2017
If only I knew exactly how
she did this experiments
I know all this supplementary
information could be useful but will
people really remember the format? Is
it worth all the hassle?I wish I could get the
numbers from this
graph - the pdf is not
much use.
I wish I had
recorded things at
the start the way I
do now…..
Typical Laboratory 9

WHATS THE STORY IN BALAMORY,
WOULDN'T YOU LIKE TO KNOW?
10

User Focus
Semantic Rigour
blog3
LabTrove
myTea
More
Tea
Smart
Tea
oreChem
Frey & Bird
TeaTrove
11

13/01/2017
The Trove Software
12www.labtrove.org

OPEN SOURCE WEB BASED
„ LabTrove - E-Science and Jisc Funding
„ Open Source Software – code available
„ Hosted on Southampton servers or researchers own hardware
„ Entries stored as ASCII XML, Files native format
„ Support for basic research needs in a flexible way
„ Allow researchers to use their own tools
„ Export and Archive abilities
„ Business Model and Community
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13/01/2017
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LABTROVE AND USER DEFINED
METADATA
13/01/2017
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17
Comment on Figures

18
Linking
Bi-directional
linking can
extended to
a group of
Troves

19

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21
Text Analysis and
Lookup Services

BlogMyData Project - Godiva
13/01/2017
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Accessibility
and Usability
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24
Templates

discussion
cc: sjdunphy - https://www.flickr.com/photos/19888921@N00
25

Figure 7. Visualization of posts as a network of resources.
Milsted AJ, Hale JR, Frey JG, Neylon C (2013) LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards
a Marked Up Record of Work in a Bioscience Research Laboratory. PLoS ONE 8(7): e67460.
doi:10.1371/journal.pone.0067460
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067460
13/01/2017
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ARCHIVE
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13/01/2017
LabTrove Open Notebooks
Mat Todd’s Malaria Project
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Select
entries
(all)
Export as HTML
“static” copy
Zip and send to
repository
LabTrove Notebooks
13/01/2017
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13/01/2017
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DataCite DOI

http://royalsocietypublishing.org/content/371/1983/20120090.jnl_roysco_tab_art
Use of Deep Zoom technique
31

Electronic
Laboratory
Notebooks
ELNs
Comparison with
traditional paper
notebooks
Communication
Collaboration
Sharing
Linking
Curating
• Higher Quality Record
• Natural linking to data
and external resources
• Easier Collaboration
• Improved planning
• Improved discussions
• Efficiency gain in
production of
presentations/reports
• Change the nature of
Professor/Student
interactions
Impact on researchers
13/01/2017
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LAB ECOSYSTEM
„ ELN is not something to be considered in isolation
„ Needs to be considered as part of a whole (digital) lab
ecosystem
33

• Without middleware • With middleware
34
Middleware: The SRF LabBroker
Software:
Get the data into the Trove before the
users even look

35

36
SLACK

37
Experimental data & analysis available via a
database

FUTURE
38

User Focus
Semantic Rigour
blog3
LabTrove
myTea
More
Tea
Smart
Tea
oreChem
Frey & Bird
TeaTrove
39

PLATFORMS
cc: hjl - https://www.flickr.com/photos/92605333@N00
40

Ontologycc: Rich Anderson - https://www.flickr.com/photos/99105016@N00
41

COMMUNITYcc: quinn.anya - https://www.flickr.com/photos/53326337@N00
42
Research to Product

All I am saying is that now is the time to
develop the technology to deflect an
asteroid
We must speed up the knowledge discovery process
13/01/2017
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Trust me Mort - no electronic communications
superhighway, no matter how vast and sophisticated,
will ever replace the art of the schmooze
Thank you for listening
44

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