"Writing a Story" Electronic Laboratory Notebooks - ORC Seminar Univeristy of Southampton

Writing a Story –
Electronic Laboratory
Notebooks
ORC Seminar
Bill Brocklesby and Jeremy Frey
12 June 2014 1

24/06/2014 2ORC Electronic Lab Notebooks

Outline
• Introduction
• Open Access vs Intelligent Access to
Data
• Digital Notebooks - Advantages
• The Trove Software
• Ultrafast X-Ray Example
• Data Citation
• The Future

Review Article
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
Chem. Soc. Rev., 2013,42, 8157-8175
DOI: 10.1039/C3CS60122F
This article is licensed under a Creative Commons
Attribution 3.0

Data Curation in the Chemical Sciences
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http://dx.doi.org/10.3789/isqv25no3.2013.02
ORC Electronic Lab Notebooks

Intelligent Open Access to Data
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6ORC Electronic Lab Notebooks

StructureGate

THE NARRATIVE
What is the story? What is the why?

Faraday’s laboratory notebooks
are also remarkable in the amount
of detail that they give about the
design and setting up of
experiments, interspersed with
comments about their outcome
and thoughts of a more
philosophical kind. All are couched
in plain language, with many vivid
phrases of delightful spontaneity….
Peter Day, ‘The Philosopher’s Tree: A Selection of Michael
Faraday’s Writings’

The integrity of science as a discipline rests on the ability of
scientists to reproduce the claims of others.
While none of the organic chemistry journals go to the same
lengths as Organic Syntheses, where each procedure must be
reproduced as described in an independent laboratory before
publication, ……..
sufficient detail so that the procedures can be reproduced and
provide sufficient data to establish the structures …….
This information is necessary for the review process …… to base
their experiments on published work.Methods are as important as the data

24/06/2014
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

Archiving of data
• Experiments are often repeated
– Data stored locally on a
computer and can’t be found
– Handwriting can’t be read
– Laboratory notebooks lost or
damaged
– Correct data not recorded
first time round
http://www.ecs.soton.ac.uk/regenesis/pictures
24/06/2014

24/06/2014
The Trove Software
13
www.labtrove.org

BlogMyData Project - Godiva
24/06/2014

LabTrove and User defined metadata

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

ULTRA FAST X-RAY GROUP

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

DATA CITATION
Supplementary data linked to laboratory notebooks

doi: 10.1098/rsta.2005.1630 Phil. Trans.
R. Soc. A 15 August 2005 vol. 363 no.
1833 2075-2095

Kenji Takeda, Graeme Earl, Jeremy Frey, Simon
Keay, and Alex Wade
Enhancing research publications using Rich
Interactive Narratives Phil. Trans. R. Soc. A. 2013
371 20120090; doi:10.1098/rsta.2012.0090
24/06/2014
Use of Deep Zoom technique
Data covers a huge range of scale and type
New ideas for presenting to avoid overload

Select
entries
(all)
Export as HTML “static”
copy
Zip and send to
repository
LabTrove Notebooks

Chemical Biology
Paper in PLoS
• Export of the entire laboratory
notebook (LabTrove) and deposit with
FigShare.
• At 50 Mb it exceeded the upload limit
of the journal!

http://ses.library.usyd.edu.au/handle/2123/10461
Example from Mat Todd
University of Sydney

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DataCite DOI

Open Notebook
Science
• Certainly not always the way to work!
– IPR, Commercial, long term projects, recognition
issues, etc
• But
– Makes connection much easier if the data and
processes are “Open”
– Easy to export & access of “Linked-Data”
24/06/2014
It is not necessary to change.
Survival is not mandatory.
W. Edwards Deming

24/06/2014
LabTrove Open Notebooks
Mat Todd’s Malaria Project

DATA EXPLOSION
CRYSTALLOGRAPHY E-
CRYSTALS
Built on the ePrints system used at Southampton as a repository for
research outputs

24/06/2014
Graph/Network provides
intuitive navigation

DISSEMINATION IS PART
OF THE RESEARCH
Bringing dissemination in to the lab… use and
re-use of data… the digital research notebook

Change in the whole way we design and build
24/06/2014
3D Printers: A radical change to the experimental section
of a paper!

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
24/06/2014

Open Data

LabTrove -> RSS -> Email / Twitter

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
24/06/2014

"Writing a Story" Electronic Laboratory Notebooks - ORC Seminar Univeristy of Southampton

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"Writing a Story" Electronic Laboratory Notebooks - ORC Seminar Univeristy of Southampton