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
•...
Review Article
Laboratory notebooks in the digital era: the role of
ELNs in record keeping for chemistry and other
science...
Data Curation in the Chemical Sciences
24/06/2014 5
http://dx.doi.org/10.3789/isqv25no3.2013.02
ORC Electronic Lab Noteboo...
Intelligent Open Access to Data
24/06/2014
6ORC Electronic Lab Notebooks
StructureGate
24/06/2014 7ORC Electronic Lab Notebooks
THE NARRATIVE
What is the story? What is the why?
24/06/2014 8ORC Electronic Lab Notebooks
Faraday’s laboratory notebooks
are also remarkable in the amount
of detail that they give about the
design and setting up ...
The integrity of science as a discipline rests on the ability of
scientists to reproduce the claims of others.
While none ...
24/06/2014
If only I knew exactly how
she did this experiments
I know all this supplementary
information could be useful b...
Archiving of data
• Experiments are often repeated
– Data stored locally on a
computer and can’t be found
– Handwriting ca...
24/06/2014
The Trove Software
13
www.labtrove.org
ORC Electronic Lab Notebooks
24/06/2014 14ORC Electronic Lab Notebooks
BlogMyData Project - Godiva
24/06/2014
15ORC Electronic Lab Notebooks
LabTrove and User defined metadata
24/06/2014 16ORC Electronic Lab Notebooks
Figure 7. Visualization of posts as a network of resources.
Milsted AJ, Hale JR, Frey JG, Neylon C (2013) LabTrove: A Ligh...
ULTRA FAST X-RAY GROUP
24/06/2014 18ORC Electronic Lab Notebooks
Electronic
Laboratory
Notebooks
ELNs
Comparison with
traditional paper
notebooks
Communication
Collaboration
Sharing
Linki...
DATA CITATION
Supplementary data linked to laboratory notebooks
24/06/2014 20ORC Electronic Lab Notebooks
doi: 10.1098/rsta.2005.1630 Phil. Trans.
R. Soc. A 15 August 2005 vol. 363 no.
1833 2075-2095
24/06/2014 21ORC Electronic ...
Kenji Takeda, Graeme Earl, Jeremy Frey, Simon
Keay, and Alex Wade
Enhancing research publications using Rich
Interactive N...
Select
entries
(all)
Export as HTML “static”
copy
Zip and send to
repository
LabTrove Notebooks
24/06/2014 23ORC Electroni...
Chemical Biology
Paper in PLoS
• Export of the entire laboratory
notebook (LabTrove) and deposit with
FigShare.
• At 50 Mb...
http://ses.library.usyd.edu.au/handle/2123/10461
Example from Mat Todd
University of Sydney
24/06/2014 25ORC Electronic La...
24/06/2014 26
DataCite DOI
ORC Electronic Lab Notebooks
Open Notebook
Science
• Certainly not always the way to work!
– IPR, Commercial, long term projects, recognition
issues, e...
24/06/2014
LabTrove Open Notebooks
Mat Todd’s Malaria Project
28ORC Electronic Lab Notebooks
DATA EXPLOSION
CRYSTALLOGRAPHY E-
CRYSTALS
Built on the ePrints system used at Southampton as a repository for
research ou...
24/06/2014
Graph/Network provides
intuitive navigation
31ORC Electronic Lab Notebooks
DISSEMINATION IS PART
OF THE RESEARCH
Bringing dissemination in to the lab… use and
re-use of data… the digital research n...
Change in the whole way we design and build
24/06/2014
3D Printers: A radical change to the experimental section
of a pape...
All I am saying is that now is the time to
develop the technology to deflect an
asteroid
We must speed up the knowledge di...
Open Data
24/06/2014 36ORC Electronic Lab Notebooks
LabTrove -> RSS -> Email / Twitter
24/06/2014 37ORC Electronic Lab Notebooks
Trust me Mort - no electronic communications
superhighway, no matter how vast and sophisticated,
will ever replace the art...
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"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

  1. 1. Writing a Story – Electronic Laboratory Notebooks ORC Seminar Bill Brocklesby and Jeremy Frey 12 June 2014 1
  2. 2. 24/06/2014 2ORC Electronic Lab Notebooks
  3. 3. Outline • Introduction • Open Access vs Intelligent Access to Data • Digital Notebooks - Advantages • The Trove Software • Ultrafast X-Ray Example • Data Citation • The Future 24/06/2014 3ORC Electronic Lab Notebooks
  4. 4. 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 24/06/2014 4ORC Electronic Lab Notebooks
  5. 5. Data Curation in the Chemical Sciences 24/06/2014 5 http://dx.doi.org/10.3789/isqv25no3.2013.02 ORC Electronic Lab Notebooks
  6. 6. Intelligent Open Access to Data 24/06/2014 6ORC Electronic Lab Notebooks
  7. 7. StructureGate 24/06/2014 7ORC Electronic Lab Notebooks
  8. 8. THE NARRATIVE What is the story? What is the why? 24/06/2014 8ORC Electronic Lab Notebooks
  9. 9. 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’ 24/06/2014 9ORC Electronic Lab Notebooks
  10. 10. 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 10ORC Electronic Lab Notebooks
  11. 11. 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 11ORC Electronic Lab Notebooks
  12. 12. 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 12ORC Electronic Lab Notebooks
  13. 13. 24/06/2014 The Trove Software 13 www.labtrove.org ORC Electronic Lab Notebooks
  14. 14. 24/06/2014 14ORC Electronic Lab Notebooks
  15. 15. BlogMyData Project - Godiva 24/06/2014 15ORC Electronic Lab Notebooks
  16. 16. LabTrove and User defined metadata 24/06/2014 16ORC Electronic Lab Notebooks
  17. 17. 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 24/06/2014 17ORC Electronic Lab Notebooks
  18. 18. ULTRA FAST X-RAY GROUP 24/06/2014 18ORC Electronic Lab Notebooks
  19. 19. 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 24/06/2014 19ORC Electronic Lab Notebooks
  20. 20. DATA CITATION Supplementary data linked to laboratory notebooks 24/06/2014 20ORC Electronic Lab Notebooks
  21. 21. doi: 10.1098/rsta.2005.1630 Phil. Trans. R. Soc. A 15 August 2005 vol. 363 no. 1833 2075-2095 24/06/2014 21ORC Electronic Lab Notebooks
  22. 22. 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 22ORC Electronic Lab Notebooks
  23. 23. Select entries (all) Export as HTML “static” copy Zip and send to repository LabTrove Notebooks 24/06/2014 23ORC Electronic Lab Notebooks
  24. 24. 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! 24/06/2014 24ORC Electronic Lab Notebooks
  25. 25. http://ses.library.usyd.edu.au/handle/2123/10461 Example from Mat Todd University of Sydney 24/06/2014 25ORC Electronic Lab Notebooks
  26. 26. 24/06/2014 26 DataCite DOI ORC Electronic Lab Notebooks
  27. 27. 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 27ORC Electronic Lab Notebooks
  28. 28. 24/06/2014 LabTrove Open Notebooks Mat Todd’s Malaria Project 28ORC Electronic Lab Notebooks
  29. 29. DATA EXPLOSION CRYSTALLOGRAPHY E- CRYSTALS Built on the ePrints system used at Southampton as a repository for research outputs 24/06/2014 29ORC Electronic Lab Notebooks
  30. 30. 24/06/2014 Graph/Network provides intuitive navigation 31ORC Electronic Lab Notebooks
  31. 31. DISSEMINATION IS PART OF THE RESEARCH Bringing dissemination in to the lab… use and re-use of data… the digital research notebook 24/06/2014 32ORC Electronic Lab Notebooks
  32. 32. Change in the whole way we design and build 24/06/2014 3D Printers: A radical change to the experimental section of a paper! 34ORC Electronic Lab Notebooks
  33. 33. 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 35ORC Electronic Lab Notebooks
  34. 34. Open Data 24/06/2014 36ORC Electronic Lab Notebooks
  35. 35. LabTrove -> RSS -> Email / Twitter 24/06/2014 37ORC Electronic Lab Notebooks
  36. 36. 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 38ORC Electronic Lab Notebooks
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