"writing a story" electronic laboratory notebooks - orc seminar univeristy of...

1

Writing a Story – Electronic Laboratory NotebooksORC Seminar

Bill Brocklesby and Jeremy Frey12 June 2014

18/04/2023 ORC Electronic Lab Notebooks 2


Outline• Introduction

• Open Access vs Intelligent Access to Data

• Digital Notebooks - Advantages

• The Trove Software

• Ultrafast X-Ray Example

• Data Citation

• The Future


Review ArticleLaboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciencesColin L. Bird, Cerys Willoughby and Jeremy G. Frey Chem. Soc. Rev., 2013,42, 8157-8175

DOI: 10.1039/C3CS60122FThis article is licensed under a Creative Commons Attribution 3.0


Data Curation in the Chemical Sciences

http://dx.doi.org/10.3789/isqv25no3.2013.02

ORC Electronic Lab Notebooks 6

Intelligent Open Access to Data 18/04/2023


StructureGate


THE NARRATIVEWhat 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


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

18/04/2023


The Trove Software

www.labtrove.org


BlogMyData Project - Godiva

18/04/2023


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.0067460http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067460

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067460


ULTRA FAST X-RAY GROUP


ElectronicLaboratoryNotebooks

ELNs

Comparison with traditional paper

notebooks

Communication Collaboration

SharingLinking

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 researchers18/04/2023


DATA CITATIONSupplementary 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

Use of Deep Zoom technique

Data covers a huge range of scale and typeNew 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


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”

18/04/2023

It is not necessary to change.

Survival is not mandatory.W. Edwards Deming

ORC Electronic Lab Notebooks 2818/04/2023

LabTrove Open Notebooks Mat Todd’s Malaria Project


DATA EXPLOSIONCRYSTALLOGRAPHY E-CRYSTALS

Built on the ePrints system used at Southampton as a repository for research outputs


18/04/2023

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

18/04/2023


Change in the whole way we design and build

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

18/04/2023


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

18/04/2023

"writing a story" electronic laboratory notebooks - orc seminar univeristy of...

Data & Analytics