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Contributions of Jean-Claude Bradley
to the vision and execution of
Open Notebook Science
Andrew SID Lang, Oral Roberts Un...
Why Open?
Q: Why did you decide to adopt an open approach?
A: In thinking about what has meaning for me as a
scientist, I realized t...
Open Source Science
Open Source Science >>
Open Notebook Science
Influenced by: Peter Murray-Rust & Beth Ritter-Guth
http://drexel-coas-elearning.blogspot.com/2006/0...
Open Notebook Science
Jean-Claude Bradley
Dec 11, 2008
NIST
Associate Professor of Chemistry
Drexel University
The current paradigm of doing and
sharing science in chemistry
1. Design experiments based on
established or potentially n...
What kind of (chemical) worldview
has this approach created?
1. Selective bias towards which
experiment are even attempted...
Open and Closed Science
Traditional
Lab Notebook
(unpublished)
Traditional
Journal
Article
Open Access
Journal Article
Ope...
Motivation: Faster Science, Better Science
Where is Science headed?
WE ARE HERE
There are NO FACTS,
only measurements embedded
within assumptions
Open Notebook Science maintains
the integrity of data pr...
TRUST
PROOF
Open Notebook Science Challenge
Co-conceived with Cameron Neylon
https://www.flickr.com/photos/24801682@N08/2824469941/
ht...
359 ONS Experiments
4,640 CC0 non-aqueous solubilities
28,645 CC0 melting points
http://figshare.com/articles/Jean_Claude_...
Where is Science headed?
WE ARE HERE
Open Notebook Science >>
• He gave soooooo much early feedback on how ChemSpider
could serve the community – the first advisory group member
• For ...
Feeding ONS MP Data into ChemSpider
 ONS data deposited into ChemSpider and linked out to ONS pages
Feeding ONS Sol. Data into ChemSpider
 ONS Solubility Challenge
Linking to ONS Data from ChemSpider
Building Teaching Tools
• JC loved to use technology to TEACH. He used freely
available tools to do so – including ChemSpi...
ChemSpider Spectra
www.SpectralGame.com
http://www.jcheminf.com/content/1/1/9
Collaborations in Openness
• JC believed in HIGH-QUALITY data
• He invested himself, and his students, in validating,
chec...
Supporting Open Data
JC and Drug Discovery
• JC cared passionately about neglected disease research
• Many of our conversations were around bet...
Journal of Cheminformatics Issue
 Seven articles already published and three more in the
pipeline. Submit yours before th...
Contributions of Jean-Claude Bradley to the vision and execution of Open Notebook Science
Contributions of Jean-Claude Bradley to the vision and execution of Open Notebook Science
Contributions of Jean-Claude Bradley to the vision and execution of Open Notebook Science
Contributions of Jean-Claude Bradley to the vision and execution of Open Notebook Science
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Contributions of Jean-Claude Bradley to the vision and execution of Open Notebook Science

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For the majority of chemists driven to share their data openly Jean-Claude (JC) Bradley will forever be the father of Open Notebook Science (ONS). Having coined the term in 2006 JC spent the next few years working to educate us in the ONS philosophy, developing tools, systems and even games for the community. This presentation will provide an overview of JC’s contributions to Open Notebook Science by examining some of the various projects that he conducted with his students and collaboratively. The outcome of the work he led includes a number of open datasets that have been used by scientists around the world, online prediction models that are accessible to anyone, games that have been played by thousands of scientists and an enormous collection of presentations, video tutorials and Open Courseware that will likely be references for the Open Notebook Science movement for many years to come.

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Contributions of Jean-Claude Bradley to the vision and execution of Open Notebook Science

  1. 1. Contributions of Jean-Claude Bradley to the vision and execution of Open Notebook Science Andrew SID Lang, Oral Roberts University Antony J Williams, ChemConnector
  2. 2. Why Open?
  3. 3. Q: Why did you decide to adopt an open approach? A: In thinking about what has meaning for me as a scientist, I realized that the work I was doing wasn’t having the kind of impact that I would like it to have, and it was not benefitting mankind in the way I would have hoped. I concluded that this was partly a consequence of secrecy. However, I couldn’t be open with the project I was then working on, because I was collaborating with someone who didn’t feel the same way as me. My decision to do open science meant cutting ties with my previous collaborators. Having done that in 2005, I started the project UsefulChem. http://www.infotoday.com/it/sep10/Poynder.shtml Interview With Jean-Claude Bradley The Impact of Open Notebook Science by Richard Poynder
  4. 4. Open Source Science
  5. 5. Open Source Science >>
  6. 6. Open Notebook Science Influenced by: Peter Murray-Rust & Beth Ritter-Guth http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
  7. 7. Open Notebook Science Jean-Claude Bradley Dec 11, 2008 NIST Associate Professor of Chemistry Drexel University
  8. 8. The current paradigm of doing and sharing science in chemistry 1. Design experiments based on established or potentially new theories. 2. Execute and record experimental outcomes in private notebooks. 3. When a sufficient narrative emerges selective experimental data are combined to publish, with a limited amount of “supplementary supporting data”
  9. 9. What kind of (chemical) worldview has this approach created? 1. Selective bias towards which experiment are even attempted. 2. Overconfidence in our understanding since deviant or ambiguous results are rarely reported.
  10. 10. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks RESEARCH TEACHING
  11. 11. Motivation: Faster Science, Better Science
  12. 12. Where is Science headed? WE ARE HERE
  13. 13. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  14. 14. TRUST PROOF
  15. 15. Open Notebook Science Challenge Co-conceived with Cameron Neylon https://www.flickr.com/photos/24801682@N08/2824469941/ http://usefulchem.blogspot.com/2008/09/open-notebook-science-challenge.html
  16. 16. 359 ONS Experiments 4,640 CC0 non-aqueous solubilities 28,645 CC0 melting points http://figshare.com/articles/Jean_Claude_Bradley_Open_Melting_Point_Datset/1031637
  17. 17. Where is Science headed? WE ARE HERE
  18. 18. Open Notebook Science >>
  19. 19. • He gave soooooo much early feedback on how ChemSpider could serve the community – the first advisory group member • For ChemSpider he contributed his students to perform crowdsourced curation and annotation • JC tapped into ChemSpider a lot for validated data and integration to his ONS wikis • He deposited data onto ChemSpider so we could link directly • His Open Notebook Science data was made available to over 10,000 scientists a day via ChemSpider JC took.. and he GAVE AWAY
  20. 20. Feeding ONS MP Data into ChemSpider  ONS data deposited into ChemSpider and linked out to ONS pages
  21. 21. Feeding ONS Sol. Data into ChemSpider  ONS Solubility Challenge
  22. 22. Linking to ONS Data from ChemSpider
  23. 23. Building Teaching Tools • JC loved to use technology to TEACH. He used freely available tools to do so – including ChemSpider services
  24. 24. ChemSpider Spectra
  25. 25. www.SpectralGame.com http://www.jcheminf.com/content/1/1/9
  26. 26. Collaborations in Openness • JC believed in HIGH-QUALITY data • He invested himself, and his students, in validating, checking and re-measuring data • He demanded openness of data, free of restrictions and constraints • Do his efforts make a difference???
  27. 27. Supporting Open Data
  28. 28. JC and Drug Discovery • JC cared passionately about neglected disease research • Many of our conversations were around better data-sharing for the various groups • We continue in our mission to help…
  29. 29. Journal of Cheminformatics Issue  Seven articles already published and three more in the pipeline. Submit yours before the end of the year!

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