Jean-Claude Bradley discusses Open Notebook Science on April 15, 2009 at the NASA Goddard Space Flight Center. This includes recent material such as ONS logos, the ChemTiles and Spectral Games, automated backup of Google Spreadsheets and automated solubility determinations using web services called from within Google Spreadsheets.

1. Open Notebook Science
NASA
Goddard Space Flight Center
Jean-Claude Bradley
Associate Professor of Chemistry
Drexel University
April 15, 2009

2. Open and Closed Science
Open Notebook
Traditional Traditional
Open Access Science (full
Lab Notebook Journal
Journal Article transparency)
(unpublished) Article
RESEARCH
OPEN
CLOSED
TEACHING
Archived
Lectures
Traditional Assigned Lectures
Notes
Paper problems Public and
public
Textbook public free online
F2F lectures
textbooks

3. Motivation: Faster Science, Better Science

4. Open Notebook Science Logos
(Andy Lang, Shirley Wu)
Sharing: how much and when

5. Where is Science headed?
WE ARE HERE

6. There are NO FACTS,
only measurements embedded
within assumptions
Open Notebook Science maintains
the integrity of data provenance by
making assumptions explicit

7. TRUST
PROOF

8. The solubility of 4-chlorobenzaldehyde

9. The Log makes Assumptions Explicit

10. The Rationale of Findings Explicit

11. Raw Data Made Public
Splatter?
Some liquid

12. YouTube for demonstrating experimental set-up

13. Calculations Made Public on
Google Spreadsheets

14. Revision History on
Google Spreadsheets

15. Wiki Page History

16. Comparing Wiki Page Versions

17. Proof of Purity with interactive NMR
spectrum using JSpecView and JCAMP-DX

18. Indexing Molecules on Google

19. Linking to Molecules in Chemistry
Databases

20. Experimental Spectra and User-
Deposited Data on ChemSpider

21. Open Data JCAMP spectra for education
(Andy Lang, Tony Williams)
(Andy Lang, Tony Williams, Robert Lancashire)

22. Database Curation via Game Playing

23. Over 50,000 spectrum views so far -
worldwide

24. Link Spectral Game to Open Educational
Content

25. Remixing Code and Content (Andy
Lang)

26. Prizes not Punishment to motivate
students

27. NMR game in Second Life (Andy Lang)

28. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)

29. Imine Formation Mechanism:
talk to the molecules!

30. Student Projects in Second Life

31. Spring 09 projects: networking in
Second Life and FriendFeed

32. Crowdsourcing Solubility Data

33. ONS Challenge Students

34. ONS Challenge Judges

35. Teaching Lab: Brent Friesen
(Dominican University)

36. Solubility Experiment List

37. Summary of Solubility Experiments

38. Solubilities collected in a Google
Spreadsheet

39. Rajarshi Guha’s Live Web Query
using Google Viz API

40. Substructure Searching of solubility data

41. Rajarshi Guha and Andy Lang:
Chemical Space Explorer

42. Andy Lang: Chemical Space Explorer in
Second Life

43. From Wikipedia to…

44. …the lab notebook and raw data

45. Including links to the literature

47. Temperature info automatically
plotted

48. Exploring Solubility in Second Life (Andy Lang)

49. Pierre Lindenbaum’s Solubility Data
as RDF Triples

50. Results and Workflows in Machine-
Friendly Format

51. Experiments in Chemical Markup Language

52. UsefulChem Workflows in
myExperiment

53. UsefulChem Project: Open Primary
Research in Drug Design using Web2.0
tools
Rajarshi Guha Tsu-Soo Tan
Docking
Indiana U Nanyang Inst.
JC Bradley
Synthesis
Drexel U
Phil Rosenthal Dan Zaharevitz
Testing
UCSF NCI
(malaria) (tumors)

54. Malaria Target: falcipain-2
involved in hemoglobin metabolism
Dana.org

55. Architecture: Distributed, Interlinked and
Redundant
BLOG
CDD WIKI
Nature FriendFeed
Precedings
JoVE
ChemSpider GoogleDocs
Mailing List

56. Where’s the Beef?

57. Link to Lab Notebook Page in Wiki

58. Link to Docking Procedure
(Rajarshi Guha)

59. Link to Docking Results:
Lists of SMILES in GoogleDocs
(Rajarshi Guha)

60. Comparing Experiments
Ugi Master Table

61. Reaction to Optimize
•Concentration (0.4, 0.2, 0.07 M)
•Solvent (methanol, ethanol, acetonitrile, THF)
•Excess of some reagents (1.2 eq.)

62. Mettler-Toledo MiniMapper

63. Mettler-Toledo MiniBlock System

64. XML reports from MiniMapper robot

65. GoogleDoc to program and report

66. Paper written on Wiki

67. References to papers, blog posts,
lab notebook pages, raw data

68. ChemSpider Automated Mark-up of
Chemical Names

69. Paper on Journal of Visualized
Experiments (JoVE)

70. Pre-print on Nature Precedings

71. Reaction Optimization Visualization in
Second Life

73. Collaborative Drug Discovery (CDD) Database

74. Outcome of Guha-Bradley-Rosenthal
collboration

75. Google Spreadsheet linked to
Open Web Services
= Chemistry Dashboard

76. Semi-Automated Measurement of
solubility via web service analysis
of JCAMP-DX files
(Andy Lang)

77. Archiving and Curation of ONS and
other new forms of scholarship?

78. Publishing Google Spreadsheets as XLS

79. Other Open Notebooks
Gus Rosania’s Notebook (recently terminated)

80. Cameron Neylon’s Notebook

81. Anthony Salvagno’s Notebook
(Steve Koch group)

82. Acknowledgements
Khalid Mirza (Drexel)

Jenny Hale (Southampton U.)

David Bulger (Oral Roberts U.)

Tim Bohinsky (Drexel)

Kevin Owens (Drexel)

Tom Osborne (Mettler-Toledo)

Antony Williams (ChemSpider)

Andrew Lang (Oral Roberts U.)

Rajarshi Guha (Indiana U.)

Cameron Neylon (Southampton U.)
