Jean-Claude Bradley presents on "Open Notebook Science and other Science2.0 Approaches to Communicate Research" at the University of Pennsylvania Library.

1. Open Notebook Science and other Science2.0 Approaches to Communicate Research Jean-Claude Bradley January 21, 2010 University of Pennsylvania Associate Professor of Chemistry Drexel University

2. The NaH oxidation controversy

3. Information spreads quickly through the blogosphere

4. 15% NMR yield

6. Khalid Mirza and Marshall Moritz

8. Top results on a Google search

9. How bad is our current system? Try to find the solubility EGCG?

10. =2.3 g/L WTF?!

11. The End of the Chain of Provenance

12. The Scandal of Bell’s Lab Notebook

13. Motivation: Faster Science, Better Science

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

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

16. TRUST PROOF

17. The solubility of 4-chlorobenzaldehyde

18. The Log makes Assumptions Explicit

19. The Rationale of Findings Explicit

20. Raw Data Made Public Splatter? Some liquid

21. YouTube for demonstrating experimental set-up

22. Calculations Made Public on Google Spreadsheets

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

24. Link to Docking Procedure (Rajarshi Guha)

25. Revision History on Google Spreadsheets

26. Wiki Page History

27. Comparing Wiki Page Versions

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

29. Linking to Molecules in Chemistry Databases

30. Experimental Spectra and User-Deposited Data on ChemSpider

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

32. Database Curation via Game Playing

33. Over 100,000 spectrum views so far - worldwide

34. Link Spectral Game to Open Educational Content

35. NMR game in Second Life (Andy Lang)

36. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?

37. Crowdsourcing Solubility Data

38. ONS Submeta Award Winners

39. ONS Challenge Judges

40. ONS Challenge Judges

41. Teaching Lab: Brent Friesen (Dominican University)

42. Solubility Experiment List

43. Solubilities collected in a Google Spreadsheet

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

45. Rajarshi Guha and Andy Lang: Chemical Space Explorer

46. WE ARE HERE How can the scientific process become more automated?

47. The Robot Scientist

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

50. Solubility Prediction (Andy Lang’s Model)

51. Solubility prediction can generate requests for additional measurements

52. Solvent mixture and temperature: multidimensional solubility data Actual Data (4-nitrobenzaldehyde) From quadratic regression of 5D space Feeds DoSol Sheet the next points to measure to best cover the space

53. Understanding in addition to empirical modeling Missed in a prior publication on solubility for this compound

54. Data provenance: From Wikipedia to…

55. … the lab notebook and raw data

56. Including links to the literature

57. Pierre Lindenbaum’s Solubility Data as RDF Triples

59. Mettler-Toledo MiniMapper

60. Mettler-Toledo MiniBlock System

61. XML reports from MiniMapper robot

62. GoogleDoc to program and report

63. Paper written on Wiki

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

65. Paper on Journal of Visualized Experiments (JoVE)

66. Pre-print on Nature Precedings

67. ChemSpider Automated Mark-up of Chemical Names

68. BUT… Open Access: the Choice that Keeps Giving.. and Giving…

69. Beware of your addiction to metrics: redundancy will reduce them

70. Cameron Neylon’s Notebooks Other Open Notebooks

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

72. Educational “Open Notebooks”

73. Educational “Open Notebooks”

74. Educational “Open Notebooks”

75. Crowdsourcing ChemInfo Resource Collection

76. 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 Where do Libraries fit in the communication of science and education in the Open/Closed Continuum?

78. The ONS backup spreadsheet and ONSPreserver (Andy Lang)

79. Publishing Google Spreadsheets as XLS

80. Librarians and Science 2.0 "The Internet Archive is a 501(c)(3) non-profit that was founded to build an Internet library, with the purpose of offering permanent access for researchers, historians, and scholars to historical collections that exist in digital format." The internet Archive is not practical for practitioners of Open Notebook Science or Science 2.0

81. Good concept but.....

82. Most pages look like this....

83. Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL:http://spreadsheets.google.com/pub?key=plwwufp30hfq0udnEmRD1aQ&output=xls. Accessed: 2009-12-11. (Archived by WebCite® at http://www.webcitation.org/5lx5ry3BV )

84. Possible role for libraries: citation to objective third party archives of digital scholarship

85. More about the ONSarchive project: