Jean-Claude Bradley presents on October 9, 2009 at the Northeastern Regional Meeting of the American Chemical Society in Hartford. This talk, entitled "Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Science", was part of a symposium on Publishing and Promoting Chemistry in the Internet Age. It consists of an overview of Open Notebook Science with some new content on solubility prediction algorithms written by Andrew Lang and a few example of students taking a Chemical Information Retrieval class at Drexel University using research logs on a wiki to flesh out their projects.

1. Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Science Jean-Claude Bradley October 9, 2009 Northeast Regional Meeting of the American Chemical Society 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. Motivation: Faster Science, Better Science

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

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

12. TRUST PROOF

13. The solubility of 4-chlorobenzaldehyde

14. The Log makes Assumptions Explicit

15. The Rationale of Findings Explicit

16. Raw Data Made Public Splatter? Some liquid

17. YouTube for demonstrating experimental set-up

18. Calculations Made Public on Google Spreadsheets

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

20. Link to Docking Procedure (Rajarshi Guha)

21. Revision History on Google Spreadsheets

22. Wiki Page History

23. Comparing Wiki Page Versions

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

25. Linking to Molecules in Chemistry Databases

26. Experimental Spectra and User-Deposited Data on ChemSpider

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

28. Database Curation via Game Playing

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

30. Link Spectral Game to Open Educational Content

31. NMR game in Second Life (Andy Lang)

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

33. Crowdsourcing Solubility Data

34. ONS Submeta Award Winners

35. ONS Challenge Judges

36. Teaching Lab: Brent Friesen (Dominican University)

37. Solubility Experiment List

38. Solubilities collected in a Google Spreadsheet

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

40. Rajarshi Guha and Andy Lang: Chemical Space Explorer

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

42. The Robot Scientist

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

45. Solubility Prediction (Andy Lang’s Model)

46. Solubility prediction can generate requests for additional measurements

47. 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

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

49. Data provenance: From Wikipedia to…

50. … the lab notebook and raw data

51. Including links to the literature

52. Pierre Lindenbaum’s Solubility Data as RDF Triples

54. Mettler-Toledo MiniMapper

55. Mettler-Toledo MiniBlock System

56. XML reports from MiniMapper robot

57. GoogleDoc to program and report

58. Paper written on Wiki

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

60. Paper on Journal of Visualized Experiments (JoVE)

61. Pre-print on Nature Precedings

62. ChemSpider Automated Mark-up of Chemical Names

63. Cameron Neylon’s Notebooks Other Open Notebooks

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

65. Educational “Open Notebooks”

66. Educational “Open Notebooks”

67. Educational “Open Notebooks”

68. Crowdsourcing ChemInfo Resource Collection