Jean-Claude Bradley presents "Accelerating Discovery by Sharing: a case for Open Notebook Science" at the National Breast Cancer Coalition Annual Advocacy Conference in Arlington, VA on May 1, 2011.

1. Accelerating Discovery by Sharing: a case for Open Notebook Science Jean-Claude Bradley May 1, 2011 National Breast Cancer Coalition Annual Advocacy Conference Associate Professor of Chemistry Drexel University

3. Industry is Sharing More

4. Opportunities for Competitive Collaboration

5. Some Initiatives Promoting More Openness in Drug Discovery

6. Motivation: Faster Science, Better Science

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

8. TRUST PROOF

9. First record then abstract structure In order to be discoverable use Google friendly formats (simple HTML, no login) In order to be replicable use free hosted tools (Wikispaces, Google Spreadsheets) Strategy for an Open Notebook:

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

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

12. The Ugi Reaction

13. Outcome of Guha-Bradley-Rosenthal collaboration

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

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

16. Crowdsourcing Solubility Data

17. ONS Challenge Judges

18. ONS Challenge Award Winners

19. Solubilities collected in a Google Spreadsheet

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

21. Data provenance: From Wikipedia to…

22. … the lab notebook and raw data

23. Interactive NMR spectra using JSpecView and JCAMP-DX

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

25. Raw Data As Images Splatter? Some liquid

26. YouTube for demonstrating experimental set-up

27. The importance of raw data availability Missed in a prior publication on solubility for this compound

28. Case study: Chemical Information Retrieval course at Drexel (Fall 2009/2010) Leveraging the educational system to contribute new science

29. The Chemical Information Validation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course

30. The Chemical Information Validation Explorer (Andrew Lang)

31. Discovering outliers for melting points (stdev/average)

32. Investigating the m.p. inconsistencies of EGCG

33. Investigating the m.p. inconsistencies of cyclohexanone

34. Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting points

35. Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling points

36. Sigma-Aldrich, Acros and Wolfram Alpha apparently DO NOT use the same sources for flash points

37. Most popular data sources

38. Alfa Aesar donates melting points to the public

39. Open Melting Point Explorer

40. Outliers MDPI dataset EPI (via ChemSpider)

41. Outliers Alfa Aesar

42. Inconsistencies and SMILES problems within MDPI dataset

43. MDPI Dataset labeled with High Trust Level

44. Open Melting Point Datasets

45. Open Random Forest modeling of Open Melting Point data using CDK descriptors (Andrew Lang) R2 = 0.78, TPSA and nHdon most important

46. Melting point prediction service

47. Other Web Services… (Andrew Lang) General Transparent Solubility Prediction

48. Convenient web services for solubility measurement and prediction (Andrew Lang)

49. Integration of Multiple Web Services to Recommend Solvents for Reactions (Andrew Lang)

50. Using melting point for temperature dependent solubility prediction

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

54. Solubility Prediction (Andy Lang uses Abraham Model)

55. Reaction Attempts Book

56. Reaction Attempts Book: Reactants listed Alphabetically

58. Dynamic links to private tagged Mendeley collections (Andrew Lang)

59. All ONS web services

60. For all Formats of ONS Projects

61. ONS Challenge Solubility Book cited for nanotechnology application

62. Visualizing molecule-researcher connection maps reveals link between 2 Open Notebooks (Todd and Bradley) (Don Pellegrino)

63. The Intersection of Open Notebooks (Bradley/Todd) and IP implications Open Notebook could have blocked patent if done earlier

64. Decanoic acid Water NaCl

65. Phrase searching for useful solubility applications

66. Search for applications of solubility for breast cancer research

67. Solubility prediction for Taxol using Abraham descriptors Pred Exp

68. Predicted temperature dependent solubility of Taxol in water (M)