Jean-Claude Bradley presents on "Open Notebook Science for Collaborative Drug Discovery" on July 23, 2009.

1. Open Notebook Science for Collaborative Drug Discovery Jean-Claude Bradley July 23, 2009 BrightTALK Associate Professor of Chemistry Drexel University

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

3. The Robot Scientist

5. 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.

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

7. Outcome of Guha-Bradley-Rosenthal collboration

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

9. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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

10. Motivation: Faster Science, Better Science

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

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

13. TRUST PROOF

14. The solubility of 4-chlorobenzaldehyde

15. The Log makes Assumptions Explicit

16. Results and Workflows in Machine-Friendly Format

17. The Rationale of Findings Explicit

18. Raw Data Made Public Splatter? Some liquid

19. YouTube for demonstrating experimental set-up

20. Calculations Made Public on Google Spreadsheets

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

22. Link to Docking Procedure (Rajarshi Guha)

23. Revision History on Google Spreadsheets

24. Wiki Page History

25. Comparing Wiki Page Versions

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

27. Linking to Molecules in Chemistry Databases

28. Experimental Spectra and User-Deposited Data on ChemSpider

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

30. Database Curation via Game Playing

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

32. Link Spectral Game to Open Educational Content

33. NMR game in Second Life (Andy Lang)

34. Crowdsourcing Solubility Data

35. ONS Challenge Students

36. ONS Challenge Judges

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

38. Teaching Lab: Brent Friesen (Dominican University)

39. Solubility Experiment List

40. Solubilities collected in a Google Spreadsheet

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

42. Rajarshi Guha and Andy Lang: Chemical Space Explorer

44. 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

45. Comparing Experiments Ugi Master Table

46. Crowdsourcing Reaction Requests: DoUgi sheet

47. Raw data reveal a problem Missed in a prior publication on solubility for this compound

48. Data provenance: From Wikipedia to…

49. … the lab notebook and raw data

50. Including links to the literature

51. Collaborative Drug Discovery (CDD) Database

53. Mettler-Toledo MiniMapper

54. Mettler-Toledo MiniBlock System

55. XML reports from MiniMapper robot

56. GoogleDoc to program and report

57. Best Yield: 66% 0.4 M methanol 1.2 eq imine

58. Reaction Optimization Visualization in Second Life

59. Paper written on Wiki

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

61. Paper on Journal of Visualized Experiments (JoVE)

62. Pre-print on Nature Precedings

63. ChemSpider Automated Mark-up of Chemical Names

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

65. Cameron Neylon’s Notebooks Other Open Notebooks

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