Jean-Claude Bradley presents an overview of Open Notebook Science at a Columbia panel on Open Science on February 19, 2009. The content of this presentation is targeted to a library services audience.

1. Open Notebook Science Jean-Claude Bradley Feb 19, 2009 Columbia University Libraries Panel on Open Science Associate Professor of Chemistry Drexel University

2. Motivation: Faster Science, Better Science

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

4. TRUST PROOF

5. The solubility of 4-chlorobenzaldehyde

6. The Log makes Assumptions Explicit

7. The Rationale of Findings Explicit

8. Raw Data Made Public Splatter? Some liquid

9. YouTube for demonstrating experimental set-up

10. Calculations Made Public on Google Spreadsheets

11. Revision History on Google Spreadsheets

12. Wiki Page History

13. Comparing Wiki Page Versions

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

15. Linking to Molecules in Chemistry Databases

16. Experimental Spectra and User-Deposited Data on ChemSpider

17. The Spectra Game (Andy Lang, Tony Williams)

19. NMR game in Second Life (Andy Lang)

20. Crowdsourcing Solubility Data

21. ONS Challenge Students

22. ONS Challenge Judges

23. Teaching Lab: Brent Friesen (Dominican University)

24. Solubility Experiments

25. Solubilities collected in a Google Spreadsheet

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

27. Substructure Searching of solubility data

28. Rajarshi Guha and Andy Lang: Chemical Space Explorer

29. Andy Lang: Chemical Space Explorer in Second Life

30. From Wikipedia to…

31. … the lab notebook and raw data

32. Including links to the literature

33. Temperature info automatically plotted

34. Exploring Solubility in Second Life (Andy Lang)

35. 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.

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

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

38. Where’s the Beef?

39. Link to Lab Notebook Page in Wiki

40. Link to Docking Procedure (Rajarshi Guha)

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

42. Outcome of Guha-Bradley-Rosenthal collboration

43. Collaborative Drug Discovery (CDD) Database

45. Paper written on Wiki

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

47. Paper on Journal of Visualized Experiments (JoVE)

48. Pre-print on Nature Precedings

49. Potential Trends for the Future of Chemistry Fast, Fuzzy, Open, Automated, Green, Crowdsourced, Simple (e.g. mix and filter)

50. Gus Rosania’s Notebook Other Open Notebooks

51. Cameron Neylon’s Notebook

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