Jean-Claude Bradley presents a talk on Open Notebook Science at the Association of College and Research Libraries on Feb 17, 2009. This presentation includes all of the relevant work up to this date, including the Spectra Game, the ONS solubility challenge and the main data viewers developed by Andy Lang and Rajarshi Guha for the web and Second Life.

1. Open Notebook Science Jean-Claude Bradley Feb 17, 2009 Association of College and Research Libraries Associate Professor of Chemistry Drexel University

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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures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

3. Motivation: Faster Science, Better Science

4. Where is Science headed? WE ARE HERE

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

6. TRUST PROOF

7. The solubility of 4-chlorobenzaldehyde

8. The Log makes Assumptions Explicit

9. The Rationale of Findings Explicit

10. Raw Data Made Public Splatter? Some liquid

11. YouTube for demonstrating experimental set-up

12. Calculations Made Public on Google Spreadsheets

13. Revision History on Google Spreadsheets

14. Wiki Page History

15. Comparing Wiki Page Versions

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

17. Indexing Molecules on Google

18. Linking to Molecules in Chemistry Databases

19. Experimental Spectra and User-Deposited Data on ChemSpider

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

22. NMR game in Second Life (Andy Lang)

23. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)

24. Imine Formation Mechanism: talk to the molecules!

25. Student Projects in Second Life

26. Crowdsourcing Solubility Data

27. ONS Challenge Students

28. ONS Challenge Judges

29. Teaching Lab: Brent Friesen (Dominican University)

30. Solubility Experiments

31. Solubilities collected in a Google Spreadsheet

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

33. Substructure Searching of solubility data

34. Rajarshi Guha and Andy Lang: Chemical Space Explorer

35. Andy Lang: Chemical Space Explorer in Second Life

36. From Wikipedia to…

37. … the lab notebook and raw data

38. Including links to the literature

40. Temperature info automatically plotted

41. Exploring Solubility in Second Life (Andy Lang)

42. Pierre Lindenbaum’s Solubility Data as RDF Triples

43. Results and Workflows in Machine-Friendly Format

44. Experiments in Chemical Markup Language

45. UsefulChem Workflows in myExperiment

46. 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.

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

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

49. Where’s the Beef?

50. Link to Lab Notebook Page in Wiki

51. Link to Docking Procedure (Rajarshi Guha)

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

53. Comparing Experiments Ugi Master Table

55. Mettler-Toledo MiniMapper

56. Mettler-Toledo MiniBlock System

57. XML reports from MiniMapper robot

58. GoogleDoc to program and report

59. Paper written on Wiki

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

61. ChemSpider Automated Mark-up of Chemical Names

62. Paper on Journal of Visualized Experiments (JoVE)

63. Pre-print on Nature Precedings

64. Reaction Optimization Visualization in Second Life

66. Collaborative Drug Discovery (CDD) Database

67. Outcome of Guha-Bradley-Rosenthal collboration

68. Google Spreadsheet linked to Open Web Services = Chemistry Dashboard

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

70. Gus Rosania’s Notebook Other Open Notebooks

71. Cameron Neylon’s Notebook

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