1. Open Notebook Science for Collaborative Drug Development Jean-Claude Bradley Sept 5, 2008 University of Manchester E-Learning Coordinator College of Arts and Sciences 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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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. Motivations for ONS Faster Science Better Science

4. A recent example in Southampton Sept 3, 2008 usefulchem.wikispaces.com/exp207

5. Investigating solubilities in organic solvents Boc-glycine vanillinglucoseNaCl

6. The lab notebook page

7. The Log: No Insider Information

8. The Results in a GoogleDoc reliable unreliable

10. Representation in the Neylon notebook

11. Open Notebook Science Grand Challenge design procedures to determine the solubility of compounds in organic solvents teams or individuals welcome Open Notebooks will be validated by experts “mystery prizes” for creativity, productivity, reproducibility and other metrics of scientific quality details coming soon….. Round one

12. 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.

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

14. Where’s the Beef?

15. Link to Lab Notebook Page in Wiki

16. Link to Molecules

17. Link to Docking Procedure (Rajarshi Guha)

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

19. Link to Raw Data with JSpecView (data in JCAMP-DX format) (by Robert Lancashire)

20. Using ChemSpider to archive compound characterization

21. Conclusion is Fully Supported

22. Table of Contents

23. Indexing the Experiments in Google

24. Searching with Google Custom Search

25. How are people finding our experiments? NMR in TFA Phenylacetaldehyde c4h6o2 nmr methylene chloride/methanol h'nmr of benzophenone sulfuric acid pka tertbutylamine tosyl isocyanide amino furan dichloromethane polar? Reaction between Benzaldehyde and NaBH4 phosphoric acid pka veratraldehyde wiki kinetics boc deprotection Rf value in polar solvent why glycerol is immiscible with ether side reaction of imines 5.8 ppm nmr nmr cdcl3 chloroform side reaction diasterotopic wiki adding anhydrous MgSO4 to the dichlormethane ether extraction hnmr doublet of doublet Boc-protected NMR chromatotron recipe triplet cdcl3 "13c nmr" Specific CompoundsExperimental Conditions

26. How are people finding UsefulChem? free downloading chemistry video organic chemistry project + high school how to make poster in second life organic chem. quiz 3d periodic tables animation protein docking docking animation why are acid-base reactions exothermic? lysosomal targets protease and malaria cheminformatics project proposal automated reactions malaria review project synthesis CHEMISTRY WEB 2.0 projects on QSAR & drug design chemistry experiment results database EducationalBig Picture

27. How Should Open Notebook Science be Used?

34. How did this experiment evolve? Third party timestamp

35. http://usefulchem.wikispaces.com/page/diff/Exp037/1577428

36. Comparing wiki page versions

38. http://usefulchem.wikispaces.com/SO+Research+Report

39. Comparing Experiments Ugi Master Table

40. YouTube for demonstrating experimental set-up

41. Older Males Prefer Organic Chemistry!

42. Mailing List Facilitates inter-group collaboration

43. Outcome of Guha-Bradley-Rosenthal collboration

44. Collaborative Drug Discovery (CDD) Database

46. Interacting with NMR spectra (JCAMP-DX) in Second Life

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

48. 3D molecules in Second Life

49. Imine Formation Mechanism: talk to the molecules!

50. Gus Rosania’s Notebook

51. Cameron Neylon’s Notebook

52. Results in Machine-Friendly Format

53. Mettler-Toledo MiniMapper

54. Mettler-Toledo MiniBlock System

55. GoogleDoc to program and report

56. XML reports from MiniMapper robot

57. Writing Code in the Murray-Rust House

58. Experiments in Chemical Markup Language

59. Paper written on Wiki

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

61. Pre-print on Nature Precedings

62. Methanol 0.4M xs of imine best

63. Paper on Journal of Visualized Experiments (JoVE)

64. Where is Science headed? WE ARE HERE

65. Conclusion Communicate first Communicate first Standardize second Standardize second In a Science2.0 world redundancy is king In a Science2.0 world redundancy is king