This talk covers Open Notebook Science from an information technology perspective . Although solubility measurements and chemical reactions are mentioned the focus is more on how information is stored, retrieved and used using free and hosted services such as Blogger, GoogleDocs, Wikispaces, ChemSpider, CDD and others. The UsefulChem project and the Open Notebook Science Challenge are highlighted.

1. Open Notebook Science Jean-Claude Bradley Nov 11, 2008 Drexel iSchool 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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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. Crowdsourcing Solubility Data

21. Solubility Experiments

22. “ Validated” Solubilities in Google Spreadsheet

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

24. Pierre Lindenbaum’s Solubility Data as RDF Triples

25. Results and Workflows in Machine-Friendly Format

26. UsefulChem Workflows in myExperiment

27. Experiments in Chemical Markup Language

28. 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.

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

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

31. Where’s the Beef?

32. Link to Lab Notebook Page in Wiki

33. Link to Docking Procedure (Rajarshi Guha)

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

35. Comparing Experiments Ugi Master Table

37. Mettler-Toledo MiniMapper

38. Mettler-Toledo MiniBlock System

39. XML reports from MiniMapper robot

40. GoogleDoc to program and report

41. Paper written on Wiki

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

43. ChemSpider Automated Mark-up of Chemical Names

44. Paper on Journal of Visualized Experiments (JoVE)

45. Pre-print on Nature Precedings

46. Reaction Optimization Visualization in Second Life

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

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

49. 3D molecules in Second Life

50. Imine Formation Mechanism: talk to the molecules!

52. Collaborative Drug Discovery (CDD) Database

53. Outcome of Guha-Bradley-Rosenthal collboration

54. Gus Rosania’s Notebook

55. Cameron Neylon’s Notebook