The document discusses the concept of open notebook science, which emphasizes full transparency in scientific research by making data and findings publicly accessible. It highlights various tools and methods used to enhance collaboration and communication in scientific experiments, including the use of Google spreadsheets, wiki pages, and online databases. The goal is to accelerate scientific discovery and improve the integrity of data by making assumptions and raw data explicit.

1. Open Notebook Science Jean-Claude Bradley Dec 11, 2008 NIST 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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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. ONS Challenge Students

22. ONS Challenge Judges

23. Solubility Experiments

24. Solubilities collected in a Google Spreadsheet

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

26. Pierre Lindenbaum’s Solubility Data as RDF Triples

27. Results and Workflows in Machine-Friendly Format

28. UsefulChem Workflows in myExperiment

29. Experiments in Chemical Markup Language

30. 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.

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

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

33. Where’s the Beef?

34. Link to Lab Notebook Page in Wiki

35. Link to Docking Procedure (Rajarshi Guha)

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

37. Comparing Experiments Ugi Master Table

38. Concentration (0.4, 0.2, 0.07 M) Solvent (methanol, ethanol, acetonitrile, THF) Excess of some reagents (1.2 eq.) Reaction to Optimize

39. Mettler-Toledo MiniMapper

40. Mettler-Toledo MiniBlock System

41. XML reports from MiniMapper robot

42. GoogleDoc to program and report

43. Paper written on Wiki

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

45. ChemSpider Automated Mark-up of Chemical Names

46. Paper on Journal of Visualized Experiments (JoVE)

47. Pre-print on Nature Precedings

48. Reaction Optimization Visualization in Second Life

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

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

51. 3D molecules in Second Life

52. Imine Formation Mechanism: talk to the molecules!

53. Exploring Solubility in Second Life (Andy Lang)

55. Collaborative Drug Discovery (CDD) Database

56. Outcome of Guha-Bradley-Rosenthal collboration

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

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

59. Gus Rosania’s Notebook

60. Cameron Neylon’s Notebook

61. Acknowledgements Khalid Mirza (Drexel) Kevin Owens (Drexel) Tim Bohinsky (Drexel) James Giammarco (Drexel) Tom Osborne (Mettler-Toledo) Antony Williams (ChemSpider) Andrew Lang (Oral Roberts U.) Cameron Neylon (Southampton U.)