1. Open Notebook Science and Cheminformatics
Indiana University Cheminformatics Class
Jean-Claude Bradley
E-Learning Coordinator
College of Arts and Sciences
Associate Professor of Chemistry
Drexel University
March 25, 2008

2. Open and Closed Science
Open Notebook
Science (full transparency)
Traditional
Lab Notebook
(unpublished)
Traditional
Journal Article
Open Access Journal Article
RESEARCH
OPEN
CLOSED
TEACHING
Archived Lectures Public and free online textbooks
Lectures Notes public
Traditional
Paper Textbook
F2F lectures
Assigned problems public

3. What is the role of blogging in scientific research transparency?
UsefulChem
BLOG
Mailing List
WIKI
GoogleDocs

4. Discussing Funding

5. Supporting Funding Initiatives

6. Highlight Popular Media Coverage

7. Highlight Peer-Reviewed Coverage

8. Announce Collaborator: Gus Rosania

9. Announce Collaborator: Matthias Zeller

10. Announce Collaborator: Phil Rosenthal

11. Discuss Presentations in Real Life

12. Discuss Presentations in Second Life

13. Showcase Science in New Media

14. Showcase Teaching in New Media
Hiro Sheridan’s Molecule Rezzer takes SMILES, InChI or InChIKeys

15. Alerts to Broader Impact Opportunities

16. Science Philosophy

17. Where’s the Beef?

18. Link to Lab Notebook Page in Wiki

19. Link to Molecules

20. Link to Experimental Plan

21. Link to Docking Procedure (Rajarshi Guha)

22. Link to Docking Results (Rajarshi Guha)

23. Procedure Section

24. Link to Raw Data with JSpecView (data in JCAMP-DX format)

25. Conclusion is Fully Supported

26. Indexing the Experiments in Google

27. Comparing Experiments

28. The Most Important Section!

29. Results in Machine-Friendly Format

30. Comparing Results in a Table

31. Table of Contents

32. Recent Changes in Wiki

33. Tracking Versions of Wiki Pages

34. Comparing Versions of Wiki Pages

35. How are people finding our experiments?

36. Telling the story of the failures

37. Mailing List Facilitates inter-group collaboration

38. Open Primary Research in Drug Design using Web2
Open Primary Research in Drug Design using Web2.0 tools (blogs, wikis, Second Life, mailing lists)
Rajarshi Guha
Indiana U
Tsu-Soo Tan
Nanyang Inst.
Docking
JC Bradley
Drexel U
Synthesis
Phil Rosenthal
UCSF
(malaria)
Dan Zaharevitz
NCI
(tumors)
Testing

39. Gus Rosania’s Notebook

40. Cameron Neylon’s Notebook

41. Automation in UsefulChem

42. CMLRSS feed on Bioclipse

43. Graphical Mining of Data with JSpecView
usefulchem.wikispaces.com/Exp070 (48h 7 min)

44. Using ExcelVBA to automate kinetics analysis

45. Specify NMR regions and internal standard

46. NMR spectra of monitoring samples calculated

47. Reaction profile plotted automatically

48. Next Step: Reading JCAMP-DX files in Second Life

49. Where is Science headed?
WE ARE HERE