1. Cheminformatics and Open Notebook Science Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University April 6, 2008 American Chemical Society CINF session

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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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. Open Primary Research in Drug Design using Web2.0 tools (blogs, wikis, Second Life, mailing lists) Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.

4. BLOG WIKI Mailing List GoogleDocs UsefulChem ChemSpider CDD

5. Where’s the Beef?

6. Link to Lab Notebook Page in Wiki

7. Link to Molecules

8. Link to Experimental Plan

9. Link to Docking Procedure (Rajarshi Guha)

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

11. Procedure Section

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

13. Using ExcelVBA to automate kinetics analysis using JCAMP-DX files

14. Reaction profile plotted automatically

15. Using ChemSpider to archive compound characterization

16. Next Step: Reading JCAMP-DX files in Second Life (Andy Lang)

17. The Most Important Section! The Log

18. Conclusion is Fully Supported

19. Indexing the Experiments in Google

20. Searching with Google Custom Search

21. 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

22. 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

23. Table of Contents

24. Comparing Experiments Ugi Master Table

25. Predicting Precipitates Rajarshi Guha’s Model MESA Analytics Model

26. Results in Machine-Friendly Format

27. Comparing Results in a Table

28. Why a Wiki?

29. Tracking Versions of Wiki Pages

30. Comparing Versions of Wiki Pages

31. Telling the story of the failures

32. Mailing List Facilitates inter-group collaboration

33. Collaborative Drug Discovery (CDD) Database

34. Exporting Assay Results from CDD

35. Collaboration with Brent Friesen’s Teaching Lab at Dominican U.

36. Gus Rosania’s Notebook

37. Cameron Neylon’s Notebook

38. Where is Science headed? WE ARE HERE