1. Cheminformatics in Open Notebook Science Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University July 29, 2008 Advanced Informatics in Chemistry Education At BCCE, Indiana U.

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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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. Older Males Prefer Organic Chemistry!

4. 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.

5. BLOG WIKI Mailing List GoogleDocs UsefulChem ChemSpider CDD

6. Where’s the Beef?

7. Link to Lab Notebook Page in Wiki

8. Link to Molecules

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 ChemSpider to archive compound characterization

14. ChemSpider predicted vs. experimental NMRs

15. The Most Important Section! The Log

16. Conclusion is Fully Supported

17. Table of Contents

18. Indexing the Experiments in Google

19. Searching with Google Custom Search

20. 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

21. 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

22. How Should Open Notebook Science be Used?

29. How did this experiment evolve? Third party timestamp

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

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

36. Comparing Experiments Ugi Master Table

37. Collaborative Drug Discovery (CDD) Database

38. YouTube for demonstrating experimental set-up

39. Mailing List Facilitates inter-group collaboration

41. Imine Formation Mechanism: talk to the molecules!

42. Interacting with NMR spectra (JCAMP-DX)

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

45. Gus Rosania’s Notebook

46. Cameron Neylon’s Notebook

47. Using ExcelVBA to automate kinetics analysis

48. Reaction profile plotted automatically

49. Results in Machine-Friendly Format

50. Mettler-Toledo MiniMapper

51. Mettler-Toledo MiniBlock System

54. Where is Science headed? WE ARE HERE

55. 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