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Cheminformatics in Open Notebook Science

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

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Cheminformatics in Open Notebook Science

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  1. Cheminformatics in Open Notebook Science Advanced Informatics in Chemistry Education At BCCE, Indiana U. Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University July 29, 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 Open and Closed Science Open Notebook Science (full transparency) Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article RESEARCH OPEN CLOSED TEACHING Archived Lectures Public and free online textbooks Lectures Notes public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. Older Males Prefer Organic Chemistry!

  4. 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

  5. UsefulChem BLOG CDD WIKI ChemSpider GoogleDocs Mailing List

  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? Specific Compounds Experimental Conditions 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"

  21. How are people finding UsefulChem? Educational Big Picture 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

  22. How Should Open Notebook Science be Used?

  23. How did this experiment evolve? Third party timestamp

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

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

  26. Comparing ExperimentsUgi Master Table

  27. Collaborative Drug Discovery (CDD) Database

  28. YouTube for demonstrating experimental set-up

  29. Mailing List Facilitates inter-group collaboration

  30. Imine Formation Mechanism: talk to the molecules!

  31. Interacting with NMR spectra (JCAMP-DX)

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

  33. Gus Rosania’s Notebook

  34. Cameron Neylon’s Notebook

  35. Using ExcelVBA to automate kinetics analysis

  36. Reaction profile plotted automatically

  37. Results in Machine-Friendly Format

  38. Mettler-Toledo MiniMapper

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