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Cheminformatics and Open Notebook Science

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

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Cheminformatics and Open Notebook Science

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  1. Cheminformatics and Open Notebook Science American Chemical Society CINF session Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University April 6, 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 Open and Closed Science Open Notebook Science (full transparency) Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article RESEARCH OPEN CLOSED TEACHING Archived Lectures Public and free online textbooks Lectures Notes public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. 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

  4. UsefulChem BLOG CDD WIKI ChemSpider GoogleDocs Mailing List

  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? 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"

  22. 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

  23. Table of Contents

  24. Comparing ExperimentsUgi 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

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