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Open Notebook Science for Collaborative Drug Development

Open Notebook Science for Collaborative Drug Development. University of Manchester. Jean-Claude Bradley. E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University. Sept 5, 2008. Open and Closed Science . Open Notebook

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Open Notebook Science for Collaborative Drug Development

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  1. Open Notebook Science for Collaborative Drug Development University of Manchester Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University Sept 5, 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 Open and Closed Science Open Notebook Science (full transparency) Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article RESEARCH OPEN CLOSED TEACHING Archived Lectures Public and free online textbooks Lectures Notes public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. Motivations for ONS • Faster Science • Better Science

  4. A recent example in Southampton Sept 3, 2008 usefulchem.wikispaces.com/exp207

  5. Investigating solubilities in organic solvents Boc-glycine vanillin glucose NaCl

  6. The lab notebook page

  7. The Log: No Insider Information

  8. The Results in a GoogleDoc reliable unreliable

  9. Representation in the Neylon notebook

  10. Open Notebook Science Grand Challenge Round one • design procedures to determine the solubility of compounds in organic solvents • teams or individuals welcome • Open Notebooks will be validated by experts • “mystery prizes” for creativity, productivity, reproducibility and other metrics of scientific quality • details coming soon…..

  11. UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Rajarshi Guha Indiana U Tsu-Soo Tan Nanyang Inst. Docking JC Bradley Drexel U Synthesis Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Testing

  12. Architecture: Distributed, Interlinked and Redundant BLOG CDD WIKI Nature Precedings FriendFeed JoVE ChemSpider GoogleDocs Mailing List

  13. Where’s the Beef?

  14. Link to Lab Notebook Page in Wiki

  15. Link to Molecules

  16. Link to Docking Procedure (Rajarshi Guha)

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

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

  19. Using ChemSpider to archive compound characterization

  20. Conclusion is Fully Supported

  21. Table of Contents

  22. Indexing the Experiments in Google

  23. Searching with Google Custom Search

  24. 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"

  25. 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

  26. How Should Open Notebook Science be Used?

  27. How did this experiment evolve? Third party timestamp

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

  29. Comparing wiki page versions

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

  31. Comparing ExperimentsUgi Master Table

  32. YouTube for demonstrating experimental set-up

  33. Older Males Prefer Organic Chemistry!

  34. Mailing List Facilitates inter-group collaboration

  35. Outcome of Guha-Bradley-Rosenthal collboration

  36. Collaborative Drug Discovery (CDD) Database

  37. Interacting with NMR spectra (JCAMP-DX) in Second Life

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

  39. 3D molecules in Second Life

  40. Imine Formation Mechanism: talk to the molecules!

  41. Gus Rosania’s Notebook

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