Open Notebook Science in 15 minutes


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Presented at Drexel University on Oct 10, 2008 in the chemistry department faculty mini-symposium. A quick summary of Open Notebook Science and its application to drug discovery.

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Open Notebook Science in 15 minutes

  1. 1. The Synthesis of anti-malarial compounds using Open Notebook Science Jean-Claude Bradley Oct 10, 2008 Drexel MiniSymposium Associate Professor of Chemistry Drexel University
  2. 2. Motivation: Faster Science, Better Science
  3. 3. Malaria Target: falcipain-2 involved in hemoglobin metabolism
  4. 4. UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools 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. 5. BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE
  6. 6. Where’s the Beef?
  7. 7. Link to Lab Notebook Page in Wiki
  8. 8. Link to Molecules
  9. 9. Link to Docking Procedure (Rajarshi Guha)
  10. 10. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  11. 11. Link to Raw Data with JSpecView (data in JCAMP-DX format) (by Robert Lancashire)
  12. 12. Conclusion is Fully Supported
  13. 13. How did this experiment evolve? Third party timestamp
  14. 14. Comparing wiki page versions
  15. 15. Comparing Experiments Ugi Master Table
  16. 16. <ul><li>Concentration (0.4, 0.2, 0.07 M) </li></ul><ul><li>Solvent (methanol, ethanol, acetonitrile, THF) </li></ul><ul><li>Excess of some reagents (1.2 eq.) </li></ul>Reaction to Optimize
  17. 17. Mettler-Toledo MiniBlock System
  18. 18. Mettler-Toledo MiniMapper
  19. 19. XML reports from MiniMapper robot
  20. 20. GoogleDoc to program and report
  21. 21. Paper written on Wiki
  22. 22. References to papers, blog posts, lab notebook pages, raw data
  23. 23. Paper on Journal of Visualized Experiments (JoVE)
  24. 24. Pre-print on Nature Precedings
  25. 25. Best Yield: 66% 0.4 M methanol 1.2 eq imine
  26. 26. Methanol 0.4M xs of imine best
  27. 27. Outcome of Guha-Bradley-Rosenthal collboration
  28. 28. Measuring Solubilities in Southampton with Cameron Neylon Sept 3, 2008
  29. 29. Investigating solubilities in organic solvents Boc-glycine vanillin glucose NaCl
  30. 30. The Results in a GoogleDoc reliable unreliable
  31. 32. Acknowledgements <ul><li>Khalid Mirza (Drexel) </li></ul><ul><li>Kevin Owens (Drexel) </li></ul><ul><li>Tim Bohinsky (Drexel) </li></ul><ul><li>James Giammarco (Drexel) </li></ul><ul><li>Tom Osborne (Mettler-Toledo) </li></ul><ul><li>Antony Williams (ChemSpider) </li></ul><ul><li>Andrew Lang (Oral Roberts U.) </li></ul><ul><li>Cameron Neylon (Southampton U.) </li></ul>
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