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NSF eChemistry workshop


NSF workshop on sharing data in chemistry in Washington, DC on Oct 23, 2008.

NSF workshop on sharing data in chemistry in Washington, DC on Oct 23, 2008.

Published in Education , Technology
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  • 1. Open Notebook Science Jean-Claude Bradley Oct 23, 2008 NSF eChemistry Workshop Associate Professor of Chemistry Drexel University
  • 2. Motivation: Faster Science, Better Science
  • 3. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  • 4. Measuring Solubilities in Southampton with Cameron Neylon Sept 3, 2008
  • 5. Investigating solubilities in organic solvents Boc-glycine vanillin glucose NaCl
  • 6. The Results in a GoogleDoc reliable unreliable
  • 7. The solubility of 4-chlorobenzaldehyde
  • 8. Open Chemistry Crowdsourcing
  • 9. 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.
  • 10. Malaria Target: falcipain-2 involved in hemoglobin metabolism
  • 11. BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE
  • 12. Where’s the Beef?
  • 13. Link to Lab Notebook Page in Wiki
  • 14. Link to Molecules
  • 15. Link to Docking Procedure (Rajarshi Guha)
  • 16. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  • 17. Link to Raw Data with JSpecView (data in JCAMP-DX format) (by Robert Lancashire)
  • 18. Conclusion is Fully Supported
  • 19. How did this experiment evolve? Third party timestamp
  • 20. Comparing wiki page versions
  • 21. Comparing Experiments Ugi Master Table
  • 22.
    • Concentration (0.4, 0.2, 0.07 M)
    • Solvent (methanol, ethanol, acetonitrile, THF)
    • Excess of some reagents (1.2 eq.)
    Reaction to Optimize
  • 23. Mettler-Toledo MiniBlock System
  • 24. Mettler-Toledo MiniMapper
  • 25. XML reports from MiniMapper robot
  • 26. GoogleDoc to program and report
  • 27. Paper written on Wiki
  • 28. References to papers, blog posts, lab notebook pages, raw data
  • 29. Paper on Journal of Visualized Experiments (JoVE)
  • 30. Pre-print on Nature Precedings
  • 31. Outcome of Guha-Bradley-Rosenthal collboration
  • 32. Acknowledgements
    • Khalid Mirza (Drexel)
    • Kevin Owens (Drexel)
    • Tim Bohinsky (Drexel)
    • James Giammarco (Drexel)
    • Tom Osborne (Mettler-Toledo)
    • Antony Williams (ChemSpider)
    • Andrew Lang (Oral Roberts U.)
    • Cameron Neylon (Southampton U.)