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NSF eChemistry workshop

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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.

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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 usefulchem.wikispaces.com/exp207
  • 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 Dana.org
  • 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.)