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Open Notebook Science in 15 minutes
 

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.

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 Open Notebook Science in 15 minutes Presentation Transcript

    • The Synthesis of anti-malarial compounds using Open Notebook Science Jean-Claude Bradley Oct 10, 2008 Drexel MiniSymposium Associate Professor of Chemistry Drexel University
    • Motivation: Faster Science, Better Science
    • Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
    • 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.
    • BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE
    • Where’s the Beef?
    • Link to Lab Notebook Page in Wiki
    • Link to Molecules
    • Link to Docking Procedure (Rajarshi Guha)
    • Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
    • Link to Raw Data with JSpecView (data in JCAMP-DX format) (by Robert Lancashire)
    • Conclusion is Fully Supported
    • How did this experiment evolve? Third party timestamp
    • Comparing wiki page versions
    • Comparing Experiments Ugi Master Table
      • Concentration (0.4, 0.2, 0.07 M)
      • Solvent (methanol, ethanol, acetonitrile, THF)
      • Excess of some reagents (1.2 eq.)
      Reaction to Optimize
    • Mettler-Toledo MiniBlock System
    • Mettler-Toledo MiniMapper
    • XML reports from MiniMapper robot
    • GoogleDoc to program and report
    • Paper written on Wiki
    • References to papers, blog posts, lab notebook pages, raw data
    • Paper on Journal of Visualized Experiments (JoVE)
    • Pre-print on Nature Precedings
    • Best Yield: 66% 0.4 M methanol 1.2 eq imine
    • Methanol 0.4M xs of imine best
    • Outcome of Guha-Bradley-Rosenthal collboration
    • Measuring Solubilities in Southampton with Cameron Neylon Sept 3, 2008 usefulchem.wikispaces.com/exp207
    • Investigating solubilities in organic solvents Boc-glycine vanillin glucose NaCl
    • The Results in a GoogleDoc reliable unreliable
    •  
    • 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.)