Download - Open Notebook Science in 15 minutes
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The Synthesis of anti-malarial compounds using
Open Notebook Science
Jean-Claude Bradley
Oct 10, 2008
Drexel MiniSymposium
Associate Professor of ChemistryDrexel University
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Motivation: Faster Science, Better Science
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Malaria Target: falcipain-2 involved in hemoglobin metabolism
Dana.org
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UsefulChem Project:UsefulChem Project: Open Primary Open Primary Research in Drug Design using Web2.0 Research in Drug Design using Web2.0
toolstools
Docking
Synthesis
Testing
Rajarshi GuhaIndiana U
JC BradleyDrexel U
Phil RosenthalUCSF
(malaria)
Dan ZaharevitzNCI
(tumors)
Tsu-Soo TanNanyang Inst.
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BLOGWIKI
Mailing List
GoogleDocs
Architecture: Distributed,
Interlinked and Redundant
ChemSpider
CDD
FriendFeedNature Precedin
gs JoVE
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Where’s the Beef?Where’s the Beef?
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Link to Lab Notebook Page in Link to Lab Notebook Page in WikiWiki
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Link to MoleculesLink to Molecules
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Link to Docking Procedure Link to Docking Procedure (Rajarshi Guha)(Rajarshi Guha)
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Link to Docking Results: Link to Docking Results: Lists of SMILES in GoogleDocs Lists of SMILES in GoogleDocs
(Rajarshi Guha)(Rajarshi Guha)
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Link to Raw Data with Link to Raw Data with JSpecViewJSpecView
(data in JCAMP-DX format)(data in JCAMP-DX format)(by Robert Lancashire)(by Robert Lancashire)
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Conclusion is Fully SupportedConclusion is Fully Supported
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How did this How did this experiment experiment
evolve?evolve?
Third party timestamp
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Comparing wiki page Comparing wiki page versionsversions
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Comparing ExperimentsComparing ExperimentsUgi Master TableUgi Master Table
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•Concentration (0.4, 0.2, 0.07 M)•Solvent (methanol, ethanol, acetonitrile, THF)•Excess of some reagents (1.2 eq.)
Reaction to Optimize
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Mettler-Toledo MiniBlock System
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Mettler-Toledo MiniMapper
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XML reports from MiniMapper robot
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GoogleDoc to program and report
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Paper written on Wiki
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References to papers, blog posts, lab notebook pages, raw
data
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Paper on Journal of Visualized Experiments (JoVE)
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Pre-print on Nature Precedings
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Best Yield: 66%
0.4 M methanol 1.2 eq imine
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Methanol 0.4M xs of imine Methanol 0.4M xs of imine bestbest
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Outcome of Guha-Bradley-Outcome of Guha-Bradley-Rosenthal collborationRosenthal collboration
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Measuring Solubilities in Southampton with Cameron
Neylon
Sept 3, 2008 usefulchem.wikispaces.com/exp207
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Investigating solubilities in organic solvents
Boc-glycine vanillin glucose NaCl
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The Results in a GoogleDoc
reliable
unreliable
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AcknowledgementsAcknowledgements
Khalid Mirza (Drexel)Khalid Mirza (Drexel) Kevin Owens (Drexel)Kevin Owens (Drexel) Tim Bohinsky (Drexel)Tim Bohinsky (Drexel) James Giammarco (Drexel)James Giammarco (Drexel) Tom Osborne (Mettler-Toledo)Tom Osborne (Mettler-Toledo) Antony Williams (ChemSpider)Antony Williams (ChemSpider) Andrew Lang (Oral Roberts U.)Andrew Lang (Oral Roberts U.) Cameron Neylon (Southampton U.)Cameron Neylon (Southampton U.)