Open Notebook Science and Malaria
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Open Notebook Science and Malaria
Jean-Claude Bradley
Drexel University
September 6, 2007
Chemists Without Borders
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Malaria is a Logical Application Malaria is a Logical Application of Open Scienceof Open Science
•Very large problem: 300-500 million cases per year with one million deaths
•Not a lucrative market: IP control less important
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Open and Closed ScienceOpen and Closed Science
TraditionalLab Notebook(unpublished)
TraditionalJournal Article
Open Access Journal Article
Open Notebook Science (full transparency)
CLOSED
OPEN
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Where is Science headed?Where is Science headed?
WE ARE HEREWE ARE HERE
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The Robot ScientistThe Robot Scientist
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How will this happen?How will this happen?
Self-organizing redundant processesSelf-organizing redundant processes Agents can participate with zero or Agents can participate with zero or
near-zero cost (free hosted services – near-zero cost (free hosted services – e.g. Google)e.g. Google)
Fully Open Access (Read and Write)Fully Open Access (Read and Write) Publication of all aspects of the Publication of all aspects of the
scientific process: Open Source scientific process: Open Source Science / Science / Open Notebook ScienceOpen Notebook Science
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How can machines know what How can machines know what is important?is important?
Ask the humansAsk the humans
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UsefulChem BlogUsefulChem Blog
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What chemists think is What chemists think is important in 2005important in 2005
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Find-A-DrugFind-A-Drug
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Diketopiperazine LibraryDiketopiperazine LibraryEvolves to: on pot Evolves to: on pot
Ugi Ugi reaction/cyclizationreaction/cyclization
First iteration: First iteration: Solid Support Solid Support
SynthesisSynthesis
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The Molecules BlogThe Molecules Blog
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The Experiments BlogThe Experiments Blog
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Comments from peersComments from peers
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The UsefulChem WikiThe UsefulChem Wiki
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Telling the story of the failuresTelling the story of the failures
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Experiments moved to wikiExperiments moved to wiki
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Experiment HistoryExperiment History
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Experiment EditsExperiment Edits
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Third Party Time-Stamp on Third Party Time-Stamp on Experiment VersionsExperiment Versions
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Monitoring experimental Monitoring experimental progressprogress
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How are people finding our How are people finding our experiments?experiments?
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Molecules found by InChIMolecules found by InChI
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usefulchem.blogspot.comusefulchem.blogspot.com
The blog as an integrative The blog as an integrative tooltool
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usefulchem.wikispaces.com/Exp049usefulchem.wikispaces.com/Exp049
The wiki as the laboratory The wiki as the laboratory notebooknotebook
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Graphical Mining of Data with Graphical Mining of Data with JSpecViewJSpecView
usefulchem.wikispaces.com/Exp070 (48h 7 min)usefulchem.wikispaces.com/Exp070 (48h 7 min)
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Processing Molecules on Processing Molecules on ChemSpiderChemSpider
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The CombiUgi ProjectThe CombiUgi Project
Focus on cheap starting materials and a product that precipitate easily from solution
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Open Primary Research in Drug Design Open Primary Research in Drug Design using Web2.0 toolsusing Web2.0 tools
(blogs, wikis, Second Life, mailing (blogs, wikis, Second Life, mailing lists)lists)
Docking
Synthesis
Testing
Rajarshi GuhaIndiana U
JC BradleyDrexel U
Phil RosenthalUCSF
(malaria)
Dan ZaharevitzNCI
(tumors)
Tsu-Soo TanNanyang Inst.
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UsefulChem and Open UsefulChem and Open Science in Second LifeScience in Second Life
scifooliveson.wikispaces.com