Cheminformatics in Open Notebook Science Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University July 29, 2008 Advanced Informatics in Chemistry Education At BCCE, Indiana U.
Open Notebook Science BCCE 2008
May 06, 2015
This is a presentation by Jean-Claude Bradley at the Biennial Conference for Chemical Education (BCCE) on July 29, 2008. The talk starts with an overview of Open Notebook Science using a wiki as a public lab notebook. An example of the usefulness of publishing failed experiments is detailed, showing how the version history of the wiki can be used to track the evolution of an organic chemistry experiment. Near the end of the talk an example of using automation to optimize a Ugi reaction is mentioned.
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Cheminformatics in Open Notebook Science
Jean-Claude Bradley
E-Learning Coordinator College of Arts and Sciences
Associate Professor of ChemistryDrexel University
July 29, 2008
Advanced Informatics in Chemistry EducationAt BCCE, Indiana U.
Open and Closed Science Open and Closed Science
TraditionalLab Notebook(unpublished)
TraditionalJournal Article
Open Access Journal Article
Open Notebook Science (full transparency)
CLOSED OPEN
TraditionalPaper TextbookF2F lectures
Lectures Notes public
Assigned problems public
Archived Lectures Public and free online textbooks
RESEARCH
TEACHING
Older Males Prefer
Organic Chemistry!
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.
BLOG
WIKI
Mailing List
GoogleDocs
UsefulChem
ChemSpider
CDD
Where’s the Beef?Where’s the Beef?
Link to Lab Notebook Page in Link to Lab Notebook Page in WikiWiki
Link to MoleculesLink to Molecules
Link to Docking Procedure Link to Docking Procedure (Rajarshi Guha)(Rajarshi Guha)
Link to Docking Results: Link to Docking Results: Lists of SMILES in GoogleDocs Lists of SMILES in GoogleDocs
(Rajarshi Guha)(Rajarshi Guha)
Procedure SectionProcedure Section
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)
Using ChemSpider to archive Using ChemSpider to archive compound characterizationcompound characterization
ChemSpider predicted vs. experimental ChemSpider predicted vs. experimental NMRsNMRs
The Most Important Section!The Most Important Section!The LogThe Log
Conclusion is Fully SupportedConclusion is Fully Supported
Table of ContentsTable of Contents
Indexing the Experiments in Indexing the Experiments in GoogleGoogle
Searching with Searching with Google Custom SearchGoogle Custom Search
How are people finding our How are people finding our experiments?experiments?
NMR in TFAPhenylacetaldehydec4h6o2 nmrmethylene chloride/methanolh'nmr of benzophenonesulfuric acid pkatertbutylaminetosyl isocyanideamino furandichloromethane polar?Reaction between Benzaldehyde and NaBH4phosphoric acid pkaveratraldehyde wiki
kinetics boc deprotectionRf value in polar solvent why glycerol is immiscible with etherside reaction of imines5.8 ppm nmrnmr cdcl3 chloroform side reactiondiasterotopic wikiadding anhydrous MgSO4 to the dichlormethane ether extractionhnmr doublet of doubletBoc-protected NMRchromatotron recipetriplet cdcl3 "13c nmr"
Specific Compounds Experimental Conditions
How are people finding How are people finding UsefulChem?UsefulChem?
free downloading chemistry videoorganic chemistry project + high schoolhow to make poster in second lifeorganic chem. quiz3d periodic tablesanimation protein dockingdocking animationwhy are acid-base reactions exothermic?
lysosomal targetsprotease and malariacheminformatics project proposalautomated reactionsmalaria review project synthesisCHEMISTRY WEB 2.0projects on QSAR & drug designchemistry experiment results database
Educational Big Picture
How Should Open Notebook How Should Open Notebook Science be Used?Science be Used?
How did this How did this experiment experiment
evolve?evolve?
Third party timestamp
http://usefulchem.wikispaces.com/page/diff/Exp037/1577428
http://usefulchem.wikispaces.com/SO+Research+Report
Comparing ExperimentsComparing ExperimentsUgi Master TableUgi Master Table
Collaborative Drug Discovery (CDD) Collaborative Drug Discovery (CDD) DatabaseDatabase
YouTube for demonstrating experimental YouTube for demonstrating experimental set-upset-up
Mailing List Facilitates inter-Mailing List Facilitates inter-group collaborationgroup collaboration
Imine Formation Mechanism: talk to the molecules!
Interacting with NMR spectra (JCAMP-DX)
Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
Gus Rosania’s NotebookGus Rosania’s Notebook
Cameron Neylon’s NotebookCameron Neylon’s Notebook
Using ExcelVBA to automate Using ExcelVBA to automate kinetics analysiskinetics analysis
Reaction profile plotted Reaction profile plotted automaticallyautomatically
Results in Machine-Friendly Results in Machine-Friendly FormatFormat
Mettler-Toledo MiniMapper
Mettler-Toledo MiniBlock System
Where is Science headed?Where is Science headed?
WE ARE HEREWE ARE HERE
ConclusionConclusion
Communicate firstCommunicate first Standardize secondStandardize second In a Science2.0 world redundancy is In a Science2.0 world redundancy is
kingking
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