Cheminformatics and Open Notebook Science Jean-Claude Bradley E-Learning Coordinator College of Arts...
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Transcript of Cheminformatics and Open Notebook Science Jean-Claude Bradley E-Learning Coordinator College of Arts...
Cheminformatics and Open Notebook Science
Jean-Claude Bradley
E-Learning Coordinator College of Arts and Sciences
Associate Professor of ChemistryDrexel University
April 6, 2008
American Chemical Society CINF session
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TraditionalLab Notebook(unpublished)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
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 Experimental PlanLink to Experimental Plan
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 ExcelVBA to automate Using ExcelVBA to automate kinetics analysis using JCAMP-kinetics analysis using JCAMP-
DX filesDX files
Reaction profile plotted Reaction profile plotted automaticallyautomatically
Using ChemSpider to archive Using ChemSpider to archive compound characterizationcompound characterization
Next Step: Reading JCAMP-DX Next Step: Reading JCAMP-DX files in Second Life (Andy files in Second Life (Andy
Lang)Lang)
The Most Important Section!The Most Important Section!The LogThe Log
Conclusion is Fully SupportedConclusion is Fully Supported
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
Table of ContentsTable of Contents
Comparing ExperimentsComparing ExperimentsUgi Master TableUgi Master Table
Predicting PrecipitatesPredicting PrecipitatesRajarshi Guha’s Model
MESA Analytics Model
Results in Machine-Friendly Results in Machine-Friendly FormatFormat
Comparing Results in a TableComparing Results in a Table
Why a Wiki?Why a Wiki?
Tracking Versions of Wiki Tracking Versions of Wiki PagesPages
Comparing Versions of Wiki Comparing Versions of Wiki PagesPages
Telling the story of the failuresTelling the story of the failures
Mailing List Facilitates inter-Mailing List Facilitates inter-group collaborationgroup collaboration
Collaborative Drug Discovery (CDD) Collaborative Drug Discovery (CDD) DatabaseDatabase
Exporting Assay Results from CDDExporting Assay Results from CDD
Collaboration with Brent Collaboration with Brent Friesen’s Teaching Lab at Friesen’s Teaching Lab at
Dominican U.Dominican U.
Gus Rosania’s NotebookGus Rosania’s Notebook
Cameron Neylon’s NotebookCameron Neylon’s Notebook
Where is Science headed?Where is Science headed?
WE ARE HEREWE ARE HERE