processing drug discovery raw data collaboratively and openly using open notebook science...
TRANSCRIPT
Processing drug discovery raw data collaboratively and openly using Open
Notebook Science
Jean-Claude Bradley
E-Learning Coordinator College of Arts and Sciences
Associate Professor of ChemistryDrexel University
August 20, 2008
American Chemical Society
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TraditionalLab Notebook(unpublished)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 using Web2.0 tools
(blogs, wikis, Second Life, mailing 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?
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)
Procedure Section
Link to Raw Data with JSpecView
(data in JCAMP-DX format)(by Robert Lancashire)
Using ChemSpider to archive compound characterization
ChemSpider predicted vs. experimental NMRs
The Most Important Section!The Log
Conclusion is Fully Supported
Table of Contents
Indexing the Experiments in Google
Searching with Google Custom Search
How are people finding our 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 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 Science be Used?
How did this experiment
evolve?
Third party timestamp
http://usefulchem.wikispaces.com/page/diff/Exp037/1577428
http://usefulchem.wikispaces.com/SO+Research+Report
Comparing ExperimentsUgi Master Table
YouTube for demonstrating experimental set-up
Older Males Prefer
Organic Chemistry!
Mailing List Facilitates inter-group collaboration
Outcome of Guha-Bradley-Rosenthal collboration
Collaborative Drug Discovery (CDD) Database
Interacting with NMR spectra (JCAMP-DX) in Second Life
Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
Using ExcelVBA to automate kinetics analysis
Reaction profile plotted automatically
3D molecules in Second Life
Imine Formation Mechanism: talk to the molecules!
Gus Rosania’s Notebook
Cameron Neylon’s Notebook
Results in Machine-Friendly Format
Mettler-Toledo MiniMapper
Mettler-Toledo MiniBlock System
GoogleDoc to program and report
XML reports from MiniMapper robot
Methanol 0.4M xs of imine best
Where is Science headed?
WE ARE HERE
Conclusion
Communicate first Standardize second In a Science2.0 world redundancy is
king