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 Chemistry Drexel University August 20, 2008 American Chemical Society
Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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 Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang 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 TFA Phenylacetaldehyde c4h6o2 nmr methylene chloride/methanol h'nmr of benzophenone sulfuric acid pka tertbutylamine tosyl isocyanide amino furan dichloromethane polar? Reaction between Benzaldehyde and NaBH4 phosphoric acid pka veratraldehyde wiki kinetics boc deprotection Rf value in polar solvent why glycerol is immiscible with ether side reaction of imines 5.8 ppm nmr nmr cdcl3 chloroform side reaction diasterotopic wiki adding anhydrous MgSO4 to the dichlormethane ether extraction hnmr doublet of doublet Boc-protected NMR chromatotron recipe triplet cdcl3 "13c nmr" Specific CompoundsExperimental Conditions
How are people finding UsefulChem? free downloading chemistry video organic chemistry project + high school how to make poster in second life organic chem. quiz 3d periodic tables animation protein docking docking animation why are acid-base reactions exothermic? lysosomal targets protease and malaria cheminformatics project proposal automated reactions malaria review project synthesis CHEMISTRY WEB 2.0 projects on QSAR & drug design chemistry experiment results database EducationalBig Picture
How Should Open Notebook Science be Used?
How did this experiment evolve? Third party timestamp
Comparing Experiments Ugi 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 (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 Communicate first Standardize second Standardize second In a Science2.0 world redundancy is king In a Science2.0 world redundancy is king