Processing drug discovery rawdata collaboratively and openlyusing 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 ScienceOpen and Closed Science
Traditional
Lab Notebook
(unpublished)
Traditional
JournalArticle
Open AccessJournal Article
Open Notebook
Science (fulltransparency)
CLOSED
OPEN
Traditional
PaperTextbook
F2F lectures
LecturesNotespublic
Assignedproblemspublic
ArchivedLecturesPublic andfree onlinetextbooks
RESEARCH
TEACHING
Open Primary Research in Drug Designusing Web2.0 tools(blogs, wikis, Second Life, mailing lists)Open Primary Research in Drug Designusing 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?Where’s the Beef?
Link to Lab Notebook Page in WikiLink to Lab Notebook Page in Wiki
Link to MoleculesLink to Molecules
Link to Docking Procedure(Rajarshi Guha)Link to Docking Procedure(Rajarshi Guha)
Link to Docking Results:Lists of SMILES in GoogleDocs(Rajarshi Guha)Link to Docking Results:Lists of SMILES in GoogleDocs(Rajarshi Guha)
Procedure SectionProcedure Section
Link to Raw Data with JSpecView(data in JCAMP-DX format)(by Robert Lancashire)Link to Raw Data with JSpecView(data in JCAMP-DX format)(by Robert Lancashire)
Using ChemSpider to archivecompound characterizationUsing ChemSpider to archivecompound characterization
ChemSpider predicted vs. experimental NMRsChemSpider predicted vs. experimental NMRs
The Most Important Section!The LogThe Most Important Section!The Log
Conclusion is Fully SupportedConclusion is Fully Supported
Table of ContentsTable of Contents
Indexing the Experiments in GoogleIndexing the Experiments in Google
Searching withGoogle Custom SearchSearching withGoogle Custom Search
How are people finding ourexperiments?How are people finding ourexperiments?
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 Benzaldehydeand NaBH4
phosphoric acid pka
veratraldehyde wiki
kinetics boc deprotection
Rf value in polar solvent
why glycerol is immiscible withether
side reaction of imines
5.8 ppm nmr
nmr cdcl3 chloroform side reaction
diasterotopic wiki
adding anhydrous MgSO4 to thedichlormethane ether extraction
hnmr doublet of doublet
Boc-protected NMR
chromatotron recipe
triplet cdcl3 "13c nmr"
Specific Compounds
Experimental Conditions
How are people findingUsefulChem?How are people findingUsefulChem?
free downloading chemistry video
organic chemistry project + highschool
how to make poster in second life
organic chem. quiz
3d periodic tables
animation protein docking
docking animation
why are acid-base reactionsexothermic?
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 resultsdatabase
Educational
Big Picture
How Should Open NotebookScience be Used?How Should Open NotebookScience be Used?
How did thisexperimentevolve?How did thisexperimentevolve?
Third party timestamp
http://usefulchem.wikispaces.com/page/diff/Exp037/1577428
http://usefulchem.wikispaces.com/SO+Research+Report
Comparing ExperimentsUgi Master TableComparing ExperimentsUgi Master Table
YouTube for demonstrating experimental set-upYouTube for demonstrating experimental set-up
Older MalesPreferOrganicChemistry!
Mailing List Facilitates inter-groupcollaborationMailing List Facilitates inter-groupcollaboration
Outcome of Guha-Bradley-RosenthalcollborationOutcome of Guha-Bradley-Rosenthalcollboration
Collaborative Drug Discovery (CDD) DatabaseCollaborative 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 automatekinetics analysisUsing ExcelVBA to automatekinetics analysis
Reaction profile plottedautomaticallyReaction profile plottedautomatically
3D molecules in Second Life
Imine Formation Mechanism:
talk to the molecules!
Gus Rosania’s NotebookGus Rosania’s Notebook
Cameron Neylon’s NotebookCameron Neylon’s Notebook
Results in Machine-Friendly FormatResults 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 bestMethanol 0.4M xs of imine best
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 kingIn a Science2.0 world redundancy is king