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TraditionalLab Notebook(unpublished)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