Open Notebook Science for Collaborative Drug

Development

Jean-Claude Bradley

Sept 5, 2008

University of Manchester

E-Learning Coordinator College of Arts and Sciences

Associate Professor of ChemistryDrexel University

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TraditionalLab Notebook(unpublished)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

Motivations for ONS Motivations for ONS

•Faster Science•Better Science

A recent example in Southampton

Sept 3, 2008 usefulchem.wikispaces.com/exp207

Investigating solubilities in organic solvents

Boc-glycine vanillin glucose NaCl

The lab notebook page

The Log: No Insider Information

The Results in a GoogleDoc

reliable

unreliable

Representation in the Neylon notebook

Open Notebook Science Grand Challenge

•design procedures to determine the solubility of compounds in organic solvents•teams or individuals welcome•Open Notebooks will be validated by experts•“mystery prizes” for creativity, productivity, reproducibility and other metrics of scientific quality•details coming soon…..

Round one

UsefulChem Project:UsefulChem Project: Open Primary Open Primary Research in Drug Design using Web2.0 Research in Drug Design using Web2.0

toolstools

Docking

Synthesis

Testing

Rajarshi GuhaIndiana U

JC BradleyDrexel U

Phil RosenthalUCSF

(malaria)

Dan ZaharevitzNCI

(tumors)

Tsu-Soo TanNanyang Inst.

BLOGWIKI

Mailing List

GoogleDocs

Architecture: Distributed,

Interlinked and Redundant

ChemSpider

CDD

FriendFeedNature Precedin

gs JoVE

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 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)

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 ChemSpider to archive Using ChemSpider to archive compound characterizationcompound characterization

Conclusion is Fully SupportedConclusion is Fully Supported

Table of ContentsTable of Contents

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

How Should Open Notebook How Should Open Notebook Science be Used?Science be Used?

How did this How did this experiment experiment

evolve?evolve?

Third party timestamp

http://usefulchem.wikispaces.com/page/diff/Exp037/1577428

Comparing wiki page Comparing wiki page versionsversions

http://usefulchem.wikispaces.com/SO+Research+Report

Comparing ExperimentsComparing ExperimentsUgi Master TableUgi Master Table

YouTube for demonstrating experimental YouTube for demonstrating experimental set-upset-up

Older Males Prefer

Organic Chemistry!

Mailing List Facilitates inter-Mailing List Facilitates inter-group collaborationgroup collaboration

Outcome of Guha-Bradley-Outcome of Guha-Bradley-Rosenthal collborationRosenthal collboration

Collaborative Drug Discovery (CDD) Collaborative Drug Discovery (CDD) DatabaseDatabase

Interacting with NMR spectra (JCAMP-DX) in Second Life

Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)

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 Results in Machine-Friendly FormatFormat

Mettler-Toledo MiniMapper

Mettler-Toledo MiniBlock System

GoogleDoc to program and report

XML reports from MiniMapper robot

Writing Code in the Murray-Rust House

Experiments in Chemical Markup Language

Paper written on Wiki

References to papers, blog posts, lab notebook pages, raw

data

Pre-print on Nature Precedings

Methanol 0.4M xs of imine Methanol 0.4M xs of imine bestbest

Paper on Journal of Visualized Experiments (JoVE)

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 In a Science2.0 world redundancy is

kingking