Open Notebook Science

Jean-Claude Bradley

Oct 23, 2008

NSF eChemistry Workshop

Associate Professor of ChemistryDrexel University

Motivation: Faster Science, Better Science

There are NO FACTS, only measurements embedded

within assumptions

Open Notebook Science maintains the integrity of data

provenance by making assumptions explicit

Measuring Solubilities in Southampton with Cameron

Neylon

Sept 3, 2008 usefulchem.wikispaces.com/exp207

Investigating solubilities in organic solvents

Boc-glycine vanillin glucose NaCl

The Results in a GoogleDoc

reliable

unreliable

The solubility of 4-chlorobenzaldehyde

Open Chemistry Crowdsourcing

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.

Malaria Target: falcipain-2 involved in hemoglobin metabolism

Dana.org

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)

Conclusion is Fully SupportedConclusion is Fully Supported

How did this How did this experiment experiment

evolve?evolve?

Third party timestamp

Comparing wiki page Comparing wiki page versionsversions

Comparing ExperimentsComparing ExperimentsUgi Master TableUgi Master Table

•Concentration (0.4, 0.2, 0.07 M)•Solvent (methanol, ethanol, acetonitrile, THF)•Excess of some reagents (1.2 eq.)

Reaction to Optimize

Mettler-Toledo MiniBlock System

Mettler-Toledo MiniMapper

XML reports from MiniMapper robot

GoogleDoc to program and report

Paper written on Wiki

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

data

Paper on Journal of Visualized Experiments (JoVE)

Pre-print on Nature Precedings

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

AcknowledgementsAcknowledgements

Khalid Mirza (Drexel)Khalid Mirza (Drexel) Kevin Owens (Drexel)Kevin Owens (Drexel) Tim Bohinsky (Drexel)Tim Bohinsky (Drexel) James Giammarco (Drexel)James Giammarco (Drexel) Tom Osborne (Mettler-Toledo)Tom Osborne (Mettler-Toledo) Antony Williams (ChemSpider)Antony Williams (ChemSpider) Andrew Lang (Oral Roberts U.)Andrew Lang (Oral Roberts U.) Cameron Neylon (Southampton U.)Cameron Neylon (Southampton U.)