Cheminformatics in Open Notebook Science

Jean-Claude Bradley

E-Learning Coordinator College of Arts and Sciences

Associate Professor of ChemistryDrexel University

July 29, 2008

Advanced Informatics in Chemistry EducationAt BCCE, Indiana U.

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TraditionalLab Notebook(unpublished)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

Older Males Prefer

Organic Chemistry!

Open Primary Research in Drug Design Open Primary Research in Drug Design using Web2.0 toolsusing Web2.0 tools

(blogs, wikis, Second Life, mailing (blogs, wikis, Second Life, mailing lists)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?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)

Procedure SectionProcedure Section

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

ChemSpider predicted vs. experimental ChemSpider predicted vs. experimental NMRsNMRs

The Most Important Section!The Most Important Section!The LogThe Log

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

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

Comparing ExperimentsComparing ExperimentsUgi Master TableUgi Master Table

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

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

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

Imine Formation Mechanism: talk to the molecules!

Interacting with NMR spectra (JCAMP-DX)

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

Gus Rosania’s NotebookGus Rosania’s Notebook

Cameron Neylon’s NotebookCameron Neylon’s Notebook

Using ExcelVBA to automate Using ExcelVBA to automate kinetics analysiskinetics analysis

Reaction profile plotted Reaction profile plotted automaticallyautomatically

Results in Machine-Friendly Results in Machine-Friendly FormatFormat

Mettler-Toledo MiniMapper

Mettler-Toledo MiniBlock System

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

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