Enhancing Scientific Communication through Open Notebook Science

Jean-Claude Bradley

E-Learning Coordinator College of Arts and Sciences

Associate Professor of ChemistryDrexel University

April 16, 2008

Scholar 2 Scholar Symposium: How Web 2.0 is Changing Scholarly Communication

What is Web 2.0?What is Web 2.0?

Source: Markus Angermeier and Tim O’Reilly, Wikipedia

Some of my friends……Some of my friends……

Evaluating and Creating Evaluating and Creating RelationshipsRelationships

A Few Examples from FriendFeedA Few Examples from FriendFeed

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TraditionalLab Notebook(unpublished)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

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

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 (Rajarshi Guha)(Rajarshi Guha)

Link to Raw Data with Link to Raw Data with JSpecViewJSpecView

Conclusion is Fully SupportedConclusion is Fully Supported

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

Using ChemSpider to archive Using ChemSpider to archive compound characterizationcompound characterization

Comparing Experiments with Comparing Experiments with GoogleDocsGoogleDocs

Predicting PrecipitatesPredicting PrecipitatesRajarshi Guha’s Model

MESA Analytics Model

The Most Important Section!The Most Important Section!

Results in Machine-Friendly Results in Machine-Friendly FormatFormat

Table of ContentsTable of Contents

Recent Changes in WikiRecent Changes in Wiki

Tracking Versions of Wiki Tracking Versions of Wiki PagesPages

Comparing Versions of Wiki Comparing Versions of Wiki PagesPages

Telling the story of the failuresTelling the story of the failures

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

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

What about the blog?What about the blog?Discussing Funding Discussing Funding

Supporting Funding Initiatives Supporting Funding Initiatives

Highlight Popular Media Highlight Popular Media Coverage Coverage

Highlight Peer-Reviewed Highlight Peer-Reviewed Coverage Coverage

Announce Collaborator: Announce Collaborator: Gus Rosania Gus Rosania

Announce Collaborator: Announce Collaborator: Matthias Zeller Matthias Zeller

Announce Collaborator: Announce Collaborator: Phil Rosenthal Phil Rosenthal

Discuss Presentations in Real Discuss Presentations in Real LifeLife

Discuss Presentations in Discuss Presentations in Second LifeSecond Life

Showcase Science in New Showcase Science in New MediaMedia

Showcase Teaching in New Showcase Teaching in New MediaMedia

Alerts to Broader Impact Alerts to Broader Impact OpportunitiesOpportunities

Science PhilosophyScience Philosophy

Gus Rosania’s NotebookGus Rosania’s Notebook

Cameron Neylon’s NotebookCameron Neylon’s Notebook

Collaboration with Brent Collaboration with Brent Friesen’s Teaching Lab at Friesen’s Teaching Lab at

Dominican UniversityDominican University

http://ochemonline.pbwiki.com/Ugi%20Synthesis%20Collaborative%20Project

Where is Science headed?Where is Science headed?

WE ARE HEREWE ARE HERE

AcknowledgementsAcknowledgements

Khalid MirzaEmily Messner

Shannon OsebackTim BohinskiDave StrumfelsJames GiammarcoLin ChengSean GardnerJessica ColditzAlicia Holsey