Open Notebook Science using Blogs and Wikis

Jean-Claude Bradley

E-Learning Coordinator College of Arts and Sciences

Drexel University

March 27, 2007

American Chemical Society Symposium on Communicating Chemistry

Open and Closed ScienceOpen and Closed Science

TraditionalLab Notebook(unpublished)

TraditionalJournal Article

Open Access Journal Article

Open Notebook Science (full transparency)

CLOSED

OPEN

Where is Science headed?Where is Science headed?

WE ARE HEREWE ARE HERE

The Robot ScientistThe Robot Scientist

How will this happen?How will this happen?

Self-organizing redundant processesSelf-organizing redundant processes Agents can participate with zero or near-zero Agents can participate with zero or near-zero

cost (free hosted services – e.g. Google)cost (free hosted services – e.g. Google) Fully Open Access (Read and Write)Fully Open Access (Read and Write) Publication of all aspects of the scientific Publication of all aspects of the scientific

process: Open Source Science / process: Open Source Science / Open Open Notebook ScienceNotebook Science

Using semantically rich formats and Using semantically rich formats and automation at zero publication cost – is this automation at zero publication cost – is this the way to the technological singularity?the way to the technological singularity?

How can machines know what How can machines know what is important?is important?

Ask the humansAsk the humans

UsefulChem BlogUsefulChem Blog

What chemists think is What chemists think is important in 2005important in 2005

Find-A-DrugFind-A-Drug

Diketopiperazine LibraryDiketopiperazine LibraryEvolves to: on pot Evolves to: on pot

Ugi Ugi reaction/cyclizationreaction/cyclization

First iteration: First iteration: Solid Support Solid Support

SynthesisSynthesis

The Molecules BlogThe Molecules Blog

The Experiments BlogThe Experiments Blog

Comments from peersComments from peers

The UsefulChem WikiThe UsefulChem Wiki

Telling the story of the failuresTelling the story of the failures

Experiments moved to wikiExperiments moved to wiki

Experiment HistoryExperiment History

Experiment EditsExperiment Edits

Third Party Time-Stamp on Third Party Time-Stamp on Experiment VersionsExperiment Versions

Monitoring experimental Monitoring experimental progressprogress

How are people finding our How are people finding our experiments?experiments?

Molecules found by InChIMolecules found by InChI

usefulchem.blogspot.comusefulchem.blogspot.com

The blog as an integrative The blog as an integrative tooltool

usefulchem.wikispaces.com/Exp049usefulchem.wikispaces.com/Exp049

The wiki as the laboratory The wiki as the laboratory notebooknotebook

Open science connectivityOpen science connectivity

More info on open source science here

http://usefulchem.wikispaces.com

Automation in UsefulChemAutomation in UsefulChem

CMLRSS feed on BioclipseCMLRSS feed on Bioclipse

Graphical Mining of Data with Graphical Mining of Data with JSpecViewJSpecView

usefulchem.wikispaces.com/Exp070 (48h 7 min)usefulchem.wikispaces.com/Exp070 (48h 7 min)

Using ExcelVBA to automate Using ExcelVBA to automate kinetics analysiskinetics analysis

Specify NMR regions and Specify NMR regions and internal standardinternal standard

NMR spectra of monitoring NMR spectra of monitoring samples calculatedsamples calculated

Reaction profile plotted Reaction profile plotted automaticallyautomatically

UsefulChem in Second LifeUsefulChem in Second Life

Display blog post as posterDisplay blog post as poster

Click on Images for Click on Images for DescriptionsDescriptions

Click on the Blue Obelisk for a Click on the Blue Obelisk for a Chemistry QuizChemistry Quiz

Thanks Beth and Eloise!Thanks Beth and Eloise!

neurodatabase.orgneurodatabase.org

Raw Experimental DataRaw Experimental Data

Selected Experiments (some Selected Experiments (some failed)failed)

Orgprepdaily.wordpress.comOrgprepdaily.wordpress.com

Orgprepdaily.wordpress.comOrgprepdaily.wordpress.com

Vendor ReliabilityVendor Reliability

Generalized ProtocolsGeneralized Protocols

Openwetware.orgOpenwetware.org

Lab Notebook for intra-group Lab Notebook for intra-group communicationcommunication

Openwetware.orgOpenwetware.org

Discussing HypothesesDiscussing Hypotheses

RRResearch.blogspot.comRRResearch.blogspot.com

Feedback for the Automation Feedback for the Automation ComponentComponent

Also – Rich Apodaca, Christoph Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-RustSteinbeck, Peter Murray-Rust