open notebook science using blogs and wikis jean-claude bradley e-learning coordinator college of...
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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TraditionalLab Notebook(unpublished)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