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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
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Open and Closed Science
Open and Closed Science
Traditional
Lab Notebook
(unpublished)
Traditional
Journal
Article
Open Access
Journal Article
Open Notebook
Science (full
transparency)
CLOSED
OPEN
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Where is Science headed?
WE ARE HERE
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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The Robot Scientist
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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How will this happen?
Self-organizing redundant processes
Self-organizing redundant processes
Agents can participate with zero or near-zero cost
Agents can participate with zero or near-zero cost
(free hosted services ­ e.g. Google)
(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 process:
Publication of all aspects of the scientific process:
Open Source Science /
Open Source Science /
Open Notebook Science
Open Notebook Science
Using semantically rich formats and automation at
Using semantically rich formats and automation at
zero publication cost ­ is this the way to the
zero publication cost ­ is this the way to the
technological singularity?
technological singularity?
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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How can machines know what is
important?
Ask the humans
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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UsefulChem Blog
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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What chemists think is important in
2005
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Find-A-Drug
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Diketopiperazine Library
Evolves to: on pot Ugi
reaction/cyclization
First iteration: Solid
Support Synthesis
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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The Molecules Blog
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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The Experiments Blog
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Comments from peers
Comments from peers
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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The UsefulChem Wiki
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Telling the story of the failures
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Experiments moved to wiki
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Experiment History
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Experiment Edits
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Third Party Time-Stamp on
Experiment Versions
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Monitoring experimental progress
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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How are people finding our
experiments?
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Molecules found by InChI
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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usefulchem.blogspot.com
The blog as an integrative tool
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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usefulchem.wikispaces.com/Exp049
The wiki as the laboratory notebook
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Open science connectivity
Open science connectivity
More info
on open
source
science
here
http://usefulchem.wikispaces.com
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Automation in UsefulChem
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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CMLRSS feed on Bioclipse
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Graphical Mining of Data with
JSpecView
usefulchem.wikispaces.com/Exp070 (48h 7 min)
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Using ExcelVBA to automate
kinetics analysis
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Specify NMR regions and internal
standard
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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NMR spectra of monitoring samples
calculated
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Reaction profile plotted
automatically
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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UsefulChem in Second Life
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Display blog post as poster
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Click on Images for Descriptions
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Click on the Blue Obelisk for a
Chemistry Quiz
Thanks Beth and Eloise!
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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neurodatabase.org
Raw Experimental Data
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Selected Experiments (some failed)
Orgprepdaily.wordpress.com
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Orgprepdaily.wordpress.com
Vendor Reliability
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Generalized Protocols
Openwetware.org
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Lab Notebook for intra-group
communication
Openwetware.org
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Discussing Hypotheses
RRResearch.blogspot.com
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Feedback for the Automation
Component
Also ­ Rich Apodaca, Christoph
Steinbeck, Peter Murray-Rust
Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007
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Nature Precedings : doi:10.1038/npre.2007.39.1 : Posted 11 Jun 2007