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Open Notebook Science:Research in Real Time
Jean-Claude Bradley
E-Learning Coordinator College of Arts and Sciences
Associate Professor of ChemistryDrexel University
Nov 27, 2007
Sigma XiSwarthmore College Chapter
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TraditionalLab Notebook(unpublished)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
How will this happen?How will this happen? Self-organizing redundant processesSelf-organizing redundant processes
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
Malaria is a Logical Application Malaria is a Logical Application of Open Scienceof Open Science
•Very large problem: 300-500 million cases per year with one million deaths
•Not a lucrative market: IP control less important
Diketopiperazine LibraryDiketopiperazine LibraryEvolves to: on pot Evolves to: on pot
Ugi Ugi reaction/cyclizationreaction/cyclization
First iteration: First iteration: Solid Support Solid Support
SynthesisSynthesis
usefulchem.blogspot.comusefulchem.blogspot.com
The blog as an integrative The blog as an integrative tooltool
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)
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.
Mailing List Facilitates inter-Mailing List Facilitates inter-group collaborationgroup collaboration
Open science connectivityOpen science connectivity
More info on open source science here
http://usefulchem.wikispaces.com
Selected Experiments (some Selected Experiments (some failed)failed)
Orgprepdaily.wordpress.comOrgprepdaily.wordpress.com
Lab Notebook for intra-group Lab Notebook for intra-group communicationcommunication
Openwetware.orgOpenwetware.org
UsefulChem and Open UsefulChem and Open Science in Second LifeScience in Second Life
scifooliveson.wikispaces.com
QuestionQuestion: Is it really a good thing to let anyone who thinks : Is it really a good thing to let anyone who thinks they have a scientific breakthrough have access to free, they have a scientific breakthrough have access to free, open, public, Googleable media? open, public, Googleable media?
YESYES QuestionQuestion: What if I make a mistake in my data, never fix it, : What if I make a mistake in my data, never fix it,
no one catches it, and then someone dies because a no one catches it, and then someone dies because a medical decision was based on my "findings"? Isn't this medical decision was based on my "findings"? Isn't this exactly why we have formal peer review in formal exactly why we have formal peer review in formal publications? publications?
Peer review is not designed to catch errors from the Peer review is not designed to catch errors from the analysis of raw dataanalysis of raw data
Open Notebook Science is more difficult where Open Notebook Science is more difficult where human subjects are involvedhuman subjects are involved
QuestionQuestion: Who is the audience for science blogs and wikis : Who is the audience for science blogs and wikis anyway? Scientists or laypeople? anyway? Scientists or laypeople?
For UsefulChem, wiki is for chemists, blog for wider For UsefulChem, wiki is for chemists, blog for wider audienceaudience
QuestionQuestion: Can you get published if you've already posted : Can you get published if you've already posted your results to your blog/wiki? your results to your blog/wiki?
We’ll find out….We’ll find out…. QuestionQuestion: Can scientists establish their : Can scientists establish their
credibility/reputation by writing blogs and wikis? credibility/reputation by writing blogs and wikis? Certainly we’ve found collaborators this wayCertainly we’ve found collaborators this way
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