Transcript Open Notebook Science: Research in Real Time Sigma Xi Swarthmore College Chapter Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University Nov 27,

Open Notebook Science:
Research in Real Time
Sigma Xi
Swarthmore College Chapter
Jean-Claude Bradley
E-Learning Coordinator
College of Arts and Sciences
Associate Professor of Chemistry
Drexel University
Nov 27, 2007
Open and Closed Science
Traditional
Lab Notebook
(unpublished)
Traditional
Journal
Article
Open Access
Journal Article
Open Notebook
Science (full
transparency)
RESEARCH
OPEN
CLOSED
TEACHING
Traditional
Paper
Textbook
F2F lectures
Lectures
Notes
public
Assigned
problems
public
Archived
Lectures
Public and
free online
textbooks
Where is Science headed?
WE ARE HERE
The Robot Scientist
How will this happen?
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Self-organizing redundant processes
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Fully Open Access (Read and Write)
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Publication of all aspects of the scientific
process: Open Source Science / Open
Notebook Science
Using semantically rich formats and
automation at zero publication cost – is this
the way to the technological singularity?
How can machines know what is
important?
Ask the humans
UsefulChem Blog
What chemists think is important in
2005
Malaria is a Logical Application of
Open Science
•Very large problem: 300-500 million cases
per year with one million deaths
•Not a lucrative market: IP control less
important
Find-A-Drug
Diketopiperazine Library
First iteration: Solid
Support Synthesis
Evolves to: on pot Ugi
reaction/cyclization
The Molecules Blog
The Experiments Blog
Comments from peers
The UsefulChem Wiki
Telling the story of the failures
Experiments moved to wiki
Experiment History
Experiment Edits
Third Party Time-Stamp on
Experiment Versions
Monitoring experimental progress
Table of Contents View
The blog as an integrative tool
usefulchem.blogspot.com
How are people finding our
experiments?
Molecules found by InChI
Processing Molecules on ChemSpider
Graphical Mining of Data with
JSpecView
usefulchem.wikispaces.com/Exp070 (48h 7 min)
Student assignments on a wiki
Student assignment on NMR using live
research data and JSpecView
Using ExcelVBA to automate
kinetics analysis
Specify NMR regions and internal
standard
NMR spectra of monitoring
samples calculated
Reaction profile plotted
automatically
Open Primary Research in Drug Design
using Web2.0 tools
(blogs, wikis, Second Life, mailing lists)
Rajarshi Guha
Indiana U
JC Bradley
Drexel U
Phil Rosenthal
UCSF
(malaria)
Docking
Tsu-Soo Tan
Nanyang Inst.
Synthesis
Testing
Dan Zaharevitz
NCI
(tumors)
Mailing List Facilitates inter-group
collaboration
Open science connectivity
More info
on open
source
science
here
http://usefulchem.wikispaces.com
CombiUgi Virtual Libraries
Falcipain-2 inhibitor?
Khalid Mirza
http://usefulchem.wikispaces.com/Exp148
More Flexible Scientific Publication
Raw Experimental Data
neurodatabase.org
Selected Experiments (some
failed)
Orgprepdaily.wordpress.com
Generalized Protocols
Openwetware.org
Vendor Reliability
Orgprepdaily.wordpress.com
Lab Notebook for intra-group
communication
Openwetware.org
Discussing Hypotheses
RRResearch.blogspot.com
Cameron Neylon’s Notebook
UsefulChem and Open Science in
Second Life
scifooliveson.wikispaces.com
Merging Research and Teaching in Second Life
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Question: Is it really a good thing to let anyone who thinks they
have a scientific breakthrough have access to free, open, public,
Googleable media?
YES
Question: What if I make a mistake in my data, never fix it, no one
catches it, and then someone dies because a medical decision was
based on my "findings"? Isn't this exactly why we have formal peer
review in formal publications?
Peer review is not designed to catch errors from the
analysis of raw data
Open Notebook Science is more difficult where human
subjects are involved
Question: Who is the audience for science blogs and wikis anyway?
Scientists or laypeople?
For UsefulChem, wiki is for chemists, blog for wider
audience
Question: Can you get published if you've already posted your
results to your blog/wiki?
We’ll find out….
Question: Can scientists establish their credibility/reputation by
writing blogs and wikis?
Certainly we’ve found collaborators this way