Jean-Claude Bradley presents on The Role of Openness in Scientific Automation: a case for Open Notebook Science at the IJCAI'09 Workshop on Abductive and Inductive Knowledge Development in Pasadena, CA on July 12, 2009.
1. The Role of Openness in Scientific
Automation: a case for Open
Notebook Science
IJCAI'09 Workshop on Abductive and
Inductive Knowledge Development
Jean-Claude Bradley
Associate Professor of Chemistry
Drexel University
July 12, 2009
3. Why are humans good at science?
GOSSIP CURIOSITY NEED TO ART
TO KNOW CREATE
UNDERSTANDING CONTROL
PREDICTIVE MODELS
CONCEPTUAL (docking) EMPIRICAL (QSAR)
4. The standard model of how science
happens
Propose Design
hypothesis experiments
Analyze Perform
results experiments
5. The actual way much of science
happens
Think up Find collaborators Convince
something who also think what somebody to
cool/useful to you want to do is fund your
do cool cool idea
Find existing Do the work Share what you
data or (experiments) found with the
models to
world
minimize the
amount of
Usually last (and
trial and error
only a small part)
6. How can the scientific process become
more automated?
WE ARE HERE
8. How radical openness can assist in the
automation of science
Agents can participate with zero or near-
zero cost (free hosted services – e.g.
Google)
Self-organizing redundant processes
13. Open and Closed Science
Traditional Traditional Open Notebook
Lab Notebook Journal Open Access Science (full
(unpublished) Article Journal Article transparency)
RESEARCH
CLOSED OPEN
TEACHING
Lectures Archived
Traditional Assigned
Notes Lectures
Paper problems
public Public and
Textbook public free online
F2F lectures
textbooks
16. There are NO FACTS,
only measurements embedded
within assumptions
Open Notebook Science maintains
the integrity of data provenance by
making assumptions explicit
44. Solubility Measurement Requests:
DoSol sheet
•Outlier Bot: flags measurements with high standard deviation to mean
ratios
•Google Analytics queries – new solvent/solute searches
•Solubility request form – researcher in Israel requesting pyrene in
acetonitrile solubility for environmental soil contamination study
•Application based models – high priority Ugi reactants
45. Solvent mixture and temperature:
multidimensional solubility data
Actual Data From quadratic regression
(4-nitrobenzaldehyde) of 5D space
Feeds DoSol Sheet the next points to measure to best cover the space
55. UsefulChem Project: Open Primary
Research in Drug Design using Web2.0
tools
Rajarshi Guha Tsu-Soo Tan
Indiana U Docking Nanyang Inst.
JC Bradley
Drexel U Synthesis
Phil Rosenthal Dan Zaharevitz
UCSF Testing NCI
(malaria) (tumors)
63. How does Open Notebook Science fit with
traditional publication?
•Concentration (0.4, 0.2, 0.07 M)
•Solvent (methanol, ethanol, acetonitrile, THF)
•Excess of some reagents (1.2 eq.)
76. Acknowledgements
Khalid Mirza (Drexel)
Jenny Hale (Southampton U.)
David Bulger (Oral Roberts U.)
Tim Bohinsky (Drexel)
Kevin Owens (Drexel)
Tom Osborne (Mettler-Toledo)
Antony Williams (ChemSpider)
Andrew Lang (Oral Roberts U.)
Rajarshi Guha (Indiana U.)
Cameron Neylon (Southampton U.)