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

2. What is science?
FINDING OUT WHAT IS:
GOOD BAD
AND MAKING CHANGES:
BETTER CURE

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

7. The Robot Scientist

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

9. How can machines know what is
important?
Ask the humans

10. UsefulChem Blog

11. What chemists think is important in
2005

12. Find-A-Drug

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(unpublished) Article Journal Article transparency)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

14. Motivation: Faster Science, Better Science

15. Open Notebook Science Logos
(Andy Lang, Shirley Wu)
Sharing: how much and when

16. There are NO FACTS,
only measurements embedded
within assumptions
Open Notebook Science maintains
the integrity of data provenance by
making assumptions explicit

17. TRUST
PROOF

18. The solubility of 4-chlorobenzaldehyde

19. The Log makes Assumptions Explicit

20. The Rationale of Findings Explicit

21. Raw Data Made Public
Splatter?
Some liquid

22. YouTube for demonstrating experimental set-up

23. Calculations Made Public on
Google Spreadsheets

24. Revision History on
Google Spreadsheets

25. Wiki Page History

26. Comparing Wiki Page Versions

27. Proof of Purity with interactive NMR
spectrum using JSpecView and JCAMP-DX

28. Linking to Molecules in Chemistry
Databases

29. Experimental Spectra and User-
Deposited Data on ChemSpider

30. Open Data JCAMP spectra for education
(Andy Lang, Tony Williams)
(Andy Lang, Tony Williams, Robert Lancashire)

31. Database Curation via Game Playing

32. Over 50,000 spectrum views so far -
worldwide

33. Link Spectral Game to Open Educational
Content

34. NMR game in Second Life (Andy Lang)

35. Crowdsourcing Solubility Data

36. ONS Challenge Students

37. ONS Challenge Judges

38. Teaching Lab: Brent Friesen
(Dominican University)

39. Solubility Experiment List

40. Solubilities collected in a Google
Spreadsheet

41. Rajarshi Guha’s Live Web Query
using Google Viz API

42. Rajarshi Guha and Andy Lang:
Chemical Space Explorer

43. Semi-Automated Measurement of
solubility via web service analysis
of JCAMP-DX files
(Andy Lang)

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

46. Crowdsourcing Reaction Requests:
DoUgi sheet

47. Understanding in addition to empirical
modeling
Missed in a prior
publication on solubility
for this compound

48. Data provenance:
From Wikipedia to…

49. …the lab notebook and raw data

50. Including links to the literature

52. Pierre Lindenbaum’s Solubility Data
as RDF Triples

53. Results and Workflows in Machine-
Friendly Format

54. Experiments in Chemical Markup Language

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)

56. Malaria Target: falcipain-2
involved in hemoglobin metabolism
Dana.org

57. Where’s the Beef?

58. Link to Lab Notebook Page in Wiki

59. Link to Docking Procedure
(Rajarshi Guha)

60. Link to Docking Results:
Lists of SMILES in GoogleDocs
(Rajarshi Guha)

61. Outcome of Guha-Bradley-Rosenthal
collboration

62. Collaborative Drug Discovery (CDD) Database

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.)

64. Mettler-Toledo MiniMapper

65. Mettler-Toledo MiniBlock System

66. XML reports from MiniMapper robot

67. GoogleDoc to program and report

68. Paper written on Wiki

69. References to papers, blog posts,
lab notebook pages, raw data

70. Paper on Journal of Visualized
Experiments (JoVE)

71. Pre-print on Nature Precedings

72. ChemSpider Automated Mark-up of
Chemical Names

73. Archiving and Curation of ONS and
other new forms of scholarship?

74. Other Open Notebooks
Cameron Neylon’s Notebooks

75. Anthony Salvagno’s Notebook
(Steve Koch group)

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.)