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BrightTALK Open Notebook Science


Jean-Claude Bradley presents on "Open Notebook Science for Collaborative Drug Discovery" on July 23, 2009.

Jean-Claude Bradley presents on "Open Notebook Science for Collaborative Drug Discovery" on July 23, 2009.

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  • 'There are NO FACTS, only measurements embedded within assumptions.'
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  • 1. Open Notebook Science for Collaborative Drug Discovery Jean-Claude Bradley July 23, 2009 BrightTALK Associate Professor of Chemistry Drexel University
  • 2. WE ARE HERE How can the scientific process become more automated?
  • 3. The Robot Scientist
  • 4.
    • Agents can participate with zero or near-zero cost (free hosted services – e.g. Google)
    • Self-organizing redundant processes
    How radical openness can assist in the automation of science
  • 5. UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.
  • 6. Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
  • 7. Outcome of Guha-Bradley-Rosenthal collboration
  • 8. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?
  • 9. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks RESEARCH TEACHING
  • 10. Motivation: Faster Science, Better Science
  • 11. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  • 12. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  • 14. The solubility of 4-chlorobenzaldehyde
  • 15. The Log makes Assumptions Explicit
  • 16. Results and Workflows in Machine-Friendly Format
  • 17. The Rationale of Findings Explicit
  • 18. Raw Data Made Public Splatter? Some liquid
  • 19. YouTube for demonstrating experimental set-up
  • 20. Calculations Made Public on Google Spreadsheets
  • 21. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  • 22. Link to Docking Procedure (Rajarshi Guha)
  • 23. Revision History on Google Spreadsheets
  • 24. Wiki Page History
  • 25. Comparing Wiki Page Versions
  • 26. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  • 27. Linking to Molecules in Chemistry Databases
  • 28. Experimental Spectra and User-Deposited Data on ChemSpider
  • 29. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
  • 30. Database Curation via Game Playing
  • 31. Over 50,000 spectrum views so far - worldwide
  • 32. Link Spectral Game to Open Educational Content
  • 33. NMR game in Second Life (Andy Lang)
  • 34. Crowdsourcing Solubility Data
  • 35. ONS Challenge Students
  • 36. ONS Challenge Judges
  • 37. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  • 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. 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
  • 44. Solvent mixture and temperature: multidimensional solubility data Actual Data (4-nitrobenzaldehyde) From quadratic regression of 5D space Feeds DoSol Sheet the next points to measure to best cover the space
  • 45. Comparing Experiments Ugi Master Table
  • 46. Crowdsourcing Reaction Requests: DoUgi sheet
  • 47. Raw data reveal a problem 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
  • 51. Collaborative Drug Discovery (CDD) Database
  • 52.
    • Concentration (0.4, 0.2, 0.07 M)
    • Solvent (methanol, ethanol, acetonitrile, THF)
    • Excess of some reagents (1.2 eq.)
    How does Open Notebook Science fit with traditional publication?
  • 53. Mettler-Toledo MiniMapper
  • 54. Mettler-Toledo MiniBlock System
  • 55. XML reports from MiniMapper robot
  • 56. GoogleDoc to program and report
  • 57. Best Yield: 66% 0.4 M methanol 1.2 eq imine
  • 58. Reaction Optimization Visualization in Second Life
  • 59. Paper written on Wiki
  • 60. References to papers, blog posts, lab notebook pages, raw data
  • 61. Paper on Journal of Visualized Experiments (JoVE)
  • 62. Pre-print on Nature Precedings
  • 63. ChemSpider Automated Mark-up of Chemical Names
  • 64. Archiving and Curation of ONS and other new forms of scholarship?
  • 65. Cameron Neylon’s Notebooks Other Open Notebooks
  • 66. Anthony Salvagno’s Notebook (Steve Koch group)
  • 67. 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.)