BrightTALK Open Notebook Science

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  • + CharlieZhu CharlieZhu 4 months ago
    'There are NO FACTS, only measurements embedded within assumptions.'
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BrightTALK Open Notebook Science - Presentation Transcript

  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
    • 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
  4. 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.
  5. Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
  6. Outcome of Guha-Bradley-Rosenthal collboration
  7. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?
  8. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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
  9. Motivation: Faster Science, Better Science
  10. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  11. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  12. TRUST PROOF
  13. The solubility of 4-chlorobenzaldehyde
  14. The Log makes Assumptions Explicit
  15. Results and Workflows in Machine-Friendly Format
  16. The Rationale of Findings Explicit
  17. Raw Data Made Public Splatter? Some liquid
  18. YouTube for demonstrating experimental set-up
  19. Calculations Made Public on Google Spreadsheets
  20. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  21. Link to Docking Procedure (Rajarshi Guha)
  22. Revision History on Google Spreadsheets
  23. Wiki Page History
  24. Comparing Wiki Page Versions
  25. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  26. Linking to Molecules in Chemistry Databases
  27. Experimental Spectra and User-Deposited Data on ChemSpider
  28. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
  29. Database Curation via Game Playing
  30. Over 50,000 spectrum views so far - worldwide
  31. Link Spectral Game to Open Educational Content
  32. NMR game in Second Life (Andy Lang)
  33. Crowdsourcing Solubility Data
  34. ONS Challenge Students
  35. ONS Challenge Judges
  36. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  37. Teaching Lab: Brent Friesen (Dominican University)
  38. Solubility Experiment List
  39. Solubilities collected in a Google Spreadsheet
  40. Rajarshi Guha’s Live Web Query using Google Viz API
  41. Rajarshi Guha and Andy Lang: Chemical Space Explorer
  42. 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
  43. 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
  44. Comparing Experiments Ugi Master Table
  45. Crowdsourcing Reaction Requests: DoUgi sheet
  46. Raw data reveal a problem Missed in a prior publication on solubility for this compound
  47. Data provenance: From Wikipedia to…
  48. … the lab notebook and raw data
  49. Including links to the literature
  50. Collaborative Drug Discovery (CDD) Database
    • 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?
  51. Mettler-Toledo MiniMapper
  52. Mettler-Toledo MiniBlock System
  53. XML reports from MiniMapper robot
  54. GoogleDoc to program and report
  55. Best Yield: 66% 0.4 M methanol 1.2 eq imine
  56. Reaction Optimization Visualization in Second Life
  57. Paper written on Wiki
  58. References to papers, blog posts, lab notebook pages, raw data
  59. Paper on Journal of Visualized Experiments (JoVE)
  60. Pre-print on Nature Precedings
  61. ChemSpider Automated Mark-up of Chemical Names
  62. Archiving and Curation of ONS and other new forms of scholarship?
  63. Cameron Neylon’s Notebooks Other Open Notebooks
  64. Anthony Salvagno’s Notebook (Steve Koch group)
  65. 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.)

+ Jean-Claude BradleyJean-Claude Bradley, 4 months ago

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