Crowdsourcing Solubility using Open Notebook Science


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Jean-Claude Bradley presents at the American Chemical Society on August 16, 2009. The talk starts with highlighting how Open Notebook Science has been used to shed light on the recent report of using sodium hydride (NaH) as an oxidant. Next the Open Notebook Science Challenge is described, where ONS coupled to crowdsourcing is used to measure and share non-aqueous solubility data. Recent developments in using bots to contribute to the scientific process and applications to the Ugi reaction are mentioned.

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Crowdsourcing Solubility using Open Notebook Science

  1. 1. Crowdsourcing non-aqueous solubility and synthesis using Open Notebook Science Jean-Claude Bradley August 16, 2009 American Chemical Society meeting Associate Professor of Chemistry Drexel University
  2. 2. The NaH oxidation controversy
  3. 3. Information spreads quickly through the blogosphere
  4. 4. 15% NMR yield
  5. 6. Khalid Mirza and Marshall Moritz
  6. 8. Top results on a Google search
  7. 9. Motivation: Faster Science, Better Science
  8. 10. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  9. 11. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  10. 12. TRUST PROOF
  11. 13. The solubility of 4-chlorobenzaldehyde
  12. 14. The Log makes Assumptions Explicit
  13. 15. The Rationale of Findings Explicit
  14. 16. Raw Data Made Public Splatter? Some liquid
  15. 17. YouTube for demonstrating experimental set-up
  16. 18. Calculations Made Public on Google Spreadsheets
  17. 19. Revision History on Google Spreadsheets
  18. 20. Wiki Page History
  19. 21. Comparing Wiki Page Versions
  20. 22. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  21. 23. Linking to Molecules in Chemistry Databases
  22. 24. Experimental Spectra and User-Deposited Data on ChemSpider
  23. 25. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
  24. 26. Crowdsourcing Solubility Data
  25. 27. ONS Submeta Award Winners
  26. 28. ONS Challenge Judges
  27. 29. Teaching Lab: Brent Friesen (Dominican University)
  28. 30. Solubility Experiment List
  29. 31. Solubilities collected in a Google Spreadsheet
  30. 32. Rajarshi Guha’s Live Web Query using Google Viz API
  31. 33. Rajarshi Guha and Andy Lang: Chemical Space Explorer
  32. 34. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  33. 35. Solubility Measurement Requests: DoSol sheet <ul><li>Outlier Bot: flags measurements with high standard deviation to mean ratios </li></ul><ul><li>Google Analytics queries – new solvent/solute searches </li></ul><ul><li>Solubility request form – researcher in Israel requesting pyrene in acetonitrile solubility for environmental soil contamination study </li></ul><ul><li>Application based models – high priority Ugi reactants </li></ul>
  34. 36. 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
  35. 37. Crowdsourcing Reaction Requests: DoUgi sheet
  36. 38. Understanding in addition to empirical modeling Missed in a prior publication on solubility for this compound
  37. 39. Data provenance: From Wikipedia to…
  38. 40. … the lab notebook and raw data
  39. 41. Including links to the literature
  40. 42. Pierre Lindenbaum’s Solubility Data as RDF Triples
  41. 43. <ul><li>Concentration (0.4, 0.2, 0.07 M) </li></ul><ul><li>Solvent (methanol, ethanol, acetonitrile, THF) </li></ul><ul><li>Excess of some reagents (1.2 eq.) </li></ul>How does Open Notebook Science fit with traditional publication?
  42. 44. Mettler-Toledo MiniMapper
  43. 45. Mettler-Toledo MiniBlock System
  44. 46. XML reports from MiniMapper robot
  45. 47. GoogleDoc to program and report
  46. 48. Paper written on Wiki
  47. 49. References to papers, blog posts, lab notebook pages, raw data
  48. 50. Paper on Journal of Visualized Experiments (JoVE)
  49. 51. Pre-print on Nature Precedings
  50. 52. ChemSpider Automated Mark-up of Chemical Names
  51. 53. Cameron Neylon’s Notebooks Other Open Notebooks
  52. 54. Anthony Salvagno’s Notebook (Steve Koch group)
  53. 55. Acknowledgements <ul><li>Khalid Mirza (Drexel) </li></ul><ul><li>Jenny Hale (Southampton U.) </li></ul><ul><li>David Bulger (Oral Roberts U.) </li></ul><ul><li>Tim Bohinsky (Drexel) </li></ul><ul><li>Kevin Owens (Drexel) </li></ul><ul><li>Tom Osborne (Mettler-Toledo) </li></ul><ul><li>Antony Williams (ChemSpider) </li></ul><ul><li>Andrew Lang (Oral Roberts U.) </li></ul><ul><li>Rajarshi Guha (Indiana U.) </li></ul><ul><li>Cameron Neylon (Southampton U.) </li></ul>