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Science Commons Open Notebook Science Talk


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Jean-Claude Bradley presents at the Science Commons Symposium on Feb 20, 2010 at the Microsoft Campus in Redmond. The talk covers doing Open Notebook Science using free and hosted tools, including new archiving protocols developed with Andrew Lang.

Science Commons Open Notebook Science Talk

  1. 1. Using Free Hosted Web2.0 Tools for Open Notebook Science Jean-Claude Bradley February 20, 2010 Science Commons Symposium Associate Professor of Chemistry Drexel University
  2. 2. The case for Open Notebook Science <ul><li>Is our current system working? </li></ul><ul><li>Is ONS difficult or expensive to implement? </li></ul><ul><li>Does ONS prevent peer-reviewed publication? </li></ul><ul><li>Can ONS data be easily discoverable? </li></ul><ul><li>Can ONS information be easily archived and cited? </li></ul><ul><li>Is ONS compatible with IP protection? </li></ul>
  3. 3. How bad is our current system? Try to find the solubility EGCG?
  4. 4. =2.3 g/L WTF?!
  5. 5. The End of the Chain of Provenance
  6. 6. The NaH oxidation controversy
  7. 7. Information spreads quickly through the blogosphere
  8. 8. 15% NMR yield
  9. 10. Khalid Mirza and Marshall Moritz
  10. 12. Top results on a Google search
  11. 13. The Scandal of Bell’s Lab Notebook
  12. 14. Motivation: Faster Science, Better Science
  13. 15. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  14. 16. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  15. 17. TRUST PROOF
  16. 18. The solubility of 4-chlorobenzaldehyde
  17. 19. The Log makes Assumptions Explicit
  18. 20. The Rationale of Findings Explicit
  19. 21. Raw Data Made Public Splatter? Some liquid
  20. 22. YouTube for demonstrating experimental set-up
  21. 23. Calculations Made Public on Google Spreadsheets
  22. 24. Revision History on Google Spreadsheets
  23. 25. Wiki Page History
  24. 26. Comparing Wiki Page Versions
  25. 27. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  26. 28. Linking to Molecules in Chemistry Databases
  27. 29. Experimental Spectra and User-Deposited Data on ChemSpider
  28. 30. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
  29. 31. Database Curation via Game Playing
  30. 32. Over 100,000 spectrum views so far - worldwide
  31. 33. Link Spectral Game to Open Educational Content
  32. 34. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?
  33. 35. Crowdsourcing Solubility Data
  34. 36. ONS Submeta Award Winners
  35. 37. ONS Challenge Judges
  36. 38. Teaching Lab: Brent Friesen (Dominican University)
  37. 39. Solubility Experiment List
  38. 40. Solubilities collected in a Google Spreadsheet
  39. 41. Rajarshi Guha’s Live Web Query using Google Viz API
  40. 42. WE ARE HERE How can the scientific process become more automated?
  41. 43. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  42. 44. 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>
  43. 45. Solubility Prediction (Andy Lang’s Model)
  44. 46. Understanding in addition to empirical modeling Missed in a prior publication on solubility for this compound
  45. 47. Data provenance: From Wikipedia to…
  46. 48. … the lab notebook and raw data
  47. 49. Including links to the literature
  48. 50. <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?
  49. 51. Paper written on Wiki
  50. 52. References to papers, blog posts, lab notebook pages, raw data
  51. 53. Paper on Journal of Visualized Experiments (JoVE)
  52. 54. Pre-print on Nature Precedings
  53. 55. ChemSpider Automated Mark-up of Chemical Names
  54. 56. BUT… Open Access: the Choice that Keeps Giving.. and Giving…
  55. 57. Beware of your addiction to metrics: redundancy will reduce them
  56. 58. Cameron Neylon’s Notebooks Other Open Notebooks
  57. 59. Anthony Salvagno’s Notebook (Steve Koch group)
  58. 60. 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 Where do Libraries fit in the communication of science and education in the Open/Closed Continuum?
  59. 61. The Missing Pieces of the Puzzle <ul><ul><li>Automatic Backup of Science 2.0 Data </li></ul></ul><ul><ul><li>Archiving of Open Notebooks </li></ul></ul><ul><ul><li>Science 2.0 Community Needed Resources - Preservation, Cataloging, Archiving, Cite-ability </li></ul></ul>
  60. 62. Librarians and Science 2.0 &quot;The Internet Archive is a 501(c)(3) non-profit that was founded to build an Internet library, with the purpose of offering permanent access for researchers, historians, and scholars to historical collections that exist in digital format.&quot; The internet Archive is not practical for practitioners of  Open Notebook Science  or  Science 2.0 
  61. 63. Good concept but.....
  62. 64. Most pages look like this....
  63. 65. Where We Began: The ONS backup spreadsheet and ONSPreserver
  64. 66. Publishing Google Spreadsheets as XLS
  65. 67. Where We Are Now
  66. 68. ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record
  67. 69. Snapshot is Self-Contained and Live on the Internet
  68. 70. Data Disks
  69. 71. DSpace – Handle (hdl)
  70. 72. - ISBN Google Spreadsheets Google Documents Web Services ChemSpider & Indiana Real Time Linear Regression, Unit Conversions, Style Sheet, etc Data Book
  71. 75. Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL: Accessed: 2009-12-11. (Archived by WebCite® at )
  72. 76. More about the ONSarchive project:
  73. 77. Conclusions <ul><li>Is our current system working? NO </li></ul><ul><li>Is ONS difficult or expensive to implement? NO </li></ul><ul><li>Does ONS prevent peer-reviewed publication? NO – but depends of publisher </li></ul><ul><li>Can ONS data be easily discoverable? YES </li></ul><ul><li>Can ONS information be easily archived and cited? YES </li></ul><ul><li>Is ONS compatible with IP protection? Maybe to a limited extent </li></ul>