UPennONS

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Jean-Claude Bradley presents on "Open Notebook Science and other Science2.0 Approaches to Communicate Research" at the University of Pennsylvania Library.

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UPennONS

  1. 1. Open Notebook Science and other Science2.0 Approaches to Communicate Research Jean-Claude Bradley January 21, 2010 University of Pennsylvania 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. How bad is our current system? Try to find the solubility EGCG?
  8. 10. =2.3 g/L WTF?!
  9. 11. The End of the Chain of Provenance
  10. 12. The Scandal of Bell’s Lab Notebook
  11. 13. Motivation: Faster Science, Better Science
  12. 14. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  13. 15. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  14. 16. TRUST PROOF
  15. 17. The solubility of 4-chlorobenzaldehyde
  16. 18. The Log makes Assumptions Explicit
  17. 19. The Rationale of Findings Explicit
  18. 20. Raw Data Made Public Splatter? Some liquid
  19. 21. YouTube for demonstrating experimental set-up
  20. 22. Calculations Made Public on Google Spreadsheets
  21. 23. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  22. 24. Link to Docking Procedure (Rajarshi Guha)
  23. 25. Revision History on Google Spreadsheets
  24. 26. Wiki Page History
  25. 27. Comparing Wiki Page Versions
  26. 28. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  27. 29. Linking to Molecules in Chemistry Databases
  28. 30. Experimental Spectra and User-Deposited Data on ChemSpider
  29. 31. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
  30. 32. Database Curation via Game Playing
  31. 33. Over 100,000 spectrum views so far - worldwide
  32. 34. Link Spectral Game to Open Educational Content
  33. 35. NMR game in Second Life (Andy Lang)
  34. 36. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?
  35. 37. Crowdsourcing Solubility Data
  36. 38. ONS Submeta Award Winners
  37. 39. ONS Challenge Judges
  38. 40. ONS Challenge Judges
  39. 41. Teaching Lab: Brent Friesen (Dominican University)
  40. 42. Solubility Experiment List
  41. 43. Solubilities collected in a Google Spreadsheet
  42. 44. Rajarshi Guha’s Live Web Query using Google Viz API
  43. 45. Rajarshi Guha and Andy Lang: Chemical Space Explorer
  44. 46. WE ARE HERE How can the scientific process become more automated?
  45. 47. The Robot Scientist
  46. 48. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  47. 49. 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>
  48. 50. Solubility Prediction (Andy Lang’s Model)
  49. 51. Solubility prediction can generate requests for additional measurements
  50. 52. 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
  51. 53. Understanding in addition to empirical modeling Missed in a prior publication on solubility for this compound
  52. 54. Data provenance: From Wikipedia to…
  53. 55. … the lab notebook and raw data
  54. 56. Including links to the literature
  55. 57. Pierre Lindenbaum’s Solubility Data as RDF Triples
  56. 58. <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?
  57. 59. Mettler-Toledo MiniMapper
  58. 60. Mettler-Toledo MiniBlock System
  59. 61. XML reports from MiniMapper robot
  60. 62. GoogleDoc to program and report
  61. 63. Paper written on Wiki
  62. 64. References to papers, blog posts, lab notebook pages, raw data
  63. 65. Paper on Journal of Visualized Experiments (JoVE)
  64. 66. Pre-print on Nature Precedings
  65. 67. ChemSpider Automated Mark-up of Chemical Names
  66. 68. BUT… Open Access: the Choice that Keeps Giving.. and Giving…
  67. 69. Beware of your addiction to metrics: redundancy will reduce them
  68. 70. Cameron Neylon’s Notebooks Other Open Notebooks
  69. 71. Anthony Salvagno’s Notebook (Steve Koch group)
  70. 72. Educational “Open Notebooks”
  71. 73. Educational “Open Notebooks”
  72. 74. Educational “Open Notebooks”
  73. 75. Crowdsourcing ChemInfo Resource Collection
  74. 76. 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?
  75. 77. 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>
  76. 78. The ONS backup spreadsheet and ONSPreserver (Andy Lang)
  77. 79. Publishing Google Spreadsheets as XLS
  78. 80. 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 
  79. 81. Good concept but.....
  80. 82. Most pages look like this....
  81. 83. Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL:http://spreadsheets.google.com/pub?key=plwwufp30hfq0udnEmRD1aQ&output=xls. Accessed: 2009-12-11. (Archived by WebCite® at http://www.webcitation.org/5lx5ry3BV )
  82. 84. Possible role for libraries:  citation to objective third party archives of digital scholarship
  83. 85. More about the ONSarchive project:

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