NITLE Open Notebook Science Talk


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Jean-Claude Bradley and Andrew Lang present on "Open Notebook Science for Research and Teaching" on February 18, 2010 at the National Institute for Technology in Liberal Education. A few examples of the use of ONS in chemistry are outlined followed by details of the Web2.0 tools implemented. The end of the presentation covers new work on how to archive Open Notebooks and all supporting documentation.

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NITLE Open Notebook Science Talk

  1. 1. Open Notebook Science for Research and Teaching Jean-Claude Bradley February 18, 2010 National Institute for Technology in Liberal Education Associate Professor of Chemistry Drexel University Andrew Lang Professor of Mathematics Oral Roberts 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. Revision History on Google Spreadsheets
  22. 24. Wiki Page History
  23. 25. Comparing Wiki Page Versions
  24. 26. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  25. 27. Linking to Molecules in Chemistry Databases
  26. 28. Experimental Spectra and User-Deposited Data on ChemSpider
  27. 29. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
  28. 30. Database Curation via Game Playing
  29. 31. Over 100,000 spectrum views so far - worldwide
  30. 32. Link Spectral Game to Open Educational Content
  31. 33. NMR game in Second Life (Andy Lang)
  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. Solubility prediction can generate requests for additional measurements
  45. 47. 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
  46. 48. Understanding in addition to empirical modeling Missed in a prior publication on solubility for this compound
  47. 49. Data provenance: From Wikipedia to…
  48. 50. … the lab notebook and raw data
  49. 51. Including links to the literature
  50. 52. Pierre Lindenbaum’s Solubility Data as RDF Triples
  51. 53. <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?
  52. 54. Paper written on Wiki
  53. 55. References to papers, blog posts, lab notebook pages, raw data
  54. 56. Paper on Journal of Visualized Experiments (JoVE)
  55. 57. Pre-print on Nature Precedings
  56. 58. ChemSpider Automated Mark-up of Chemical Names
  57. 59. BUT… Open Access: the Choice that Keeps Giving.. and Giving…
  58. 60. Beware of your addiction to metrics: redundancy will reduce them
  59. 61. Cameron Neylon’s Notebooks Other Open Notebooks
  60. 62. Anthony Salvagno’s Notebook (Steve Koch group)
  61. 63. Educational “Open Notebooks”
  62. 64. Educational “Open Notebooks”
  63. 65. Educational “Open Notebooks”
  64. 66. Crowdsourcing ChemInfo Resource Collection
  65. 67. 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?
  66. 68. 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>
  67. 69. 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 
  68. 70. Good concept but.....
  69. 71. Most pages look like this....
  70. 72. Where We Began: The ONS backup spreadsheet and ONSPreserver
  71. 73. Publishing Google Spreadsheets as XLS
  72. 74. Where We Are Now
  73. 75. ONSPreserverLite Daily Backup of Crucial Data
  74. 76. ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record
  75. 77. Snapshot is Self-Contained and Live on the Internet
  76. 78. Data Disks
  77. 79. DSpace – Handle (hdl)
  78. 80. - ISBN Google Spreadsheets Google Documents Web Services ChemSpider & Indiana Real Time Linear Regression, Unit Conversions, Style Sheet, etc Data Book
  79. 83. Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL: Accessed: 2009-12-11. (Archived by WebCite® at )
  80. 84. More about the ONSarchive project: