OpenSciNY Open Notebook Science


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Jean-Claude Bradley presents at the OpenSciNY conference on May 14, 2010 on Open Notebooks Science and Scientific Scholarship.

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OpenSciNY Open Notebook Science

  1. 1. Open Notebook Science Jean-Claude Bradley May 14, 2010 OpenSciNY Associate Professor of Chemistry Drexel University
  2. 2. What is a Scientific Precedent? What is a Scientific Publication? What is Peer Review? What is Scholarship?
  3. 3. Asked to Review an Article…
  4. 12. “ I would never consider a claim made in a patent as blocking an author's claim of novelty.” Langmuir Editor What is a Scientific Precedent in Academia? What is a Scientific Precedent in Patent Law?
  5. 13. Chemistry Preprint Archive (Elsevier)
  6. 14. What is Scholarship?
  7. 15. What is Peer Review?
  8. 16. The Scandal of Bell’s Lab Notebook
  9. 17. How bad is our current system? Try to find the solubility EGCG?
  10. 18. =2.3 g/L WTF?!
  11. 19. The End of the Chain of Provenance
  12. 20. The NaH oxidation controversy
  13. 21. Information spreads quickly through the blogosphere
  14. 22. 15% NMR yield
  15. 24. Khalid Mirza and Marshall Moritz
  16. 26. Top results on a Google search
  17. 27. Motivation: Faster Science, Better Science
  18. 28. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  19. 29. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  20. 30. TRUST PROOF
  21. 31. The solubility of 4-chlorobenzaldehyde
  22. 32. The Log makes Assumptions Explicit
  23. 33. The Rationale of Findings Explicit
  24. 34. Raw Data Made Public Splatter? Some liquid
  25. 35. YouTube for demonstrating experimental set-up
  26. 36. Calculations Made Public on Google Spreadsheets
  27. 37. Revision History on Google Spreadsheets
  28. 38. Wiki Page History
  29. 39. Comparing Wiki Page Versions
  30. 40. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  31. 41. Linking to Molecules in Chemistry Databases
  32. 42. Experimental Spectra and User-Deposited Data on ChemSpider
  33. 43. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
  34. 44. Database Curation via Game Playing
  35. 45. Over 100,000 spectrum views so far - worldwide
  36. 46. Link Spectral Game to Open Educational Content
  37. 47. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?
  38. 48. Crowdsourcing Solubility Data
  39. 49. ONS Submeta Award Winners
  40. 50. ONS Challenge Judges
  41. 51. Teaching Lab: Brent Friesen (Dominican University)
  42. 52. Solubility Experiment List
  43. 53. Solubilities collected in a Google Spreadsheet
  44. 54. Rajarshi Guha’s Live Web Query using Google Viz API
  45. 55. WE ARE HERE How can the scientific process become more automated?
  46. 56. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  47. 57. 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. 58. Understanding in addition to empirical modeling Missed in a prior publication on solubility for this compound
  49. 59. Data provenance: From Wikipedia to…
  50. 60. … the lab notebook and raw data
  51. 61. Including links to the literature
  52. 62. <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?
  53. 63. Paper written on Wiki
  54. 64. References to papers, blog posts, lab notebook pages, raw data
  55. 65. Paper on Journal of Visualized Experiments (JoVE)
  56. 66. Pre-print on Nature Precedings
  57. 67. ChemSpider Automated Mark-up of Chemical Names
  58. 68. BUT… Open Access: the Choice that Keeps Giving.. and Giving…
  59. 69. Beware of your addiction to metrics: redundancy will reduce them
  60. 70. Cameron Neylon’s Notebooks Other Open Notebooks
  61. 71. Anthony Salvagno’s Notebook (Steve Koch group)
  62. 72. Archiving and Libraries <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>
  63. 73. 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 
  64. 74. Good concept but.....
  65. 75. Most pages look like this....
  66. 76. Where We Began: The ONS backup spreadsheet and ONSPreserver
  67. 77. Publishing Google Spreadsheets as XLS
  68. 78. ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record
  69. 79. Snapshot is Self-Contained and Live on the Internet
  70. 80. Data Disks
  71. 81. DSpace – Handle (hdl)
  72. 82. Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL: Accessed: 2009-12-11. (Archived by WebCite® at )
  73. 83. - ISBN Google Spreadsheets Google Documents Web Services ChemSpider & Indiana Real Time Linear Regression, Unit Conversions, Style Sheet, etc Data Book
  74. 86. Solubility Prediction (Andy Lang uses Abraham Model)
  75. 87. Reaction Attempts Book
  76. 88. Reaction Attempts Book: Reactants listed Alphabetically
  77. 89. For all Formats of ONS Projects
  78. 90. 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>