Columbia ONS Archiving May09


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Jean-Claude Bradley and Andrew Lang present to Columbia University on May 21, 2009 in an effort to explore what role libraries could play in archiving Open Notebook Science projects and other forms of digital scholarship.

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Columbia ONS Archiving May09

  1. 1. Libraries and digital scholarship, documenting Open Notebook Science Jean-Claude Bradley May 20, 2009 Columbia University Associate Professor of Chemistry Drexel University Andrew Lang Professor of Mathematics Oral Roberts University
  2. 2. Outline <ul><ul><li>ONS and Digital Scholarship </li></ul></ul><ul><ul><li>Roles and opportunities for Libraries </li></ul></ul>
  3. 3. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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
  4. 4. Motivation: Faster Science, Better Science
  5. 5. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  6. 6. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  8. 8. The solubility of 4-chlorobenzaldehyde
  9. 9. The Log makes Assumptions Explicit
  10. 10. The Rationale of Findings Explicit
  11. 11. Raw Data Made Public Splatter? Some liquid
  12. 12. YouTube for demonstrating experimental set-up
  13. 13. Calculations Made Public on Google Spreadsheets
  14. 14. Revision History on Google Spreadsheets
  15. 15. Wiki Page History
  16. 16. Comparing Wiki Page Versions
  17. 17. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  18. 18. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  19. 19. Indexing Molecules on Google
  20. 20. Linking to Molecules in Chemistry Databases
  21. 21. Experimental Spectra and User-Deposited Data on ChemSpider
  22. 22. Crowdsourcing Solubility Data
  23. 23. ONS Challenge Students
  24. 24. ONS Challenge Judges
  25. 25. Teaching Lab: Brent Friesen (Dominican University)
  26. 26. Solubility Experiment List
  27. 27. Summary of Solubility Experiments
  28. 28. Solubilities collected in a Google Spreadsheet
  29. 29. Rajarshi Guha’s Live Web Query using Google Viz API
  30. 30. From Wikipedia to…
  31. 31. … the lab notebook and raw data
  32. 32. Including links to the literature
  33. 33. <ul><ul><li>Concentration (0.4, 0.2, 0.07 M) </li></ul></ul><ul><ul><li>Solvent (methanol, ethanol, acetonitrile, THF) </li></ul></ul><ul><ul><li>Excess of some reagents (1.2 eq.) </li></ul></ul>Reaction to Optimize
  34. 34. Mettler-Toledo MiniMapper
  35. 35. Mettler-Toledo MiniBlock System
  36. 36. XML reports from MiniMapper robot
  37. 37. GoogleDoc to program and report
  38. 38. Paper written on Wiki
  39. 39. Paper on Journal of Visualized Experiments (JoVE)
  40. 40. References to papers, blog posts, lab notebook pages, raw data
  41. 41. Where’s the Beef?
  42. 42. Pre-print on Nature Precedings
  43. 43. ChemSpider Journal: Automated Mark-up of Chemical Names
  44. 45. Cameron Neylon’s Notebook Other Open Notebooks
  45. 46. Anthony Salvagno’s Notebook (Steve Koch group)
  46. 47. 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>
  47. 48. The ONS backup spreadsheet and ONSPreserver
  48. 49. Publishing Google Spreadsheets as XLS
  49. 50. Automatic Backup of Data
  50. 51. Archiving Open Notebooks
  51. 52. 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 
  52. 53. Good concept but.....
  53. 54. Most pages look like this....
  54. 55. Possible role for libraries:  citation to objective third party archives of digital scholarship
  55. 56. Acknowledgments <ul><ul><li>Rajendra Bose (Columbia) </li></ul></ul><ul><ul><li>Tim Bohinsky (Drexel) </li></ul></ul><ul><ul><li>David Bulger (Oral Roberts) </li></ul></ul><ul><ul><li>Rajarshi Guha (NIH) </li></ul></ul><ul><ul><li>Jenny Hale (Southampton) </li></ul></ul><ul><ul><li>Khalid Mirza (Drexel) </li></ul></ul><ul><ul><li>Cameron Neylon (Southampton) </li></ul></ul><ul><ul><li>Tom Osborne (Mettler-Toledo) </li></ul></ul><ul><ul><li>Kevin Owens (Drexel) </li></ul></ul><ul><ul><li>Antony Williams (ChemSpider) </li></ul></ul>