ACRL Open Notebook Science talk

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Jean-Claude Bradley presents a talk on Open Notebook Science at the Association of College and Research Libraries on Feb 17, 2009. This presentation includes all of the relevant work up to this date, including the Spectra Game, the ONS solubility challenge and the main data viewers developed by Andy Lang and Rajarshi Guha for the web and Second Life.

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ACRL Open Notebook Science talk

  1. 1. Open Notebook Science Jean-Claude Bradley Feb 17, 2009 Association of College and Research Libraries Associate Professor of Chemistry Drexel University
  2. 2. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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
  3. 3. Motivation: Faster Science, Better Science
  4. 4. Where is Science headed? WE ARE HERE
  5. 5. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  6. 6. TRUST PROOF
  7. 7. The solubility of 4-chlorobenzaldehyde
  8. 8. The Log makes Assumptions Explicit
  9. 9. The Rationale of Findings Explicit
  10. 10. Raw Data Made Public Splatter? Some liquid
  11. 11. YouTube for demonstrating experimental set-up
  12. 12. Calculations Made Public on Google Spreadsheets
  13. 13. Revision History on Google Spreadsheets
  14. 14. Wiki Page History
  15. 15. Comparing Wiki Page Versions
  16. 16. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  17. 17. Indexing Molecules on Google
  18. 18. Linking to Molecules in Chemistry Databases
  19. 19. Experimental Spectra and User-Deposited Data on ChemSpider
  20. 20. The Spectra Game (Andy Lang, Tony Williams)
  21. 22. NMR game in Second Life (Andy Lang)
  22. 23. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
  23. 24. Imine Formation Mechanism: talk to the molecules!
  24. 25. Student Projects in Second Life
  25. 26. Crowdsourcing Solubility Data
  26. 27. ONS Challenge Students
  27. 28. ONS Challenge Judges
  28. 29. Teaching Lab: Brent Friesen (Dominican University)
  29. 30. Solubility Experiments
  30. 31. Solubilities collected in a Google Spreadsheet
  31. 32. Rajarshi Guha’s Live Web Query using Google Viz API
  32. 33. Substructure Searching of solubility data
  33. 34. Rajarshi Guha and Andy Lang: Chemical Space Explorer
  34. 35. Andy Lang: Chemical Space Explorer in Second Life
  35. 36. From Wikipedia to…
  36. 37. … the lab notebook and raw data
  37. 38. Including links to the literature
  38. 40. Temperature info automatically plotted
  39. 41. Exploring Solubility in Second Life (Andy Lang)
  40. 42. Pierre Lindenbaum’s Solubility Data as RDF Triples
  41. 43. Results and Workflows in Machine-Friendly Format
  42. 44. Experiments in Chemical Markup Language
  43. 45. UsefulChem Workflows in myExperiment
  44. 46. UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.
  45. 47. Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
  46. 48. BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE
  47. 49. Where’s the Beef?
  48. 50. Link to Lab Notebook Page in Wiki
  49. 51. Link to Docking Procedure (Rajarshi Guha)
  50. 52. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  51. 53. Comparing Experiments Ugi Master Table
  52. 54. <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>Reaction to Optimize
  53. 55. Mettler-Toledo MiniMapper
  54. 56. Mettler-Toledo MiniBlock System
  55. 57. XML reports from MiniMapper robot
  56. 58. GoogleDoc to program and report
  57. 59. Paper written on Wiki
  58. 60. References to papers, blog posts, lab notebook pages, raw data
  59. 61. ChemSpider Automated Mark-up of Chemical Names
  60. 62. Paper on Journal of Visualized Experiments (JoVE)
  61. 63. Pre-print on Nature Precedings
  62. 64. Reaction Optimization Visualization in Second Life
  63. 66. Collaborative Drug Discovery (CDD) Database
  64. 67. Outcome of Guha-Bradley-Rosenthal collboration
  65. 68. Google Spreadsheet linked to Open Web Services = Chemistry Dashboard
  66. 69. Potential Trends for the Future of Chemistry Fast, Fuzzy, Open, Automated, Green, Crowdsourced, Simple (e.g. mix and filter)
  67. 70. Gus Rosania’s Notebook Other Open Notebooks
  68. 71. Cameron Neylon’s Notebook
  69. 72. Anthony Salvagno’s Notebook (Steve Koch group)
  70. 73. Acknowledgements <ul><li>Khalid Mirza (Drexel) </li></ul><ul><li>Jenny Hale (Southampton U.) </li></ul><ul><li>David Bulger (Oral Roberts U.) </li></ul><ul><li>Tim Bohinsky (Drexel) </li></ul><ul><li>Kevin Owens (Drexel) </li></ul><ul><li>Tom Osborne (Mettler-Toledo) </li></ul><ul><li>Antony Williams (ChemSpider) </li></ul><ul><li>Andrew Lang (Oral Roberts U.) </li></ul><ul><li>Rajarshi Guha (Indiana U.) </li></ul><ul><li>Cameron Neylon (Southampton U.) </li></ul>

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