iSchool Open Notebook Science Talk

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This talk covers Open Notebook Science from an information technology perspective . Although solubility measurements and chemical reactions are mentioned the focus is more on how information is stored, retrieved and used using free and hosted services such as Blogger, GoogleDocs, Wikispaces, ChemSpider, CDD and others. The UsefulChem project and the Open Notebook Science Challenge are highlighted.

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iSchool Open Notebook Science Talk

  1. 1. Open Notebook Science Jean-Claude Bradley Nov 11, 2008 Drexel iSchool 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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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. Crowdsourcing Solubility Data
  21. 21. Solubility Experiments
  22. 22. “ Validated” Solubilities in Google Spreadsheet
  23. 23. Rajarshi Guha’s Live Web Query using Google Viz API
  24. 24. Pierre Lindenbaum’s Solubility Data as RDF Triples
  25. 25. Results and Workflows in Machine-Friendly Format
  26. 26. UsefulChem Workflows in myExperiment
  27. 27. Experiments in Chemical Markup Language
  28. 28. 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.
  29. 29. Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
  30. 30. BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE
  31. 31. Where’s the Beef?
  32. 32. Link to Lab Notebook Page in Wiki
  33. 33. Link to Docking Procedure (Rajarshi Guha)
  34. 34. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  35. 35. Comparing Experiments Ugi Master Table
  36. 36. <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
  37. 37. Mettler-Toledo MiniMapper
  38. 38. Mettler-Toledo MiniBlock System
  39. 39. XML reports from MiniMapper robot
  40. 40. GoogleDoc to program and report
  41. 41. Paper written on Wiki
  42. 42. References to papers, blog posts, lab notebook pages, raw data
  43. 43. ChemSpider Automated Mark-up of Chemical Names
  44. 44. Paper on Journal of Visualized Experiments (JoVE)
  45. 45. Pre-print on Nature Precedings
  46. 46. Reaction Optimization Visualization in Second Life
  47. 47. Interacting with NMR spectra (JCAMP-DX) in Second Life
  48. 48. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
  49. 49. 3D molecules in Second Life
  50. 50. Imine Formation Mechanism: talk to the molecules!
  51. 52. Collaborative Drug Discovery (CDD) Database
  52. 53. Outcome of Guha-Bradley-Rosenthal collboration
  53. 54. Gus Rosania’s Notebook
  54. 55. Cameron Neylon’s Notebook
  55. 56. Acknowledgements <ul><li>Khalid Mirza (Drexel) </li></ul><ul><li>Kevin Owens (Drexel) </li></ul><ul><li>Tim Bohinsky (Drexel) </li></ul><ul><li>James Giammarco (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>Cameron Neylon (Southampton U.) </li></ul>

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