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Manchester Open Notebook Science Talk


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Jean-Claude Bradley presents on Open Notebook Science. Recent research on solubility measurements from the Neylon lab are reported.

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Manchester Open Notebook Science Talk

  1. 1. Open Notebook Science for Collaborative Drug Development Jean-Claude Bradley Sept 5, 2008 University of Manchester E-Learning Coordinator College of Arts and Sciences 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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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. Motivations for ONS <ul><li>Faster Science </li></ul><ul><li>Better Science </li></ul>
  4. 4. A recent example in Southampton Sept 3, 2008
  5. 5. Investigating solubilities in organic solvents Boc-glycine vanillin glucose NaCl
  6. 6. The lab notebook page
  7. 7. The Log: No Insider Information
  8. 8. The Results in a GoogleDoc reliable unreliable
  9. 10. Representation in the Neylon notebook
  10. 11. Open Notebook Science Grand Challenge <ul><li>design procedures to determine the solubility of compounds in organic solvents </li></ul><ul><li>teams or individuals welcome </li></ul><ul><li>Open Notebooks will be validated by experts </li></ul><ul><li>“ mystery prizes” for creativity, productivity, reproducibility and other metrics of scientific quality </li></ul><ul><li>details coming soon….. </li></ul>Round one
  11. 12. 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.
  12. 13. BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE
  13. 14. Where’s the Beef?
  14. 15. Link to Lab Notebook Page in Wiki
  15. 16. Link to Molecules
  16. 17. Link to Docking Procedure (Rajarshi Guha)
  17. 18. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  18. 19. Link to Raw Data with JSpecView (data in JCAMP-DX format) (by Robert Lancashire)
  19. 20. Using ChemSpider to archive compound characterization
  20. 21. Conclusion is Fully Supported
  21. 22. Table of Contents
  22. 23. Indexing the Experiments in Google
  23. 24. Searching with Google Custom Search
  24. 25. How are people finding our experiments? NMR in TFA Phenylacetaldehyde c4h6o2 nmr methylene chloride/methanol h'nmr of benzophenone sulfuric acid pka tertbutylamine tosyl isocyanide amino furan dichloromethane polar? Reaction between Benzaldehyde and NaBH4 phosphoric acid pka veratraldehyde wiki kinetics boc deprotection Rf value in polar solvent why glycerol is immiscible with ether side reaction of imines 5.8 ppm nmr nmr cdcl3 chloroform side reaction diasterotopic wiki adding anhydrous MgSO4 to the dichlormethane ether extraction hnmr doublet of doublet Boc-protected NMR chromatotron recipe triplet cdcl3 &quot;13c nmr&quot; Specific Compounds Experimental Conditions
  25. 26. How are people finding UsefulChem? free downloading chemistry video organic chemistry project + high school how to make poster in second life organic chem. quiz 3d periodic tables animation protein docking docking animation why are acid-base reactions exothermic? lysosomal targets protease and malaria cheminformatics project proposal automated reactions malaria review project synthesis CHEMISTRY WEB 2.0 projects on QSAR & drug design chemistry experiment results database Educational Big Picture
  26. 27. How Should Open Notebook Science be Used?
  27. 34. How did this experiment evolve? Third party timestamp
  28. 35.
  29. 36. Comparing wiki page versions
  30. 38.
  31. 39. Comparing Experiments Ugi Master Table
  32. 40. YouTube for demonstrating experimental set-up
  33. 41. Older Males Prefer Organic Chemistry!
  34. 42. Mailing List Facilitates inter-group collaboration
  35. 43. Outcome of Guha-Bradley-Rosenthal collboration
  36. 44. Collaborative Drug Discovery (CDD) Database
  37. 46. Interacting with NMR spectra (JCAMP-DX) in Second Life
  38. 47. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
  39. 48. 3D molecules in Second Life
  40. 49. Imine Formation Mechanism: talk to the molecules!
  41. 50. Gus Rosania’s Notebook
  42. 51. Cameron Neylon’s Notebook
  43. 52. Results in Machine-Friendly Format
  44. 53. Mettler-Toledo MiniMapper
  45. 54. Mettler-Toledo MiniBlock System
  46. 55. GoogleDoc to program and report
  47. 56. XML reports from MiniMapper robot
  48. 57. Writing Code in the Murray-Rust House
  49. 58. Experiments in Chemical Markup Language
  50. 59. Paper written on Wiki
  51. 60. References to papers, blog posts, lab notebook pages, raw data
  52. 61. Pre-print on Nature Precedings
  53. 62. Methanol 0.4M xs of imine best
  54. 63. Paper on Journal of Visualized Experiments (JoVE)
  55. 64. Where is Science headed? WE ARE HERE
  56. 65. Conclusion <ul><li>Communicate first </li></ul><ul><li>Standardize second </li></ul><ul><li>In a Science2.0 world redundancy is king </li></ul>