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NIST Dec08 Open Notebook Science Talk


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Jean-Claude Bradley presented on Open Notebook Science at the NIST Social Media Day on December 11, 2008. The talks starts with an overview of ONS and how it is being used to assess solubility measurements being crowdsourced in the ONS Challenge and Submeta Awards. The use of wikis, blogs, Google Spreadsheets, YouTube, Flickr, ChemSpider and other free hosted Web2.0 tools is highlighted. The UsefulChem project, involving the synthesis of anti-malarial agents, is then briefly covered. Finally, a very recent application of using Google Spreadsheets to automatically call web services to calculate volumes and weights of chemicals needed in reactions is demonstrated (code by Rajarshi Guha).

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NIST Dec08 Open Notebook Science Talk

  1. 1. Open Notebook Science Jean-Claude Bradley Dec 11, 2008 NIST 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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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
  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. ONS Challenge Students
  22. 22. ONS Challenge Judges
  23. 23. Solubility Experiments
  24. 24. Solubilities collected in a Google Spreadsheet
  25. 25. Rajarshi Guha’s Live Web Query using Google Viz API
  26. 26. Pierre Lindenbaum’s Solubility Data as RDF Triples
  27. 27. Results and Workflows in Machine-Friendly Format
  28. 28. UsefulChem Workflows in myExperiment
  29. 29. Experiments in Chemical Markup Language
  30. 30. 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.
  31. 31. Malaria Target: falcipain-2 involved in hemoglobin metabolism
  32. 32. BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE
  33. 33. Where’s the Beef?
  34. 34. Link to Lab Notebook Page in Wiki
  35. 35. Link to Docking Procedure (Rajarshi Guha)
  36. 36. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  37. 37. Comparing Experiments Ugi Master Table
  38. 38. <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
  39. 39. Mettler-Toledo MiniMapper
  40. 40. Mettler-Toledo MiniBlock System
  41. 41. XML reports from MiniMapper robot
  42. 42. GoogleDoc to program and report
  43. 43. Paper written on Wiki
  44. 44. References to papers, blog posts, lab notebook pages, raw data
  45. 45. ChemSpider Automated Mark-up of Chemical Names
  46. 46. Paper on Journal of Visualized Experiments (JoVE)
  47. 47. Pre-print on Nature Precedings
  48. 48. Reaction Optimization Visualization in Second Life
  49. 49. Interacting with NMR spectra (JCAMP-DX) in Second Life
  50. 50. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
  51. 51. 3D molecules in Second Life
  52. 52. Imine Formation Mechanism: talk to the molecules!
  53. 53. Exploring Solubility in Second Life (Andy Lang)
  54. 55. Collaborative Drug Discovery (CDD) Database
  55. 56. Outcome of Guha-Bradley-Rosenthal collboration
  56. 57. Google Spreadsheet linked to Open Web Services = Chemistry Dashboard
  57. 58. Potential Trends for the Future of Chemistry Fast, Fuzzy, Open, Automated, Green, Crowdsourced, Simple (e.g. mix and filter)
  58. 59. Gus Rosania’s Notebook
  59. 60. Cameron Neylon’s Notebook
  60. 61. 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>