NASA Open Notebook Science Talk

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Jean-Claude Bradley discusses Open Notebook Science on April 15, 2009 at the NASA Goddard Space Flight Center. This includes recent material such as ONS logos, the ChemTiles and Spectral Games, automated backup of Google Spreadsheets and automated solubility determinations using web services called from within Google Spreadsheets.

Published in: Education, Technology

NASA Open Notebook Science Talk

  1. 1. Open Notebook Science NASA Goddard Space Flight Center Jean-Claude Bradley Associate Professor of Chemistry Drexel University April 15, 2009
  2. 2. Open and Closed Science Open Notebook Traditional Traditional Open Access Science (full Lab Notebook Journal Journal Article transparency) (unpublished) Article RESEARCH OPEN CLOSED TEACHING Archived Lectures Traditional Assigned Lectures Notes Paper problems Public and public Textbook public free online F2F lectures textbooks
  3. 3. Motivation: Faster Science, Better Science
  4. 4. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  5. 5. Where is Science headed? WE ARE HERE
  6. 6. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  7. 7. TRUST PROOF
  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. Indexing Molecules on Google
  19. 19. Linking to Molecules in Chemistry Databases
  20. 20. Experimental Spectra and User- Deposited Data on ChemSpider
  21. 21. Open Data JCAMP spectra for education (Andy Lang, Tony Williams) (Andy Lang, Tony Williams, Robert Lancashire)
  22. 22. Database Curation via Game Playing
  23. 23. Over 50,000 spectrum views so far - worldwide
  24. 24. Link Spectral Game to Open Educational Content
  25. 25. Remixing Code and Content (Andy Lang)
  26. 26. Prizes not Punishment to motivate students
  27. 27. NMR game in Second Life (Andy Lang)
  28. 28. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
  29. 29. Imine Formation Mechanism: talk to the molecules!
  30. 30. Student Projects in Second Life
  31. 31. Spring 09 projects: networking in Second Life and FriendFeed
  32. 32. Crowdsourcing Solubility Data
  33. 33. ONS Challenge Students
  34. 34. ONS Challenge Judges
  35. 35. Teaching Lab: Brent Friesen (Dominican University)
  36. 36. Solubility Experiment List
  37. 37. Summary of Solubility Experiments
  38. 38. Solubilities collected in a Google Spreadsheet
  39. 39. Rajarshi Guha’s Live Web Query using Google Viz API
  40. 40. Substructure Searching of solubility data
  41. 41. Rajarshi Guha and Andy Lang: Chemical Space Explorer
  42. 42. Andy Lang: Chemical Space Explorer in Second Life
  43. 43. From Wikipedia to…
  44. 44. …the lab notebook and raw data
  45. 45. Including links to the literature
  46. 46. Temperature info automatically plotted
  47. 47. Exploring Solubility in Second Life (Andy Lang)
  48. 48. Pierre Lindenbaum’s Solubility Data as RDF Triples
  49. 49. Results and Workflows in Machine- Friendly Format
  50. 50. Experiments in Chemical Markup Language
  51. 51. UsefulChem Workflows in myExperiment
  52. 52. UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Rajarshi Guha Tsu-Soo Tan Docking Indiana U Nanyang Inst. JC Bradley Synthesis Drexel U Phil Rosenthal Dan Zaharevitz Testing UCSF NCI (malaria) (tumors)
  53. 53. Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
  54. 54. Architecture: Distributed, Interlinked and Redundant BLOG CDD WIKI Nature FriendFeed Precedings JoVE ChemSpider GoogleDocs Mailing List
  55. 55. Where’s the Beef?
  56. 56. Link to Lab Notebook Page in Wiki
  57. 57. Link to Docking Procedure (Rajarshi Guha)
  58. 58. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  59. 59. Comparing Experiments Ugi Master Table
  60. 60. Reaction to Optimize •Concentration (0.4, 0.2, 0.07 M) •Solvent (methanol, ethanol, acetonitrile, THF) •Excess of some reagents (1.2 eq.)
  61. 61. Mettler-Toledo MiniMapper
  62. 62. Mettler-Toledo MiniBlock System
  63. 63. XML reports from MiniMapper robot
  64. 64. GoogleDoc to program and report
  65. 65. Paper written on Wiki
  66. 66. References to papers, blog posts, lab notebook pages, raw data
  67. 67. ChemSpider Automated Mark-up of Chemical Names
  68. 68. Paper on Journal of Visualized Experiments (JoVE)
  69. 69. Pre-print on Nature Precedings
  70. 70. Reaction Optimization Visualization in Second Life
  71. 71. Collaborative Drug Discovery (CDD) Database
  72. 72. Outcome of Guha-Bradley-Rosenthal collboration
  73. 73. Google Spreadsheet linked to Open Web Services = Chemistry Dashboard
  74. 74. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  75. 75. Archiving and Curation of ONS and other new forms of scholarship?
  76. 76. Publishing Google Spreadsheets as XLS
  77. 77. Other Open Notebooks Gus Rosania’s Notebook (recently terminated)
  78. 78. Cameron Neylon’s Notebook
  79. 79. Anthony Salvagno’s Notebook (Steve Koch group)
  80. 80. Acknowledgements Khalid Mirza (Drexel)  Jenny Hale (Southampton U.)  David Bulger (Oral Roberts U.)  Tim Bohinsky (Drexel)  Kevin Owens (Drexel)  Tom Osborne (Mettler-Toledo)  Antony Williams (ChemSpider)  Andrew Lang (Oral Roberts U.)  Rajarshi Guha (Indiana U.)  Cameron Neylon (Southampton U.) 

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