Columbia Talk on Open Notebook Science


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Jean-Claude Bradley presents an overview of Open Notebook Science at a Columbia panel on Open Science on February 19, 2009. The content of this presentation is targeted to a library services audience.

Published in: Technology, Education
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  • i really enjoyed this talk. inspiring work. i am artist/engineer and have been also been trying to maximize the use of free web tools as a distributed open notebook. i would love to see a more configurable version of friendfeed and some better tools for sharing svgs and cad files. i'm also interested in more 'automatic' documentation streams. for practical reasons of time and for psychological reasons of avoiding self-filtering bias. along those lines i've been trying a lot of experiments with timelapse to encapsulate some abstract views of the process. and i'm thinking about things like web browser history? or the my personal or lab bank acount? what are streams of information that already exist that might also support some documentation of the process? some of these lean more art than science but certainly we are all taking part in some great cultural experiment and anything we can do to help others repeat our work is good? or we run into the problem of toxicity of information?
    when we have this more detailed version of our process, will me move to PULL (i need your process expertise over here) models rather than the current PUSH (look at how great this is!) models which seem to dominate the landscape?
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Columbia Talk on Open Notebook Science

  1. 1. Open Notebook Science Jean-Claude Bradley Feb 19, 2009 Columbia University Libraries Panel on Open Science Associate Professor of Chemistry Drexel University
  2. 2. Motivation: Faster Science, Better Science
  3. 3. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  5. 5. The solubility of 4-chlorobenzaldehyde
  6. 6. The Log makes Assumptions Explicit
  7. 7. The Rationale of Findings Explicit
  8. 8. Raw Data Made Public Splatter? Some liquid
  9. 9. YouTube for demonstrating experimental set-up
  10. 10. Calculations Made Public on Google Spreadsheets
  11. 11. Revision History on Google Spreadsheets
  12. 12. Wiki Page History
  13. 13. Comparing Wiki Page Versions
  14. 14. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  15. 15. Linking to Molecules in Chemistry Databases
  16. 16. Experimental Spectra and User-Deposited Data on ChemSpider
  17. 17. The Spectra Game (Andy Lang, Tony Williams)
  18. 19. NMR game in Second Life (Andy Lang)
  19. 20. Crowdsourcing Solubility Data
  20. 21. ONS Challenge Students
  21. 22. ONS Challenge Judges
  22. 23. Teaching Lab: Brent Friesen (Dominican University)
  23. 24. Solubility Experiments
  24. 25. Solubilities collected in a Google Spreadsheet
  25. 26. Rajarshi Guha’s Live Web Query using Google Viz API
  26. 27. Substructure Searching of solubility data
  27. 28. Rajarshi Guha and Andy Lang: Chemical Space Explorer
  28. 29. Andy Lang: Chemical Space Explorer in Second Life
  29. 30. From Wikipedia to…
  30. 31. … the lab notebook and raw data
  31. 32. Including links to the literature
  32. 33. Temperature info automatically plotted
  33. 34. Exploring Solubility in Second Life (Andy Lang)
  34. 35. 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.
  35. 36. Malaria Target: falcipain-2 involved in hemoglobin metabolism
  36. 37. BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE
  37. 38. Where’s the Beef?
  38. 39. Link to Lab Notebook Page in Wiki
  39. 40. Link to Docking Procedure (Rajarshi Guha)
  40. 41. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  41. 42. Outcome of Guha-Bradley-Rosenthal collboration
  42. 43. Collaborative Drug Discovery (CDD) Database
  43. 44. <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
  44. 45. Paper written on Wiki
  45. 46. References to papers, blog posts, lab notebook pages, raw data
  46. 47. Paper on Journal of Visualized Experiments (JoVE)
  47. 48. Pre-print on Nature Precedings
  48. 49. Potential Trends for the Future of Chemistry Fast, Fuzzy, Open, Automated, Green, Crowdsourced, Simple (e.g. mix and filter)
  49. 50. Gus Rosania’s Notebook Other Open Notebooks
  50. 51. Cameron Neylon’s Notebook
  51. 52. Anthony Salvagno’s Notebook (Steve Koch group)
  52. 53. 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>