Open Notebook Science at ACS March07


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Here is my talk "Open Notebook Science using Blogs and Wikis" at the American Chemical Society meeting in Chicago on March 27, 2007 at the Communicating Chemistry Symposium.

The first half is basically a condensed summary of how we are using UsefulChem to do Open Science. I then demonstrate for the first time Dave's Excel code to compute kinetics from JCAMP NMR reaction profiles and the building in Second Life where Beth and Eloise have help me to set up a poster room with NMR spectra, molecules and an organic chemistry quiz.

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Open Notebook Science at ACS March07

  1. 1. Open Notebook Science using Blogs and Wikis Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Drexel University March 27, 2007 American Chemical Society Symposium on Communicating Chemistry
  2. 2. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN
  3. 3. Where is Science headed? WE ARE HERE
  4. 4. The Robot Scientist
  5. 5. <ul><li>Self-organizing redundant processes </li></ul><ul><li>Agents can participate with zero or near-zero cost (free hosted services – e.g. Google) </li></ul><ul><li>Fully Open Access (Read and Write) </li></ul><ul><li>Publication of all aspects of the scientific process: Open Source Science / Open Notebook Science </li></ul><ul><li>Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity? </li></ul>How will this happen?
  6. 6. How can machines know what is important? Ask the humans
  7. 7. UsefulChem Blog
  8. 8. What chemists think is important in 2005
  9. 9. Find-A-Drug
  10. 10. Diketopiperazine Library Evolves to: on pot Ugi reaction/cyclization First iteration: Solid Support Synthesis
  11. 11. The Molecules Blog
  12. 12. The Experiments Blog
  13. 13. Comments from peers
  14. 14. The UsefulChem Wiki
  15. 15. Telling the story of the failures
  16. 16. Experiments moved to wiki
  17. 17. Experiment History
  18. 18. Experiment Edits
  19. 19. Third Party Time-Stamp on Experiment Versions
  20. 20. Monitoring experimental progress
  21. 21. How are people finding our experiments?
  22. 22. Molecules found by InChI
  23. 23. The blog as an integrative tool
  24. 24. The wiki as the laboratory notebook
  25. 25. Open science connectivity More info on open source science here
  26. 26. Automation in UsefulChem
  27. 27. CMLRSS feed on Bioclipse
  28. 28. Graphical Mining of Data with JSpecView (48h 7 min)
  29. 29. Using ExcelVBA to automate kinetics analysis
  30. 30. Specify NMR regions and internal standard
  31. 31. NMR spectra of monitoring samples calculated
  32. 32. Reaction profile plotted automatically
  33. 33. UsefulChem in Second Life
  34. 34. Display blog post as poster
  35. 35. Click on Images for Descriptions
  36. 36. Click on the Blue Obelisk for a Chemistry Quiz Thanks Beth and Eloise!
  37. 37. Raw Experimental Data
  38. 38. Selected Experiments (some failed)
  39. 39. Vendor Reliability
  40. 40. Generalized Protocols
  41. 41. Lab Notebook for intra-group communication
  42. 42. Discussing Hypotheses
  43. 43. Feedback for the Automation Component Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-Rust