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Open Notebook Science at ACS March07
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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. ...

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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  • 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. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN
  • 3. Where is Science headed? WE ARE HERE
  • 4. The Robot Scientist
  • 5.
    • Self-organizing redundant processes
    • Agents can participate with zero or near-zero cost (free hosted services – e.g. Google)
    • Fully Open Access (Read and Write)
    • Publication of all aspects of the scientific process: Open Source Science / Open Notebook Science
    • Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity?
    How will this happen?
  • 6. How can machines know what is important? Ask the humans
  • 7. UsefulChem Blog
  • 8. What chemists think is important in 2005
  • 9. Find-A-Drug
  • 10. Diketopiperazine Library Evolves to: on pot Ugi reaction/cyclization First iteration: Solid Support Synthesis
  • 11. The Molecules Blog
  • 12. The Experiments Blog
  • 13. Comments from peers
  • 14. The UsefulChem Wiki
  • 15. Telling the story of the failures
  • 16. Experiments moved to wiki
  • 17. Experiment History
  • 18. Experiment Edits
  • 19. Third Party Time-Stamp on Experiment Versions
  • 20. Monitoring experimental progress
  • 21. How are people finding our experiments?
  • 22. Molecules found by InChI
  • 23. usefulchem.blogspot.com The blog as an integrative tool
  • 24. usefulchem.wikispaces.com/Exp049 The wiki as the laboratory notebook
  • 25. Open science connectivity More info on open source science here http://usefulchem.wikispaces.com
  • 26. Automation in UsefulChem
  • 27. CMLRSS feed on Bioclipse
  • 28. Graphical Mining of Data with JSpecView usefulchem.wikispaces.com/Exp070 (48h 7 min)
  • 29. Using ExcelVBA to automate kinetics analysis
  • 30. Specify NMR regions and internal standard
  • 31. NMR spectra of monitoring samples calculated
  • 32. Reaction profile plotted automatically
  • 33. UsefulChem in Second Life
  • 34. Display blog post as poster
  • 35. Click on Images for Descriptions
  • 36. Click on the Blue Obelisk for a Chemistry Quiz Thanks Beth and Eloise!
  • 37. neurodatabase.org Raw Experimental Data
  • 38. Selected Experiments (some failed) Orgprepdaily.wordpress.com
  • 39. Orgprepdaily.wordpress.com Vendor Reliability
  • 40. Generalized Protocols Openwetware.org
  • 41. Lab Notebook for intra-group communication Openwetware.org
  • 42. Discussing Hypotheses RRResearch.blogspot.com
  • 43. Feedback for the Automation Component Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-Rust
  • 44.