Science Blogging Conference Bradley Talk


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Open Source/Open Notebook Science Talk at the North Carolina Science Blogging Conference on Jan 20, 2007 by Jean-Claude Bradley.

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Science Blogging Conference Bradley Talk

  1. 1. Open Source/Open Notebook Science: Doing science with blogs and wikis [email_address] Jan 20, 2007 Drexel University Chemistry Department
  2. 2. Agenda <ul><li>This session will cover the dissemination of primary scientific information via blogs, wikis and other non-traditional vehicles </li></ul><ul><li>1. Types of information </li></ul><ul><ul><li>raw experimental data (Open Notebook Science) </li></ul></ul><ul><ul><li>analyzed data </li></ul></ul><ul><ul><li>hypotheses </li></ul></ul><ul><ul><li>“ failed” experiments </li></ul></ul><ul><ul><li>generalized protocols </li></ul></ul><ul><ul><li>traditional article format </li></ul></ul>
  3. 3. <ul><li>2. Issues </li></ul><ul><ul><li>Intellectual Property </li></ul></ul><ul><ul><li>Referencing and claims to priority </li></ul></ul><ul><ul><li>Academic Validation </li></ul></ul><ul><ul><li>Peer Review – mandatory and elective </li></ul></ul>
  4. 4. <ul><li>3. Opportunities </li></ul><ul><li>Increasing productivity in terms of universally usable knowledge units </li></ul><ul><li>Making explicit the nature and quantity of work in collaborations </li></ul><ul><li>Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity? </li></ul>
  5. 5. Where is Science headed? WE ARE HERE
  6. 6. The Robot Scientist
  7. 7. <ul><li>Self-organizing reduntant processes </li></ul><ul><li>Agents can participate with zero or near-zero cost (free hosted services) </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>How will this happen?
  8. 8. How can machines know what is important? Ask the humans
  9. 9. UsefulChem Blog
  10. 10. What chemists think is important in 2005
  11. 11. Find-A-Drug
  12. 12. Diketopiperazine Library Evolves to: on pot Ugi reaction/cyclization First iteration: Solid Support Synthesis
  13. 13. The Molecules Blog
  14. 14. The Experiments Blog
  15. 15. Comments from peers
  16. 16. The UsefulChem Wiki
  17. 17. Telling the story of the failures
  18. 18. Experiments moved to wiki
  19. 19. Experiment History
  20. 20. Experiment Edits
  21. 21. Third Party Time-Stamp on Experiment Versions
  22. 22. Monitoring experimental progress
  23. 23. How are people finding our experiments?
  24. 24. Molecules found by InChI
  25. 25. Automation in UsefulChem
  26. 26. CMLRSS feed on Bioclipse
  27. 27. CMLRSS feed on Bloglines
  28. 28. Open science connectivity More info on open source science here
  29. 29. Extending the interaction outside of science
  30. 30. The blog as an integrative tool
  31. 31. The wiki as the laboratory notebook
  32. 32. (2 min) Graphical Mining of Data with JSpecView
  33. 33. Raw Experimental Data
  34. 34. Selected Experiments (some failed)
  35. 35. Vendor Reliability
  36. 36. Generalized Protocols
  37. 37. Lab Notebook for intra-group communication
  38. 38. Discussing Hypotheses
  39. 39. Writing Code for the Automation Component Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-Rust