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.

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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  • 1. Open Source/Open Notebook Science: Doing science with blogs and wikis [email_address] Jan 20, 2007 Drexel University Chemistry Department
  • 2. Agenda
    • This session will cover the dissemination of primary scientific information via blogs, wikis and other non-traditional vehicles
    • 1. Types of information
      • raw experimental data (Open Notebook Science)
      • analyzed data
      • hypotheses
      • “ failed” experiments
      • generalized protocols
      • traditional article format
  • 3.
    • 2. Issues
      • Intellectual Property
      • Referencing and claims to priority
      • Academic Validation
      • Peer Review – mandatory and elective
  • 4.
    • 3. Opportunities
    • Increasing productivity in terms of universally usable knowledge units
    • Making explicit the nature and quantity of work in collaborations
    • Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity?
  • 5. Where is Science headed? WE ARE HERE
  • 6. The Robot Scientist
  • 7.
    • Self-organizing reduntant processes
    • Agents can participate with zero or near-zero cost (free hosted services)
    • Fully Open Access (Read and Write)
    • Publication of all aspects of the scientific process: Open Source Science / Open Notebook Science
    How will this happen?
  • 8. How can machines know what is important? Ask the humans
  • 9. UsefulChem Blog
  • 10. What chemists think is important in 2005
  • 11. Find-A-Drug
  • 12. Diketopiperazine Library Evolves to: on pot Ugi reaction/cyclization First iteration: Solid Support Synthesis
  • 13. The Molecules Blog
  • 14. The Experiments Blog
  • 15. Comments from peers
  • 16. The UsefulChem Wiki
  • 17. Telling the story of the failures
  • 18. Experiments moved to wiki
  • 19. Experiment History
  • 20. Experiment Edits
  • 21. Third Party Time-Stamp on Experiment Versions
  • 22. Monitoring experimental progress
  • 23. How are people finding our experiments?
  • 24. Molecules found by InChI
  • 25. Automation in UsefulChem
  • 26. CMLRSS feed on Bioclipse
  • 27. CMLRSS feed on Bloglines
  • 28. Open science connectivity More info on open source science here http://usefulchem.wikispaces.com
  • 29. Extending the interaction outside of science
  • 30. usefulchem.blogspot.com The blog as an integrative tool
  • 31. usefulchem.wikispaces.com/Exp049 The wiki as the laboratory notebook
  • 32. usefulchem.wikispaces.com/Exp049 (2 min) Graphical Mining of Data with JSpecView
  • 33. neurodatabase.org Raw Experimental Data
  • 34. Selected Experiments (some failed) Orgprepdaily.wordpress.com
  • 35. Orgprepdaily.wordpress.com Vendor Reliability
  • 36. Generalized Protocols Openwetware.org
  • 37. Lab Notebook for intra-group communication Openwetware.org
  • 38. Discussing Hypotheses RRResearch.blogspot.com
  • 39. Writing Code for the Automation Component Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-Rust
  • 40.