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Open Source/Open Notebook Science:  Doing  science with blogs and wikis  [email_address] Jan 20, 2007 Drexel University Ch...
Agenda <ul><li>This session will cover the dissemination of  primary scientific information  via blogs, wikis and other no...
<ul><li>2. Issues </li></ul><ul><ul><li>Intellectual Property  </li></ul></ul><ul><ul><li>Referencing and claims to priori...
<ul><li>3. Opportunities   </li></ul><ul><li>Increasing productivity in terms of universally usable knowledge units  </li>...
Where is Science headed? WE ARE HERE
The Robot Scientist
<ul><li>Self-organizing reduntant processes </li></ul><ul><li>Agents can participate with zero or near-zero cost (free hos...
How can machines know what is important? Ask the humans
UsefulChem Blog
What chemists think is important in 2005
Find-A-Drug
Diketopiperazine Library Evolves to: on pot Ugi reaction/cyclization First iteration: Solid Support Synthesis
The Molecules Blog
The Experiments Blog
Comments from peers
The UsefulChem Wiki
Telling the story of the failures
Experiments moved to wiki
Experiment History
Experiment Edits
Third Party Time-Stamp on Experiment Versions
Monitoring experimental progress
How are people finding our experiments?
Molecules found by InChI
Automation in UsefulChem
CMLRSS feed on Bioclipse
CMLRSS feed on Bloglines
Open science connectivity More info on open source science here http://usefulchem.wikispaces.com
Extending the interaction outside of science
usefulchem.blogspot.com The blog as an integrative tool
usefulchem.wikispaces.com/Exp049 The wiki as the laboratory notebook
usefulchem.wikispaces.com/Exp049 (2 min) Graphical Mining of Data with JSpecView
neurodatabase.org Raw Experimental Data
Selected Experiments (some failed) Orgprepdaily.wordpress.com
Orgprepdaily.wordpress.com Vendor Reliability
Generalized Protocols Openwetware.org
Lab Notebook for intra-group communication Openwetware.org
Discussing Hypotheses RRResearch.blogspot.com
Writing Code for the Automation Component Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-Rust
 
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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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Transcript of "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 http://usefulchem.wikispaces.com
  29. 29. Extending the interaction outside of science
  30. 30. usefulchem.blogspot.com The blog as an integrative tool
  31. 31. usefulchem.wikispaces.com/Exp049 The wiki as the laboratory notebook
  32. 32. usefulchem.wikispaces.com/Exp049 (2 min) Graphical Mining of Data with JSpecView
  33. 33. neurodatabase.org Raw Experimental Data
  34. 34. Selected Experiments (some failed) Orgprepdaily.wordpress.com
  35. 35. Orgprepdaily.wordpress.com Vendor Reliability
  36. 36. Generalized Protocols Openwetware.org
  37. 37. Lab Notebook for intra-group communication Openwetware.org
  38. 38. Discussing Hypotheses RRResearch.blogspot.com
  39. 39. Writing Code for the Automation Component Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-Rust

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