ACS talk on UsefulChem


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Jean-Claude Bradley's talk at the American Chemical Society on September 14, 2006 in San Francisco. This is a fairly condensed summary of the UsefulChem project at Drexel University, with plenty of examples on how to use blogs and wikis to do open source science.

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ACS talk on UsefulChem

  1. 1. UsefulChem project: Open source chemical research with blogs and wikis [email_address] September 14, 2006 American Chemical Society National meeting in San Francisco
  2. 2. Where is Science headed? WE ARE HERE
  3. 3. The Robot Scientist
  4. 4. <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 </li></ul>How will this happen?
  5. 5. How can machines know what is important? Ask the humans
  6. 6. UsefulChem Blog
  7. 7. What chemists think is important in 2005
  8. 8. Find-A-Drug
  9. 9. Diketopiperazine Library Evolves to: on pot Ugi reaction/cyclization First iteration: Solid Support Synthesis
  10. 10. The Molecules Blog
  11. 11. The Experiments Blog
  12. 12. Comments from peers
  13. 13. The UsefulChem Wiki
  14. 14. Telling the story of the failures
  15. 15. Experiments moved to wiki
  16. 16. Experiment History
  17. 17. Experiment Edits
  18. 18. Third Party Time-Stamp on Experiment Versions
  19. 19. Monitoring experimental progress
  20. 20. How are people finding our experiments?
  21. 21. Molecules found by InChI
  22. 22. Automation in UsefulChem
  23. 23. CMLRSS feed on Bioclipse
  24. 24. CMLRSS feed on Bloglines
  25. 25. The value of peer review in finding information <ul><li>Before Internet -> </li></ul><ul><ul><li>“pre-validation” saves time when searching is laborious </li></ul></ul><ul><ul><li>Fewer publications to keep track of </li></ul></ul><ul><li>After Internet -> </li></ul><ul><ul><li>online availability is more valuable when searching is fast and easy </li></ul></ul><ul><ul><li>Many new publications - who are the peers? </li></ul></ul>
  26. 26. The value of peer review in academia <ul><li>These are two separate problems: </li></ul><ul><ul><li>Communicating science </li></ul></ul><ul><ul><li>Justifying the value of scholarship </li></ul></ul>
  27. 27. Open science connectivity More info on open source science here
  28. 28. Extending the interaction outside of science
  29. 29. Next Steps <ul><li>Incorporate our molecules into Emolecules to enable substructure searching </li></ul><ul><li>Custom CMLRSS feeds (e.g. only new commercial sources found) </li></ul><ul><li>Get spectra in JCAMP format </li></ul><ul><li>Extend our collaboration with other chemists (e.g. docking data) </li></ul><ul><li>Get our anti-malarials made and tested </li></ul>
  30. 30. Acknowledgments <ul><li>Khalid Mirza (grad student) </li></ul><ul><li>James Giammarco (undergrad) </li></ul><ul><li>Lin Chen (undergrad) </li></ul><ul><li>Dave Strumfels (cheminformatics) </li></ul><ul><li>Bloggers (Egon Willighagen, Peter Murray-Rust, etc.) </li></ul>