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UsefulChem project: Open source chemical research with blogs and wikis

UsefulChem project: Open source chemical research with blogs and wikis . Jean-Claude.Bradley@drexel.edu September 14, 2006. American Chemical Society National meeting in San Francisco. Where is Science headed?. WE ARE HERE. The Robot Scientist. How will this happen?.

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UsefulChem project: Open source chemical research with blogs and wikis

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  1. UsefulChem project: Open source chemical research with blogs and wikis Jean-Claude.Bradley@drexel.edu September 14, 2006 American Chemical Society National meeting in San Francisco

  2. Where is Science headed? WE ARE HERE

  3. The Robot Scientist

  4. How will this happen? • 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

  5. How can machines know what is important? Ask the humans

  6. UsefulChem Blog

  7. What chemists think is important in 2005

  8. Find-A-Drug

  9. Diketopiperazine Library First iteration: Solid Support Synthesis Evolves to: on pot Ugi reaction/cyclization

  10. The Molecules Blog

  11. The Experiments Blog

  12. Comments from peers

  13. The UsefulChem Wiki

  14. Telling the story of the failures

  15. Experiments moved to wiki

  16. Experiment History

  17. Experiment Edits

  18. Third Party Time-Stamp on Experiment Versions

  19. Monitoring experimental progress

  20. How are people finding our experiments?

  21. Molecules found by InChI

  22. Automation in UsefulChem

  23. CMLRSS feed on Bioclipse

  24. CMLRSS feed on Bloglines

  25. The value of peer review in finding information • Before Internet -> • “pre-validation” saves time when searching is laborious • Fewer publications to keep track of • After Internet -> • online availability is more valuable when searching is fast and easy • Many new publications - who are the peers?

  26. The value of peer review in academia • These are two separate problems: • Communicating science • Justifying the value of scholarship

  27. Open science connectivity More info on open source science here http://usefulchem.wikispaces.com

  28. Extending the interaction outside of science

  29. Next Steps • Incorporate our molecules into Emolecules to enable substructure searching • Custom CMLRSS feeds (e.g. only new commercial sources found) • Get spectra in JCAMP format • Extend our collaboration with other chemists (e.g. docking data) • Get our anti-malarials made and tested

  30. Acknowledgments • Khalid Mirza (grad student) • James Giammarco (undergrad) • Lin Chen (undergrad) • Dave Strumfels (cheminformatics) • Bloggers (Egon Willighagen, Peter Murray-Rust, etc.)

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