Open Notebook Science and Malaria


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My presentation to Chemists Without Borders on September 6, 2007. I introduce the basics of the UsefulChem project and Open Notebook Science and why malaria is a particularly good target for Open Science. This includes the CombiUgi project and our collaborations with ChemSpider, Rajarshi Guha, Phil Rosenthal, Dan Zaharevitz and Tsu-Soo Tan. The final slide shows the presentation of our work on Second Life at a SciFoo Lives On session.

Published in: Business, Technology
  • @BasarBilisimTeknolojileri Notebook very nice I would recommend to anyone
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  • tq
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  • Notebook
    thank you for sharing.
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  • Hi JC. I love the way you think about doing science. I have a brother-in-law doing cutting edge research in biomedical engineering and have discussed with him the 'open science' paradigm you talk about here. His reply is something along the lines of 'It would be interesting to see a senior researcher do something like that ... but it's just not done.'

    I wanted to follow many of the links in your presentation. Did you know that if you make them live links from within the original slideshow (Keynote or PowerPoint) that functionality carries over here to slideshare? You just have to keep the links in towards the middle of the page otherwise the 'forward' and 'backward' navigation functionality overrides the active links. Thought you might like to know. ;-)

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Open Notebook Science and Malaria

  1. 1. Open Notebook Science and Malaria Jean-Claude Bradley Drexel University September 6, 2007 Chemists Without Borders
  2. 2. Malaria is a Logical Application of Open Science <ul><li>Very large problem: 300-500 million cases per year with one million deaths </li></ul><ul><li>Not a lucrative market: IP control less important </li></ul>
  3. 4. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN
  4. 5. Where is Science headed? WE ARE HERE
  5. 6. The Robot Scientist
  6. 7. <ul><li>Self-organizing redundant processes </li></ul><ul><li>Agents can participate with zero or near-zero cost (free hosted services – e.g. Google) </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?
  7. 8. How can machines know what is important? Ask the humans
  8. 9. UsefulChem Blog
  9. 10. What chemists think is important in 2005
  10. 11. Find-A-Drug
  11. 12. Diketopiperazine Library Evolves to: on pot Ugi reaction/cyclization First iteration: Solid Support Synthesis
  12. 13. The Molecules Blog
  13. 14. The Experiments Blog
  14. 15. Comments from peers
  15. 16. The UsefulChem Wiki
  16. 17. Telling the story of the failures
  17. 18. Experiments moved to wiki
  18. 19. Experiment History
  19. 20. Experiment Edits
  20. 21. Third Party Time-Stamp on Experiment Versions
  21. 22. Monitoring experimental progress
  22. 23. How are people finding our experiments?
  23. 24. Molecules found by InChI
  24. 25. The blog as an integrative tool
  25. 26. The wiki as the laboratory notebook
  26. 27. Graphical Mining of Data with JSpecView (48h 7 min)
  27. 28. Processing Molecules on ChemSpider
  28. 29. The CombiUgi Project Focus on cheap starting materials and a product that precipitate easily from solution
  29. 30. Open Primary Research in Drug Design using Web2.0 tools (blogs, wikis, Second Life, mailing lists) Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.
  30. 31. UsefulChem and Open Science in Second Life