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Open and Closed Science

Publication of all aspects of the scientific process: Open Source Science / Open ... Third Party Time-Stamp on Experiment Versions. Monitoring experimental ...

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Open and Closed Science

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  1. Open Notebook Science: Research in Real Time Sigma Xi Swarthmore College Chapter Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University Nov 27, 2007

  2. Open and Closed Science Open Notebook Science (full transparency) Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article RESEARCH OPEN CLOSED TEACHING Archived Lectures Public and free online textbooks Lectures Notes public Traditional Paper Textbook F2F lectures Assigned problems public

  3. Where is Science headed? WE ARE HERE

  4. The Robot Scientist

  5. How will this happen? • Self-organizing redundant processes • Fully Open Access (Read and Write) • Publication of all aspects of the scientific process: Open Source Science / Open Notebook Science • Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity?

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

  7. UsefulChem Blog

  8. What chemists think is important in 2005

  9. Malaria is a Logical Application of Open Science • Very large problem: 300-500 million cases per year with one million deaths • Not a lucrative market: IP control less important

  10. Find-A-Drug

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

  12. The Molecules Blog

  13. The Experiments Blog

  14. Comments from peers

  15. The UsefulChem Wiki

  16. Telling the story of the failures

  17. Experiments moved to wiki

  18. Experiment History

  19. Experiment Edits

  20. Third Party Time-Stamp on Experiment Versions

  21. Monitoring experimental progress

  22. Table of Contents View

  23. The blog as an integrative tool usefulchem.blogspot.com

  24. How are people finding our experiments?

  25. Molecules found by InChI

  26. Processing Molecules on ChemSpider

  27. Graphical Mining of Data with JSpecView usefulchem.wikispaces.com/Exp070 (48h 7 min)

  28. Student assignments on a wiki

  29. Student assignment on NMR using live research data and JSpecView

  30. Using ExcelVBA to automate kinetics analysis

  31. Specify NMR regions and internal standard

  32. NMR spectra of monitoring samples calculated

  33. Reaction profile plotted automatically

  34. Open Primary Research in Drug Design using Web2.0 tools(blogs, wikis, Second Life, mailing lists) Rajarshi Guha Indiana U Tsu-Soo Tan Nanyang Inst. Docking JC Bradley Drexel U Synthesis Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Testing

  35. Mailing List Facilitates inter-group collaboration

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

  37. CombiUgi Virtual Libraries

  38. Falcipain-2 inhibitor? Khalid Mirza http://usefulchem.wikispaces.com/Exp148

  39. More Flexible Scientific Publication

  40. Raw Experimental Data neurodatabase.org

  41. Selected Experiments (some failed) Orgprepdaily.wordpress.com

  42. Generalized Protocols Openwetware.org

  43. Vendor Reliability Orgprepdaily.wordpress.com

  44. Lab Notebook for intra-group communication Openwetware.org

  45. Discussing Hypotheses RRResearch.blogspot.com

  46. Cameron Neylon’s Notebook

  47. UsefulChem and Open Science in Second Life scifooliveson.wikispaces.com

  48. Merging Research and Teaching in Second Life

  49. Question: Is it really a good thing to let anyone who thinks they have a scientific breakthrough have access to free, open, public, Googleable media? • YES • Question: What if I make a mistake in my data, never fix it, no one catches it, and then someone dies because a medical decision was based on my "findings"? Isn't this exactly why we have formal peer review in formal publications? • Peer review is not designed to catch errors from the analysis of raw data • Open Notebook Science is more difficult where human subjects are involved • Question: Who is the audience for science blogs and wikis anyway? Scientists or laypeople? • For UsefulChem, wiki is for chemists, blog for wider audience • Question: Can you get published if you've already posted your results to your blog/wiki? • We’ll find out…. • Question: Can scientists establish their credibility/reputation by writing blogs and wikis? • Certainly we’ve found collaborators this way

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