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

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 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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

3. Where is Science headed? WE ARE HERE

4. The Robot Scientist

5. How will this happen? Self-organizing redundant processes Self-organizing redundant processes Fully Open Access (Read and Write) Fully Open Access (Read and Write) Publication of all aspects of the scientific process: Open Source Science / Open Notebook Science 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? 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 Evolves to: on pot Ugi reaction/cyclization First iteration: Solid Support Synthesis

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

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) Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.

35. Mailing List Facilitates inter-group collaboration

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

38. CombiUgi Virtual Libraries

39. Falcipain-2 inhibitor? http://usefulchem.wikispaces.com/Exp148Khalid Mirza

40. More Flexible Scientific Publication

41. neurodatabase.org Raw Experimental Data

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

43. Generalized Protocols Openwetware.org

44. Orgprepdaily.wordpress.com Vendor Reliability

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

46. Discussing Hypotheses RRResearch.blogspot.com

47. Cameron Neylon’s Notebook

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

49. Merging Research and Teaching in Second Life

50. 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? 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 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? 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 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 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? Question: Who is the audience for science blogs and wikis anyway? Scientists or laypeople? For UsefulChem, wiki is for chemists, blog for wider audience 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? Question: Can you get published if you've already posted your results to your blog/wiki? We’ll find out…. We’ll find out…. Question: Can scientists establish their credibility/reputation by writing blogs and wikis? Question: Can scientists establish their credibility/reputation by writing blogs and wikis? Certainly we’ve found collaborators this way Certainly we’ve found collaborators this way