1. Open Source/Open Notebook Science: Doing science with blogs and wikis Jean-Claude.Bradley@drexel.edu Jan 20, 2007 Drexel University Chemistry Department

2. Agenda This session will cover the dissemination of primary scientific information via blogs, wikis and other non-traditional vehicles This session will cover the dissemination of primary scientific information via blogs, wikis and other non-traditional vehicles 1. Types of information raw experimental data (Open Notebook Science) raw experimental data (Open Notebook Science) analyzed data analyzed data hypotheses hypotheses “failed” experiments “failed” experiments generalized protocols generalized protocols traditional article format traditional article format

3. 2. Issues Intellectual Property Intellectual Property Referencing and claims to priority Referencing and claims to priority Academic Validation Academic Validation Peer Review – mandatory and elective Peer Review – mandatory and elective

4. 3. Opportunities Increasing productivity in terms of universally usable knowledge units Increasing productivity in terms of universally usable knowledge units Making explicit the nature and quantity of work in collaborations Making explicit the nature and quantity of work in collaborations 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?

5. Where is Science headed? WE ARE HERE

6. The Robot Scientist

7. How will this happen? Self-organizing reduntant processes Self-organizing reduntant processes Agents can participate with zero or near- zero cost (free hosted services) Agents can participate with zero or near- zero cost (free hosted services) 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

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

9. UsefulChem Blog

10. What chemists think is important in 2005

11. Find-A-Drug

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

13. The Molecules Blog

14. The Experiments Blog

15. Comments from peers

16. The UsefulChem Wiki

17. Telling the story of the failures

18. Experiments moved to wiki

19. Experiment History

20. Experiment Edits

21. Third Party Time-Stamp on Experiment Versions

22. Monitoring experimental progress

23. How are people finding our experiments?

24. Molecules found by InChI

25. Automation in UsefulChem

26. CMLRSS feed on Bioclipse

27. CMLRSS feed on Bloglines

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

29. Extending the interaction outside of science

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

31. usefulchem.wikispaces.com/Exp049 The wiki as the laboratory notebook

32. usefulchem.wikispaces.com/Exp049 (2 min) Graphical Mining of Data with JSpecView

33. neurodatabase.org Raw Experimental Data

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

35. Orgprepdaily.wordpress.com Vendor Reliability

36. Generalized Protocols Openwetware.org

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

38. Discussing Hypotheses RRResearch.blogspot.com

39. Writing Code for the Automation Component Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-Rust