Scholar2Scholar presentation

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This is my April 16, 2008 presentation at the Scholar2Scholar conference at Drexel University. I introduce Web2.0 then show how developing anti-malarial agents can be done on blogs and wikis.

Technology Education

Enhancing Scientific Communication through Open Notebook Science Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University April 16, 2008 Scholar 2 Scholar Symposium: How Web 2.0 is Changing Scholarly Communication

What is Web 2.0? Source: Markus Angermeier and Tim O’Reilly, Wikipedia

Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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

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

BLOG WIKI Mailing List GoogleDocs UsefulChem ChemSpider CDD

Link to Docking Procedure (Rajarshi Guha)

How are people finding our experiments? NMR in TFA Phenylacetaldehyde c4h6o2 nmr methylene chloride/methanol h'nmr of benzophenone sulfuric acid pka tertbutylamine tosyl isocyanide amino furan dichloromethane polar? Reaction between Benzaldehyde and NaBH4 phosphoric acid pka veratraldehyde wiki kinetics boc deprotection Rf value in polar solvent why glycerol is immiscible with ether side reaction of imines 5.8 ppm nmr nmr cdcl3 chloroform side reaction diasterotopic wiki adding anhydrous MgSO4 to the dichlormethane ether extraction hnmr doublet of doublet Boc-protected NMR chromatotron recipe triplet cdcl3 "13c nmr" Specific Compounds Experimental Conditions

How are people finding UsefulChem? free downloading chemistry video organic chemistry project + high school how to make poster in second life organic chem. quiz 3d periodic tables animation protein docking docking animation why are acid-base reactions exothermic? lysosomal targets protease and malaria cheminformatics project proposal automated reactions malaria review project synthesis CHEMISTRY WEB 2.0 projects on QSAR & drug design chemistry experiment results database Educational Big Picture

Using ChemSpider to archive compound characterization

Predicting Precipitates Rajarshi Guha’s Model MESA Analytics Model

Collaborative Drug Discovery (CDD) Database

Mailing List Facilitates inter-group collaboration

Collaboration with Brent Friesen’s Teaching Lab at Dominican University http://ochemonline.pbwiki.com/Ugi%20Synthesis%20Collaborative%20Project

Acknowledgements Khalid Mirza Emily Messner Shannon Oseback Tim Bohinski Dave Strumfels James Giammarco Lin Cheng Sean Gardner Jessica Colditz Alicia Holsey

This is a presentation by Jean-Claude Bradley at the Biennial Conference for Chemical Education (BCCE) on July 29, 2008. The talk starts with an overview of Open Notebook Science using a wiki as a public lab notebook. An example of the usefulness of publishing failed experiments is detailed, showing how the version history of the wiki can be used to track the evolution of an organic chemistry experiment. Near the end of the talk an example of using automation to optimize a Ugi reaction is mentioned.

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Jean-Claude Bradley presented on Open Notebook Science at the NIST Social Media Day on December 11, 2008. The talks starts with an overview of ONS and how it is being used to assess solubility measurements being crowdsourced in the ONS Challenge and Submeta Awards. The use of wikis, blogs, Google Spreadsheets, YouTube, Flickr, ChemSpider and other free hosted Web2.0 tools is highlighted. The UsefulChem project, involving the synthesis of anti-malarial agents, is then briefly covered. Finally, a very recent application of using Google Spreadsheets to automatically call web services to calculate volumes and weights of chemicals needed in reactions is demonstrated (code by Rajarshi Guha).

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Scholar2Scholar presentation

1. Enhancing Scientific Communication through Open Notebook Science Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University April 16, 2008 Scholar 2 Scholar Symposium: How Web 2.0 is Changing Scholarly Communication

2. What is Web 2.0? Source: Markus Angermeier and Tim O’Reilly, Wikipedia

3. Some of my friends……

4. Evaluating and Creating Relationships

5. A Few Examples from FriendFeed

6. 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

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

8. BLOG WIKI Mailing List GoogleDocs UsefulChem ChemSpider CDD

9. Where’s the Beef?

10. Link to Lab Notebook Page in Wiki

11. Link to Molecules

12. Link to Docking Procedure (Rajarshi Guha)

13. Link to Docking Results (Rajarshi Guha)

14. Link to Raw Data with JSpecView

15. Conclusion is Fully Supported

16. Indexing the Experiments in Google

17. Searching with Google Custom Search

18. How are people finding our experiments? NMR in TFA Phenylacetaldehyde c4h6o2 nmr methylene chloride/methanol h'nmr of benzophenone sulfuric acid pka tertbutylamine tosyl isocyanide amino furan dichloromethane polar? Reaction between Benzaldehyde and NaBH4 phosphoric acid pka veratraldehyde wiki kinetics boc deprotection Rf value in polar solvent why glycerol is immiscible with ether side reaction of imines 5.8 ppm nmr nmr cdcl3 chloroform side reaction diasterotopic wiki adding anhydrous MgSO4 to the dichlormethane ether extraction hnmr doublet of doublet Boc-protected NMR chromatotron recipe triplet cdcl3 "13c nmr" Specific Compounds Experimental Conditions

19. How are people finding UsefulChem? free downloading chemistry video organic chemistry project + high school how to make poster in second life organic chem. quiz 3d periodic tables animation protein docking docking animation why are acid-base reactions exothermic? lysosomal targets protease and malaria cheminformatics project proposal automated reactions malaria review project synthesis CHEMISTRY WEB 2.0 projects on QSAR & drug design chemistry experiment results database Educational Big Picture

20. Using ChemSpider to archive compound characterization

21. Comparing Experiments with GoogleDocs

22. Predicting Precipitates Rajarshi Guha’s Model MESA Analytics Model

23. The Most Important Section!

24. Results in Machine-Friendly Format

25. Table of Contents

26. Recent Changes in Wiki

27. Tracking Versions of Wiki Pages

28. Comparing Versions of Wiki Pages

29. Telling the story of the failures

30. Collaborative Drug Discovery (CDD) Database

31. Mailing List Facilitates inter-group collaboration

32. What about the blog? Discussing Funding

33. Supporting Funding Initiatives

34. Highlight Popular Media Coverage

35. Highlight Peer-Reviewed Coverage

36. Announce Collaborator: Gus Rosania

37. Announce Collaborator: Matthias Zeller

38. Announce Collaborator: Phil Rosenthal

39. Discuss Presentations in Real Life

40. Discuss Presentations in Second Life

41. Showcase Science in New Media

42. Showcase Teaching in New Media

43. Alerts to Broader Impact Opportunities

44. Science Philosophy

45. Gus Rosania’s Notebook

46. Cameron Neylon’s Notebook

47. Collaboration with Brent Friesen’s Teaching Lab at Dominican University http://ochemonline.pbwiki.com/Ugi%20Synthesis%20Collaborative%20Project

48. Where is Science headed? WE ARE HERE

49. Acknowledgements Khalid Mirza Emily Messner Shannon Oseback Tim Bohinski Dave Strumfels James Giammarco Lin Cheng Sean Gardner Jessica Colditz Alicia Holsey

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