The Value of Openness in Research and Teaching


Published on

Jean-Claude Bradley presents at the University of Delaware Tuesday Tech Talks on February 12, 2013. The aim is to make a compelling case that openness is valuable to the educational process and augmenting scientific knowledge. Specific examples in chemistry relating to solubility, melting point and recrystallization will be detailed, as well as the technical solutions that have proved most useful.

Published in: Education
1 Like
  • Be the first to comment

No Downloads
Total views
On SlideShare
From Embeds
Number of Embeds
Embeds 0
No embeds

No notes for slide

The Value of Openness in Research and Teaching

  1. 1. The value of Openness in Research and Teaching University of Delaware Tuesday Tech Talks Jean-Claude Bradley Associate Professor of Chemistry Drexel University February 12, 2013
  2. 2. The story of the enigmatic solventSophomore Organic Chemistry lab at Drexel University Lab procedure required recrystallization from ethyl acetate and synthesis not reliable
  3. 3. Searching for a logical reason• The synthesis of DBA is widespread in organic teaching labs• Methods vary but ethyl acetate is often used to recrystallize DBA• Its use traces back to a paper from 1903• However the solubility of DBA in ethyl acetate was apparently never reported
  4. 4. Developing a rational method to choose asynthesis and recrystallization solvent – in the open Matthew McBride
  5. 5. An example of a failed experiment in an Open Notebook with useful information
  6. 6. A failed experiment reveals the importance of aldehyde solubility
  7. 7. An example of a successful experiment in an Open NotebookThis synthesis will now be used in the revised organic teaching lab manual at Drexel
  8. 8. Incomplete information from the literature can be very problematic
  9. 9. Motivation: Faster Science, Better Science
  10. 10. The Recrystallization App (Andrew Lang)
  11. 11. What are good solvents to recrystallize benzoic acid? (Andrew Lang)
  12. 12. Click on the solvent to see temp curve (Andrew Lang)
  13. 13. Deliver melting point data via App (Andrew Lang)
  14. 14. The Recrystallization App produces and usesOpen Data:• Open Solubility Collection and Models• Open Melting Point Collection and Models• Modeling depends mainly on CDK (Open Source Software with Open Descriptors)• Open Notebook Science
  15. 15. Open Melting Point DatasetsCurrently 20,000 compounds with Open MPs
  16. 16. Contributing to Science while Teaching it: Chemical Information Retrieval Class
  17. 17. The Chemical Information Validation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course
  18. 18. Each entry validated with an image
  19. 19. Alfa Aesar donates melting points to the public
  20. 20. Outliers for ethanol: Alfa Aesar and Oxford MSDS
  21. 21. Solubility Outlier List
  22. 22. Open Melting Point Explorer (Andrew Lang)
  23. 23. Searching for aldol condensations of acetone in the Reaction Attempts database (Andrew Lang)
  24. 24. Open Random Forest modeling of Open Melting Point data using CDK descriptors (Andrew Lang) R2 = 0.78, TPSA and nHdon most important
  25. 25. Melting point prediction service
  26. 26. Web services for summary data (Andrew Lang)
  27. 27. Using a Google Spreadsheet as a “dashboard interface” for reaction planning and analysis
  28. 28. Calling Google App Scripts
  29. 29. Calling Google App Scripts (Andrew Lang and Rich Apodaca)
  30. 30. Google Apps Scripts for conveniently exploring melting point data
  31. 31. A click away from an interactive NMR display (using JCAMP-DX format and ChemDoodle) (Andrew Lang)
  32. 32. Open Melting Points in Supplementary Data Pages of Wikipedia (Martin Walker)
  33. 33. Google Apps Scripts web services
  34. 34. Chemistry Google App Scripts description sheet (Andrew Lang and Rich Apodaca)
  35. 35. Open Chemical Property Matrix (OCPM)Boiling point Vapor pressure Flash point Abraham Melting point descriptors logP Aqueous Octanol solubility solubility
  36. 36. ConclusionsMore openness in chemistry can make science more efficientProvide interfaces that make sense to the end users:Open Data, Open Models and Open Source Software to modelersApps (smartphones, Google App Scripts, etc.) for chemists at the bench Acknowledgements Andrew Lang (code, modeling) Bill Acree (modeling, solubility data contribution) Antony Williams (ChemSpider services, mp data curation) Matthew McBride and Rida Atif (recrystallization and synthesis) Kayla Gogarty (OCPM)