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The Value of Openness in Research and Teaching
The document discusses the importance of openness in scientific research and teaching, particularly in organic chemistry labs at Drexel University. It highlights the development of tools and apps for improving the efficiency of recrystallization processes, emphasizes the value of sharing open data regarding solvent properties, and describes various contributions from individuals involved in this work. The overarching theme is that increased openness can lead to faster, better science through collaboration and shared resources.
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The Value of Openness in Research and Teaching
- 1. The value ofOpenness in Research and Teaching University of Delaware Tuesday Tech Talks Jean-Claude Bradley Associate Professor of Chemistry Drexel University February 12, 2013
- 2. The story ofthe enigmatic solvent Sophomore Organic Chemistry lab at Drexel University Lab procedure required recrystallization from ethyl acetate and synthesis not reliable
- 3. Searching for alogical 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. Developing a rationalmethod to choose a synthesis and recrystallization solvent – in the open Matthew McBride
- 5. An example ofa failed experiment in an Open Notebook with useful information
- 6. A failed experimentreveals the importance of aldehyde solubility
- 7. An example ofa successful experiment in an Open Notebook This synthesis will now be used in the revised organic teaching lab manual at Drexel
- 8. Incomplete information fromthe literature can be very problematic
- 9. Motivation: Faster Science,Better Science
- 10. The Recrystallization App (Andrew Lang)
- 11. What are goodsolvents to recrystallize benzoic acid? (Andrew Lang)
- 12. Click on thesolvent to see temp curve (Andrew Lang)
- 13. Deliver melting pointdata via App (Andrew Lang)
- 14. The Recrystallization Appproduces and uses Open 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. Open Melting PointDatasets Currently 20,000 compounds with Open MPs
- 16. Contributing to Sciencewhile Teaching it: Chemical Information Retrieval Class
- 17. The Chemical InformationValidation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course
- 18. Each entry validatedwith an image
- 19. Alfa Aesar donatesmelting points to the public
- 20. Outliers for ethanol:Alfa Aesar and Oxford MSDS
- 21.
- 22. Open Melting PointExplorer (Andrew Lang)
- 23. Searching for aldolcondensations of acetone in the Reaction Attempts database (Andrew Lang)
- 24. Open Random Forestmodeling of Open Melting Point data using CDK descriptors (Andrew Lang) R2 = 0.78, TPSA and nHdon most important
- 25. Melting point predictionservice
- 26. Web services forsummary data (Andrew Lang)
- 27. Using a GoogleSpreadsheet as a “dashboard interface” for reaction planning and analysis
- 28. Calling Google AppScripts
- 29. Calling Google AppScripts (Andrew Lang and Rich Apodaca)
- 30. Google Apps Scriptsfor conveniently exploring melting point data
- 31. A click awayfrom an interactive NMR display (using JCAMP-DX format and ChemDoodle) (Andrew Lang)
- 32. Open Melting Pointsin Supplementary Data Pages of Wikipedia (Martin Walker)
- 33. Google Apps Scriptsweb services
- 34. Chemistry Google AppScripts description sheet (Andrew Lang and Rich Apodaca)
- 35. Open Chemical PropertyMatrix (OCPM) Boiling point Vapor pressure Flash point Abraham Melting point descriptors logP Aqueous Octanol solubility solubility
- 36. Conclusions More openness inchemistry can make science more efficient Provide interfaces that make sense to the end users: Open Data, Open Models and Open Source Software to modelers Apps (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)