Jean-Claude Bradley presents "Open Notebook Science as an efficient means for transparency in science" on April 15, 2011 at the Drexel Nanotechnology Institute IGERT Meeting.

1. Open Notebook Science as an efficient means for transparency in science IGERT Drexel Meeting Jean-Claude Bradley Department of Chemistry Drexel University April 15, 2011

2. The current state of transparency in scientific communication Case study of melting point data

3. The Chemical Information Validation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course

4. The Chemical Information Validation Explorer (Andrew Lang)

5. Discovering outliers for melting points (stdev/average)

6. Investigating the m.p. inconsistencies of EGCG

7. Investigating the m.p. inconsistencies of cyclohexanone

8. Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting points

9. Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling points

10. Sigma-Aldrich, Acros and Wolfram Alpha apparently DO NOT use the same sources for flash points

11. Most popular data sources

12. Alfa Aesar donates melting points to the public

13. Open Melting Point Explorer

14. Outliers MDPI dataset EPI (via ChemSpider)

15. Outliers Alfa Aesar

16. Inconsistencies and SMILES problems within MDPI dataset

17. MDPI Dataset labeled with High Trust Level

18. Open Melting Point Datasets

19. Open Random Forest modeling of Open Melting Point data using CDK descriptors (Andrew Lang) R2 = 0.78, TPSA and nHdon most important

20. Melting point prediction service

21. Using melting point for temperature dependent solubility prediction

22. Motivation: Faster Science,Better Science

23. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit

24. TRUST PROOF

25. Strategy for an Open Notebook: First record then abstract structure In order to be discoverable use Google friendly formats (simple HTML, no login) In order to be replicable use free hosted tools (Wikispaces, Google Spreadsheets)

26. Crowdsourcing Solubility Data

27. Data provenance: From Wikipedia to…

28. …the lab notebook and raw data

29. Calculations Made Public on Google Spreadsheets

30. Interactive NMR spectra using JSpecView and JCAMP-DX

31. Raw Data As Images Splatter? Some liquid

32. YouTube for demonstrating experimental set-up

33. The importance of raw data availability Missed in a prior publication on solubility for this compound

34. Solubilities collected in a Google Spreadsheet

35. Rajarshi Guha’s Live Web Query using Google Viz API

36. Web services for summary data (Andrew Lang)

37. Web service calls from within a Google Spreadsheet for solubility measurement and prediction (Andrew Lang)

38. Integration of Multiple Web Services to Recommend Solvents for Reactions (Andrew Lang)

42. Reaction Attempts Book

43. Reaction Attempts Book: Reactants listed Alphabetically

44. ONS Challenge Solubility Book cited for nanotechnology application

45. Lulu.com Data Disks

46. Visualizing molecule-researcher connection maps reveals link between 2 Open Notebooks (Todd and Bradley) (Don Pellegrino)

47. All ONS web services

48. For all Formats of ONS Projects

50. Open Notebook Science offers an efficient way to make research transparent and discoverable