This document discusses open notebook science, which aims to make the scientific process more transparent and collaborative. It describes how open notebook science makes raw data, calculations, assumptions and revision histories publicly available. This allows other scientists to reproduce and build on the reported results. The document also addresses challenges around archiving and preserving open science data and notebooks so they remain accessible over the long term. It outlines current archiving solutions used by the open notebook science community such as daily backups of crucial data and semi-automated snapshots of the entire scientific record.

1. Open Notebook Science for Research and Teaching Jean-Claude Bradley February 18, 2010 National Institute for Technology in Liberal Education Associate Professor of Chemistry Drexel University Andrew Lang Professor of Mathematics Oral Roberts University

2. The NaH oxidation controversy

3. Information spreads quickly through the blogosphere

4. 15% NMR yield

6. Khalid Mirza and Marshall Moritz

8. Top results on a Google search

9. How bad is our current system? Try to find the solubility EGCG?

10. =2.3 g/L WTF?!

11. The End of the Chain of Provenance

12. The Scandal of Bell’s Lab Notebook

13. Motivation: Faster Science, Better Science

14. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when

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

16. TRUST PROOF

17. The solubility of 4-chlorobenzaldehyde

18. The Log makes Assumptions Explicit

19. The Rationale of Findings Explicit

20. Raw Data Made Public Splatter? Some liquid

21. YouTube for demonstrating experimental set-up

22. Calculations Made Public on Google Spreadsheets

23. Revision History on Google Spreadsheets

24. Wiki Page History

25. Comparing Wiki Page Versions

26. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX

27. Linking to Molecules in Chemistry Databases

28. Experimental Spectra and User-Deposited Data on ChemSpider

29. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)

30. Database Curation via Game Playing

31. Over 100,000 spectrum views so far - worldwide

32. Link Spectral Game to Open Educational Content

33. NMR game in Second Life (Andy Lang)

34. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?

35. Crowdsourcing Solubility Data

36. ONS Submeta Award Winners

37. ONS Challenge Judges

38. Teaching Lab: Brent Friesen (Dominican University)

39. Solubility Experiment List

40. Solubilities collected in a Google Spreadsheet

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

42. WE ARE HERE How can the scientific process become more automated?

43. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)

45. Solubility Prediction (Andy Lang’s Model)

46. Solubility prediction can generate requests for additional measurements

47. Solvent mixture and temperature: multidimensional solubility data Actual Data (4-nitrobenzaldehyde) From quadratic regression of 5D space Feeds DoSol Sheet the next points to measure to best cover the space

48. Understanding in addition to empirical modeling Missed in a prior publication on solubility for this compound

49. Data provenance: From Wikipedia to…

50. … the lab notebook and raw data

51. Including links to the literature

52. Pierre Lindenbaum’s Solubility Data as RDF Triples

54. Paper written on Wiki

55. References to papers, blog posts, lab notebook pages, raw data

56. Paper on Journal of Visualized Experiments (JoVE)

57. Pre-print on Nature Precedings

58. ChemSpider Automated Mark-up of Chemical Names

59. BUT… Open Access: the Choice that Keeps Giving.. and Giving…

60. Beware of your addiction to metrics: redundancy will reduce them

61. Cameron Neylon’s Notebooks Other Open Notebooks

62. Anthony Salvagno’s Notebook (Steve Koch group)

63. Educational “Open Notebooks”

64. Educational “Open Notebooks”

65. Educational “Open Notebooks”

66. Crowdsourcing ChemInfo Resource Collection

67. 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 Where do Libraries fit in the communication of science and education in the Open/Closed Continuum?

69. Librarians and Science 2.0 "The Internet Archive is a 501(c)(3) non-profit that was founded to build an Internet library, with the purpose of offering permanent access for researchers, historians, and scholars to historical collections that exist in digital format." The internet Archive is not practical for practitioners of Open Notebook Science or Science 2.0

70. Good concept but.....

71. Most pages look like this....

72. Where We Began: The ONS backup spreadsheet and ONSPreserver

73. Publishing Google Spreadsheets as XLS

74. Where We Are Now

75. ONSPreserverLite Daily Backup of Crucial Data

76. ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record

77. Snapshot is Self-Contained and Live on the Internet

78. Lulu.com Data Disks

79. DSpace – Handle (hdl)

80. Lulu.com - ISBN Google Spreadsheets Google Documents Web Services ChemSpider & Indiana Real Time Linear Regression, Unit Conversions, Style Sheet, etc Data Book

83. Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL:http://spreadsheets.google.com/pub?key=plwwufp30hfq0udnEmRD1aQ&output=xls. Accessed: 2009-12-11. (Archived by WebCite® at http://www.webcitation.org/5lx5ry3BV )

84. More about the ONSarchive project: