Talk given at the Science 2.0 Symposium organized by Greg Wilson as part of the Software Carpentry course on 29 July 2009. The talk discussed how the web can influence and improve the way we record research. http://softwarecarpentry.wordpress.com/guests/

1. A Web Native Research Record Applying the best of the web to the laboratory notebook

2. You are free to: Copy, share, adapt, or re-mix; Photograph, film, or broadcast; Blog, live-blog, or post video of; This presentation. Provided that: You attribute the work to its author and respect the rights and licenses associated with its components.

3. Neil Saunders Brian Kelly Harry Collins Tim O’Reilly Michael Nielsen Jen Dodd Greg Wilson Timo Hannay Maxine Clarke Jenny Rohn Ricardo Vidal Paulo Nuin Jenny Hale Peter Murray-Rust Deepak Singh Jon Udell Tim O’Reilly David Crotty Rafael Sidi Richard Akerman Jean-Claude Bradley Mike Ellis Liz Lyons Andy Powell Gavin Baker Peter Suber Victor Henning Sabine Hossenfelder Flickr Google Steve Wilson Andrew Milsted Frank Norman Dave de Roure Jeremy Frey John Cumbers John Cumbers Bill Flanagan ISIS LSS Group Lakshmi Shastry Catherine Jones ISIS Computing Group STFC Plausible Accuracy John Dupuis Chad Orzel Ken Shankland Martyn Bull Iain Emsley Jonathan Gray Rufus Pollock Clay Shirky Kevin Kelly Gavin Bell Shirley Wu Euan Adie Richard Curry Ian Mulvaney Jamie McQuay Atilla Csordas Pawel Szcsesny Gabriel Cavalli Matt Wood Tim Hubbard Duncan Hull Richard Grant Branwen Hide PLoS Friendfeed Bora Zivkovic Peter Binfield John Wilbanks Kaitlin Thaney The BioGang Tony Williams Egon Willighagen Martin Fenner Yaroslav Nikolaev Jon Eisen Michael Eisen Richard Akerman Jeremiah Faith Michael Barton Lee Smolin Garret Lisi Victoria Stodden Helen Berman Simon Coles Tony Hey Noel Gorelick Jon Tansley Benjamin Good Dorothea Salo Paul Walk Mitch Waldrop Björn Brembs Rich Apodaca Lorie LeJeune Bill Hooker Pedro Beltrao Mat Todd SciFoo 2008 campers Stephen Brenner

4. What is the web good for?

5. Publishing... http://flickr.com/photos/94549193@N00/3329968159/

6. ...subscribing... http://www.flickr.com/photos/orinrobertjohn/170352038 CC-BY-SA

7. ...subscribing... http://www.flickr.com/photos/alui0000/2324784482 CC-BY-SA

8. ...syndicate... ...remix... ...mashup... http://www.boingboing.net/2008/01/08/useless-beautiful-ma.html CC-BY-NC

9. (Micro)Publish Aggregate (subscribe) Syndicate (embed) Remix (re-purpose) Collaborate

10. Scientists need to...? http://commons.wikimedia.org/wiki/File:Snowscientist.JPG CC-BY

11. ...publish, subscribe...

12. ...syndicate... http://commons.wikimedia.org/wiki/File:CRC_Handbook_of_Tables_for_Organic_Compound_Identification.jpg Public Domain

13. ...remix... http://www.flickr.com/photos/lofaesofa/394290399 CC-BY

14. So far, so good right?

15. ...validate... http://www.flickr.com/photos/argonne/3465398655 CC-BY

17. ...we’re covered then?

18. No

19. Dead. Broken. Disconnected.

20. Links make the web go round http://opte.org/maps/ CC-BY-NC

21. Make science less like this... http://www.flickr.com/photos/creativecommons/1586727124/ CC-BY

22. ...and more like this http://upload.wikimedia.org/wikipedia/commons/e/ef/Network_representation_of_brain_connectivity.JPG CC-BY

23. Fragments of science Loosely coupled Tightly wired

24. What is a fragment of science?

25. Too big...

26. Too small? Not wired up. http://twitter.com/MarsPhoenix/status/839088619

27. http://biolab.isis.rl.ac.uk/projects/blog/

30. Procedure Experiment Analysis Physical objects Digital objects Laboratory procedures Computational procedures Material(s) Sample(s) Data Data

31. Automatic Blogging by Machines

32. A web of objects...

33. A web of objects...

34. A web of objects... ...and the process that connects them

35. ...but not semantic

36. Tagging goes some way... ...but how to enforce tagging?

37. Templates create a virtuous circle [table] [row] Lane[col]Sample[col]ul [/row] … [row] 4[col] [[Dna:%]] [col] [[box]] [/row] … [/table] [[Section>Procedure]] [[Procedure_Type>electrophoresis_agarose]] [[Sandpit_group>DrexelDemo]]

38. Self assembling ontology? Sequence ontology: SO:0000696 “oligo” SO:0000155 “plasmid” ...but... SO:0000006 “PCR product” or SO:0000412 “rest. fragment”? Mixing up of process of production and material type?

39. Time Material Material Material Procedure Analysis Procedure Procedure Analysis Material Procedure Data Data Data Data Data Data Sample Sample Sample Sample Sample Sample Sample

40. Time Material Material Material Procedure Analysis Procedure Procedure Analysis Material Procedure Data Data Data Data Data Data Sample Sample Sample Sample Sample Sample Sample

41. Distribute, don’t control... ...let someone else do the heavy lifting.

45. Can distribution work in practice?

46. http://onschallenge.wikispaces.com/Exp026

47. http://tinyurl.com/ons-challenge-spreadsheet

48. http://oru.edu/cccda/sl/descriptorspace/ds.php

49. http://oru.edu/cccda/sl/descriptorspace/ds.php

50. http://slurl.com/secondlife/Drexel/165/178/24

51. Time Data Data Data Data Data Data Sample Material Material Material Procedure Analysis Analysis Sample Sample Sample Sample Sample Sample Material Procedure Procedure Procedure

52. Time Data Data Data Data Data Data Sample Material Material Material Procedure Analysis Analysis Sample Sample Sample Sample Sample Sample Material Procedure Procedure Procedure Samples can be offloaded...

53. Time Data Data Data Data Data Data Sample Material Material Material Procedure Analysis Analysis Sample Sample Sample Sample Sample Sample Material Procedure Procedure Procedure Samples can be offloaded... LIMS, Database, Blog, Wiki, Spreadsheet

54. Time Data Data Data Data Data Data Sample Material Material Material Procedure Analysis Analysis Sample Sample Sample Sample Sample Sample Material Procedure Procedure Procedure Procedures are just documents…

55. What are we left with?

56. Time Data Data Data Data Data Data Sample Material Material Material Procedure Analysis Analysis Sample Sample Sample Sample Sample Sample Material Procedure Procedure Procedure

57. Time

58. A feed of links between resources Time

59. So the web-native lab record is...

60. Distributed

61. Re-uses available services

62. A (semantic) feed of relationships

63. Semantic creates UI issues

64. One last key point...

65. Realistically, the current mainstream response to these ideas looks like…

68. And if the cited objects are freely available on the web?

70. Research impact = Google PageRank

71. High PageRank = Wired into the network

72. =

73. Available

74. And available means...

75. http://flickr.com/photos/virtualsugar/316200555/ CC-BY