Web Native Laboratory Record

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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/

Web Native Laboratory Record

  1. 1. A Web Native Research Record Applying the best of the web to the laboratory notebook
  2. 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. 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. 4. What is the web good for?
  5. 5. Publishing... http://flickr.com/photos/94549193@N00/3329968159/
  6. 6. ...subscribing... http://www.flickr.com/photos/orinrobertjohn/170352038 CC-BY-SA
  7. 7. ...subscribing... http://www.flickr.com/photos/alui0000/2324784482 CC-BY-SA
  8. 8. ...syndicate... ...remix... ...mashup... http://www.boingboing.net/2008/01/08/useless-beautiful-ma.html CC-BY-NC
  9. 9. (Micro)Publish Aggregate (subscribe) Syndicate (embed) Remix (re-purpose) Collaborate
  10. 10. Scientists need to...? http://commons.wikimedia.org/wiki/File:Snowscientist.JPG CC-BY
  11. 11. ...publish, subscribe...
  12. 12. ...syndicate... http://commons.wikimedia.org/wiki/File:CRC_Handbook_of_Tables_for_Organic_Compound_Identification.jpg Public Domain
  13. 13. ...remix... http://www.flickr.com/photos/lofaesofa/394290399 CC-BY
  14. 14. So far, so good right?
  15. 15. ...validate... http://www.flickr.com/photos/argonne/3465398655 CC-BY
  16. 17. ...we’re covered then?
  17. 18. No
  18. 19. Dead. Broken. Disconnected.
  19. 20. Links make the web go round http://opte.org/maps/ CC-BY-NC
  20. 21. Make science less like this... http://www.flickr.com/photos/creativecommons/1586727124/ CC-BY
  21. 22. ...and more like this http://upload.wikimedia.org/wikipedia/commons/e/ef/Network_representation_of_brain_connectivity.JPG CC-BY
  22. 23. Fragments of science Loosely coupled Tightly wired
  23. 24. What is a fragment of science?
  24. 25. Too big...
  25. 26. Too small? Not wired up. http://twitter.com/MarsPhoenix/status/839088619
  26. 27. http://biolab.isis.rl.ac.uk/projects/blog/
  27. 30. Procedure Experiment Analysis Physical objects Digital objects Laboratory procedures Computational procedures Material(s) Sample(s) Data Data
  28. 31. Automatic Blogging by Machines
  29. 32. A web of objects...
  30. 33. A web of objects...
  31. 34. A web of objects... ...and the process that connects them
  32. 35. ...but not semantic
  33. 36. Tagging goes some way... ...but how to enforce tagging?
  34. 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]]
  35. 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?
  36. 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
  37. 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
  38. 41. Distribute, don’t control... ...let someone else do the heavy lifting.
  39. 45. Can distribution work in practice?
  40. 46. http://onschallenge.wikispaces.com/Exp026
  41. 47. http://tinyurl.com/ons-challenge-spreadsheet
  42. 48. http://oru.edu/cccda/sl/descriptorspace/ds.php
  43. 49. http://oru.edu/cccda/sl/descriptorspace/ds.php
  44. 50. http://slurl.com/secondlife/Drexel/165/178/24
  45. 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
  46. 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...
  47. 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
  48. 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…
  49. 55. What are we left with?
  50. 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
  51. 57. Time
  52. 58. A feed of links between resources Time
  53. 59. So the web-native lab record is...
  54. 60. Distributed
  55. 61. Re-uses available services
  56. 62. A (semantic) feed of relationships
  57. 63. Semantic creates UI issues
  58. 64. One last key point...
  59. 65. Realistically, the current mainstream response to these ideas looks like…
  60. 68. And if the cited objects are freely available on the web?
  61. 70. Research impact = Google PageRank
  62. 71. High PageRank = Wired into the network
  63. 72. =
  64. 73. Available
  65. 74. And available means...
  66. 75. http://flickr.com/photos/virtualsugar/316200555/ CC-BY

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