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

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Neil Saunders Brian Kelly Harry Collins Tim OReilly 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 OReilly 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 Bjrn 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/170352038CC-BY-SA 7. ...subscribing... http://www.flickr.com/photos/alui0000/2324784482CC-BY-SA 8. ...syndicate... ...remix... ...mashup... http://www.boingboing.net/2008/01/08/useless-beautiful-ma.htmlCC-BY-NC 9. (Micro)Publish Aggregate (subscribe) Syndicate (embed) Remix (re-purpose) Collaborate 10. Scientists need to...? http://commons.wikimedia.org/wiki/File:Snowscientist.JPGCC-BY 11. ...publish, subscribe... 12. ...syndicate... http://commons.wikimedia.org/wiki/File:CRC_Handbook_of_Tables_for_Organic_Compound_Identification.jpgPublic Domain 13. ...remix... http://www.flickr.com/photos/lofaesofa/394290399CC-BY 14. So far, so good right? 15. ...validate... http://www.flickr.com/photos/argonne/3465398655CC-BY 16. 17. ...were 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.JPGCC-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/ 28. 29. 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, dont control... ...let someone else do the heavy lifting. 42. 43. 44. 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 66. 67. 68. And if the cited objects are freely available on the web? 69. 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