1. Richard Grant Mat Todd Hide Plausible AccuracyPedro BeltraoJohn Branwen Rich Apodaca Dupuis Neil Saunders Steve Wilson Simon Coles Noel Tony Hey Pawel SzcsesnyRichard AkermanGorelickDave de RoureJon Tim OReilly Victoria Stodden Jeremy FreyISIS LSS GroupUdellJean-Claude Bradley Jeremiah FaithMartyn Bull Michael Barton John CumbersClay ShirkyBoraDavid CrottyHelenEgon WillighagenBrian Kelly Tony Williams Tim OReilly Berman Zivkovic Maxine ClarkeAndrew Michael NielsenFrank MitchMartin Fenner MilstedJenny Rohn NormanWaldrop WilsonGregYaroslav Nikolaev Iain Emsley Rafael Sidi Lee Smolin Lorie LeJeune JonathanHookerBill Timo Hannay GrayKen Shankland Paulo NuinDeepak Singh Shirley Wu Liz Lyons PLoS STFC Friendfeed Peter Binfield Benjamin Good Dorothea SaloPeter Murray-Rust Richard AkermanJen DoddChad Orzel Lakshmi Shastry ISIS Computing Group Jon Eisen Jenny Hale ciFoo 2008 Flanagan Bill Matt Wood Michael Eisen Jon TansleyVictor HenningGoogle Bjrn Brembs campers Rufus Pollock JohnTIM HUBBARD Gavin Bell Andy PowellHarry CollinsWilbanksMike EllisGarret LisiDUNCAN HULL Euan AdiePeter SuberGavin Baker The BioGang Sabine Hossenfelder Paul WalkFlickrKevin KellyKaitlin Thaney Richard Curry Atilla Csordas Ian Mulvaney

2. Capturing Process In silico, in the lab, and all the messy in betweens 3. Laboratory ComputationalproceduresproceduresProcedure ExperimentAnalysis DataData Material(s) Sample(s) Physical objectsDigital objects 4. http://www.ickr.com/photos/halfchinese/113968722 CC-BY 5. Data is dynamic... http://www.ickr.com/photos/idletype/282855293/ CC-BY 6. Inspiration from coding best practiceRepositories for storage/backup Strong record of who and when Roll-back, diffs, and reversionTesting as part of the process Scripting for solid replication 7. Working independently... http://www.ickr.com/photos/tswicegood/3233621766/ CC-BY-SA 8. ...data integration http://www.ickr.com/photos/tbisaacs/3087193160/ CC-BY 9. ...but commits are freetext 10. DVCS systems can provide who, when, what and differences between versionsBut it doesnt provide the relationships between objects... 11. Have a good provenance trail... http://www.ickr.com/photos/a4gpa/195354385 CC-BY-SA 12. ...but not a good map of how that relates to everything elsehttp://www.ickr.com/photos/normanbleventhalmapcenter/2674855383 CC-BY 13. If we have the map......if we capture the connections 14. http://is.gd/thVr 15. ...and on to a semantic web of data 16. ...but what about in here? http://www.ickr.com/photos/mararie/2151361243 CC-BY-SA 17. Lab book as a journal... http://www.ickr.com/photos/nbachiyski/2186228572 CC-BY 18. Blog as journal... 19. Description, date categorisation, objects, identity, accessibility......not of much interest to most people 20. http://biolab.isis.rl.ac.uk/projects/blog/ 21. http://is.gd/thMB 22. http://is.gd/thMB 23. Laboratory ComputationalproceduresproceduresProcedure ExperimentAnalysis DataData Material(s) Sample(s) Physical objectsDigital objects 24. A web of objects... 25. A web of objects... 26. A web of objects......and the processthat connects them 27. ...but still not semantic 28. Tagging goes some way... ...but how to enforce tagging? 29. 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]] 30. 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]] 31. 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]] 32. 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? 33. We need a robust ontology or controlled vocabulary for experiments... ...but with that in hand http://www.ickr.com/photos/peterkaminski/5444915 CC-BY 34. We can build a semantic web of objects ...and the processes that connect them 35. Linked open data and linked open objectshttp://is.gd/thVr 36. Building for the future? http://www.ickr.com/photos/blahowers/1382374610 CC-BY-SA 37. Capture it at source... ...in context http://ickr.com/photos/jason_burmeister/2053139930 CC-BY 38. Capture as much as possible automatically Slide adapted from original by Simon Coles 39. In silico capture the process step by step... http://www.ickr.com/photos/stevoarnold/2787234769 CC-BY 40. In silico capture the process step by step... ...one way or another thesemantics can be baked in http://www.ickr.com/photos/stevoarnold/2787234769 CC-BY 41. In the lab capture each object as it is created... 42. In the lab capture each object as it is created......and capture the plan andtrack execution step by step 43. Plan =Template = Minimal Information Foo = Semantics 44. Data repositories......as easy to use as Flickr 45. More natural interfaces... http://www.ickr.com/photos/bekathwia/2910518374 CC-BY-SA 46. More natural interfaces......to capture and communicate http://www.ickr.com/photos/bekathwia/2910518374 CC-BY-SA 47. ...Pages from a project need to be linked in a 3D web of relevance...I want to be able to annotate a...collaborator's work by drawing on it...as I would write on [their] whiteboard...Mat Todd http://is.gd/yVQKhttp://www.ickr.com/photos/andypowe11/2938538086 CC-BY 48. But who (and what) can you trust? http://www.ickr.com/photos/joi/2941559903 CC-BY 49. We trust people......not objects 50. A semantic social web of objects (and data,and process and...) 51. (Some of) thepeople I trust... ...in dierent ways and for dierent things 52. http://friendfeed.com 53. Code Data Sample Process http://friendfeed.com/lists/isisbiolab 54. Data nds the data, then people nd people.Jeff Jonas/Jon Udell via Deepak Singh 55. Its the objects that are the centre of the social interactionand not the people 56. But that can only workif these objects are... 57. http://ickr.com/photos/virtualsugar/316200555/ CC-BY 58. Connected research changes the playing eld 59. Connected research changes the playing eld...availability of resources key 60. We need to capture objects as they are created... 61. We need to capture objects as they are created... ...and to capture their relationships 62. The rest we can buildbit by bit as we go 63. Communicate rst, standardize second.Jean-Claude Bradley