Blogs Logs Pods: Smart Labs


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The design, development and use of semantic electronic laboratory notebooks and Blog based systems in smart laboratories

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Blogs Logs Pods: Smart Labs

  1. 1. Logs, Blogs and Pods Smart Electronic Laboratory Notebooks e-Research Open Meeting 2009 Reading Jeremy G. Frey School of Chemistry University of Southampton
  2. 2. Talk <ul><li>Laboratory Notebooks </li></ul><ul><li>Laboratory BlogBooks </li></ul><ul><li>Instruments and Blogjects </li></ul><ul><li>Semantic Blogs </li></ul>
  3. 3. “ The internet wasn't created for mockery! It was created so scientists from different universities could share datasets....” Simpson, H. The Simpsons (2005), Eds. Groening, M., Brooks, J.L. & Simon, S., Series 16, Episode 8, Original air date (US) 06-Feb-2005.
  4. 4. The Comb e Chem Project <ul><li>‘ End to End’ linking </li></ul><ul><ul><li>Data (life-)cycle </li></ul></ul><ul><li>Do things ‘right’ at the start </li></ul><ul><ul><li>Make sure the metadata is of high quality </li></ul></ul><ul><ul><li>Record properly at source in Digital Form </li></ul></ul><ul><li>Extensive provenance </li></ul><ul><ul><li>[email_address] </li></ul></ul><ul><li>The Chemistry Lab </li></ul><ul><ul><li>People & Machines working together </li></ul></ul>
  5. 5. The Data Explosion Exponential growth The future overwhelms the past, but the past must not be lost PDB deposited structures CCDC deposited structures
  6. 6. Chemists and programming <ul><li>Many Chemists think that they can program! </li></ul>You still use FORTRAN!! What about that! His brain uses old vacuum tubes
  7. 7. Typical laboratory conversations If only I knew exactly how she did this experiments I know all this supplementary information could be useful but will people really remember the format? Is it worth all the hassle? I wish I could get the numbers from this graph - the pdf is not much use. I wish I had recorded things at the start the way I do now…..
  8. 8. Some problems are due to the lack of information recorded at the time, others are due to loss of information over time. Supervisors and Managers I am sure we collected that information a few years ago… The details should be in her lab book….. Can you read what it says here….? Can you find the files of data that were used to make the plot?
  9. 9. Faraday’s laboratory notebooks are also remarkable in the amount of detail that they give about the design and setting up of experiments, interspersed with comments about their outcome and thoughts of a more philosophical kind. All are couched in plain language, with many vivid phrases of delightful spontaneity…. Peter Day, ‘The Philosopher’s Tree: A Selection of Michael Faraday’s Writings’
  10. 10. Mixture of text, images, plans, data
  11. 11. Electronic Laboratory Notebooks Permanent, documented and primary record of laboratory observations
  12. 12. If you are caught using the “ scrap of paper” technique, your improperly recorded data may be confiscated by your TA Observations are never collected on note pads, filter paper or other temporary paper for later transfer into a notebook
  13. 13. Attach Date Cut and Paste
  14. 14. Cross reference Ontology and Folksonomy Folksonomy (also known as collaborative tagging, social classification, social indexing, and social tagging) Provenance, Probity and Priority
  15. 15. Discussions
  16. 16. BUT – the data needs to be recorded somewhere! The data only lives if connected to the laboratory notebook to provide the context. This link while essential is often fragile.
  17. 17. Electronic Laboratory Notebooks
  18. 18. He is charged with expressing contempt for meta-data meta Key is to make recording of the metadata easy and as automated as possible
  19. 19. COSHH Leverage off things we already have to do “ We have a cunning plan”
  20. 21. Smart Tea Project - User Centred Design, Design by Analogy to ensure the correct information is captured simply and easily.
  21. 22. The Two Interfaces Planning and Review Implementation
  22. 23. Procedure
  23. 24. Into the Lab!
  24. 25. Into the Lab!
  25. 27. Plans <ul><li>Plans in advance are useful </li></ul><ul><li>This is the way things are supposed to be done </li></ul><ul><li>The Plan provides a digital context so increases the value of planning </li></ul><ul><li>Key to our ‘Smart Lab’ approach…. </li></ul><ul><li>But is it the best way? </li></ul>
  26. 28. Laboratory “Blogs” <ul><li>Laboratory notebook is a Blog </li></ul><ul><li>Encourage and facilitate collaboration </li></ul><ul><li>Flexible </li></ul><ul><li>Need a data repositories behind the B log </li></ul><ul><ul><li>R4L </li></ul></ul><ul><ul><li>E-Bank </li></ul></ul>
  27. 29. Implementation of e-lab book <ul><li>Blog based format </li></ul><ul><li>Purpose built engine </li></ul><ul><li>Fully flexible system with arbitrary metadata </li></ul><ul><li>Full record of changes (not currently easily accessible) </li></ul> / “Bio Blogs” Discussion
  28. 30. Implementation of e-lab book <ul><li>One post, one item approach </li></ul><ul><li>Procedures can be tracked back to starting materials (or forwards to products) by clicking through </li></ul><ul><li>Aim to ultimately be interpretable by machine and human </li></ul>
  29. 31. Templates
  30. 32. LIVECOP LINK <METADATA> <TITLE>album09 - jrh4880_19_competent_transformation_from_ligation</TITLE> <SIZE_X>1300</SIZE_X> <SIZE_Y>1026</SIZE_Y> <THUMB_SRC> </THUMB_SRC> <PREVIEW_SRC> </PREVIEW_SRC> <PICTURE_URL> </PICTURE_URL> </METADATA>
  31. 33. Link to objects
  32. 34. Issues <ul><li>The Physical World </li></ul><ul><li>Safety documentation </li></ul><ul><li>Patent/IP – sign-off </li></ul><ul><li>Trust </li></ul><ul><li>Will computers survive in the laboratory? </li></ul>Remember we do have a physical world to keep in sync
  33. 36.   19 June 2008 10:32   / Journal publication Test Data RESULTS! Conference reports Grant Applications Analysis Management Time Line View
  34. 37. An rdf graph of posts and links between them rendered using Welkin ( Sortase Experiment Map of the X-Ray Blog (comments not shown)
  35. 39. Environment <ul><li>Automatically record as much of the laboratory environment as possible </li></ul><ul><li>Blog for the day </li></ul>
  36. 40. Pub-Sub systems provide the flexible & extensible approach to distribution of real time laboratory monitoring & archiving Smart Laboratory Spaces
  37. 41. “ I just realized, Howard, that everything in this apartment is more sophisticated than we are”
  38. 42. Blog-jects <ul><li>Equipment become first class members of the web </li></ul><ul><li>Interacts well with Pub-Sub as items are attached to topics, topics relate the Bog items </li></ul><ul><li>With automation this evolves to a two-way communication </li></ul><ul><li>Everything has a network connection – research equipment will catch up with the fridge & other commodity goods </li></ul>
  39. 43. Blog-jects <ul><li>Equipment become first class members of the web </li></ul><ul><li>Interacts well with Pub-Sub as items are attached to topics, topics relate the Bog items </li></ul><ul><li>With automation this evolves to a two-way communication </li></ul><ul><li>Live Copy essential </li></ul>
  40. 44. Lab environment data and experimental output linked
  41. 45. Comments and Annotation A picture worth a thousand words! Chemists like to sketch!
  42. 47. Can we have both the web 2.0 Blog style and the Semantics of the ELN? YES!
  43. 49. Simple Experiment Ontology
  44. 54. Impact on researchers <ul><li>Higher Quality Record </li></ul><ul><li>Easier Collaboration </li></ul><ul><li>Improved planning </li></ul><ul><li>Improved discussions </li></ul><ul><li>Efficiency gain in production of presentations/reports </li></ul><ul><li>Change the nature of Professor/Student interactions </li></ul>
  45. 55. Influence on Meetings and Discussions <ul><li>Enable geographically / temporally separated discussions </li></ul><ul><li>Meeting preparation much less of an imposition </li></ul><ul><li>Posted material is discussed, comparison with older materials is easy </li></ul><ul><li>Change from ‘can I look at your data’ to ‘have you seen my blog post’ </li></ul>
  46. 57. Growing need for the global (virtual) equivalent of the “Tea Room”
  47. 58. Separating Data from Interpretations: A crystallography example Underlying data Intellect & Interpretation
  48. 59. Access to ALL underlying data eBank & eCrystals
  49. 60. Information Providers Information Consumers These are the same people – if we can ‘talk’ to ourselves efficiently over time then that is a good start to be able to ‘talk’ to others
  50. 63. Thanks <ul><li>RC UK, EPSRC, JISC for funding </li></ul><ul><li>Colleagues and Students from the Schools of Chemistry, Electronics & Computer Science, Mathematics </li></ul><ul><li>IBM, Microsoft </li></ul><ul><li> </li></ul><ul><li> </li></ul><ul><li> </li></ul>
  51. 64. Excerpted from the Onion : The Recording Industry Association of America announced Tuesday that it will be taking legal action against anyone discovered telling friends, acquaintances, or associates about new songs, artists, or albums. Data Sharing &quot;We are merely exercising our right to defend our intellectual properties from unauthorized peer-to-peer notification of the existence of copyrighted material.&quot; A daring daylight raid of copyright material ACS
  52. 65. Validation <ul><li>Increasing the value of data </li></ul><ul><li>How to bring all the necessary information together to enable appropriate validation </li></ul><ul><li>Increasingly difficult & expensive to achieve </li></ul>Need provenance and context otherwise just a collection of items