Ceh Conference Nsb

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Old presentation (2006!) about electronic lab notebook pilot at the Centre for Ecology and Hydrology annual conference

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Ceh Conference Nsb

  1. 1. Electronic Lab Books Nicolas Bertrand, Environmental Informatics e-Science Consultant
  2. 2. Overview <ul><li>Lab books in Science </li></ul><ul><li>Issues </li></ul><ul><li>Opportunities </li></ul><ul><li>Trial </li></ul><ul><li>Lessons learned </li></ul><ul><li>Future Direction </li></ul>
  3. 3. Scientific Lab books <ul><li>Day to day account of scientific research </li></ul><ul><li>essential information about planning, designing and running of scientific experiments </li></ul><ul><li>A component of Quality Assurance </li></ul><ul><li>Communication tool between project leader and scientist </li></ul>
  4. 4. What is a lab book? <ul><li>Hard bound </li></ul><ul><li>Diary </li></ul><ul><li>(Index) </li></ul><ul><li>Page numbers </li></ul><ul><li>Chronological </li></ul><ul><li>(Carbon copies) </li></ul><ul><li>Sketches / diagrams </li></ul><ul><li>Text </li></ul><ul><li>Raw data </li></ul><ul><li>Counter signature </li></ul>
  5. 5. Issues <ul><li>Not readily accessible </li></ul><ul><li>Not searchable </li></ul><ul><li>(Not readable) </li></ul><ul><li>Easy to loose </li></ul><ul><li>Archival, annotation, QA, reviewal and referencing of lab book material is at the very least inconsistent </li></ul>
  6. 6. Examples
  7. 7. Opportunities <ul><li>Searching </li></ul><ul><li>Archival </li></ul><ul><li>Sharing </li></ul><ul><li>Openness </li></ul><ul><li>Auditing </li></ul><ul><li>Version Control </li></ul><ul><li>Accessibility </li></ul>
  8. 8. Electronic lab notebook: call for volunteers <ul><li>Maintain in parallel a paper based lab notebook and a personal web-based lab book for a period of 3 Weeks. </li></ul><ul><li>Provide regular feedback to build a desired feature list to define requirements for an electronic lab notebook system for CEH. </li></ul>
  9. 9. The Trial <ul><li>Web diary </li></ul><ul><li>(a.k.a. Blog or </li></ul><ul><li>weblog) </li></ul><ul><li>Confluence (wiki & blog) </li></ul>
  10. 10. More about Confluence <ul><li>Commercial Java-based blog + wiki </li></ul><ul><li>Open API for extension and integration </li></ul><ul><li>Source code available for developers </li></ul><ul><li>Built on Open source technologies </li></ul><ul><li>Enterprise security </li></ul><ul><li>Attractive, user-friendly WYSIWYG interface </li></ul><ul><li>Powerful tools for structuring and searching your wiki </li></ul><ul><li>Professional features such as PDF export </li></ul>
  11. 11. Confluence Features (continued)
  12. 12. Confluence at CEH <ul><li>Environmental Informatics </li></ul><ul><li>Countryside Survey </li></ul><ul><li>Countryside Survey Steering group </li></ul><ul><li>Countryside Survey Surveyors </li></ul><ul><li>NERC Strategy Group </li></ul><ul><li>High Performance Computing and e-Science Technical Advisory Group </li></ul><ul><li>Trobit </li></ul><ul><li>CCS </li></ul><ul><li>EHFI Bids </li></ul><ul><li>Informatics Liaison Network </li></ul><ul><li>ISFG </li></ul><ul><li>Mixture Toxicity </li></ul><ul><li>edcat </li></ul><ul><li>Electronic lab book trial </li></ul><ul><li>Electronic lab book discussion wiki </li></ul>STATISTICS 701 pages 5447 versions 249 pages with attachments 1347 pages with attachments 1555 attachment versions 41 pages with comments 123 comments 52 Authors
  13. 13. Volunteers 1. Darren Sleep (QA Manager, ECP Section, Lancaster) - dsleep 2. Bob Possee (Head of Site. Virologist, Oxford) - rdpo 3. Rob Griffiths (Microbiologist, Ecologist, Oxford) - rig 4. Andrew Worgan (GIS / Organic Chemistry, Dorset) - adpw - Start date: 06 July 2006 5. Jonathan Evans (Hydrologist, Wallingforfd) - jge Start date: 24 july 2006 -- continuing to use labbook despite end of pilot 6. David Wilson (ECP, Lancaster) - drwi Start Date: 26 September 2006 7. David Williams (Field Support / Laboratory Technician, Bangor) 8. Mark Bescoby (Radiochemist, Lancaster) start date: 26 September 2006 9. Neville Llewellyn (Organic analytical chemist, Wallingford) 10. Thien Ho (Virologist, Oxford) 11. Gillian Ainsworth (Environmental Chemist, Lancaster) - Start date: 12 July 2006 12. Susan Brown (Microbiologist (amoeba), Dorset) Start date: 17 july 2006 13. Jan Dick (Landscape restoration ecologist, Edinburgh) - pulled out on 15 September 2006 14. Richard Ellis (Climate Modeller, Wallingford) Start date: 21 September 2006 continuing to use lab book despite end of pilot 15. Fai Fung (Hydrologist, Wallingford) start date: 23 September 2006
  14. 14. Issues with the trial <ul><li>Lack of support for sketching / diagrams </li></ul><ul><li>Not quite there as a replacement for a paper lab book (lab environment / field work) </li></ul><ul><li>No offline editing </li></ul>
  15. 15. In the lab Digital Pens Digital lab book upload
  16. 16. Diagrams Gliffy Confluence plugin (http://www.gliffy.com/)
  17. 17. Benefits of using Confluence <ul><li>Data sharing </li></ul><ul><li>Rich access control (closed, completely to groups, individuals) </li></ul><ul><li>Version control </li></ul><ul><li>Searchable </li></ul><ul><li>Attach diagrams, documents </li></ul><ul><li>Add semantics (tags/labels) </li></ul><ul><li>Can “subscribe” to lab books (via RSS or email notification) </li></ul><ul><li>Others can comment (effective peer review) </li></ul><ul><li>Ability to structure Lab book information (in addition to provision of diary function) </li></ul><ul><li>Content can be locked, exported (archival) </li></ul>
  18. 18. What's next? <ul><li>Confluence has the potential to be fulfill many of the requirements </li></ul><ul><li>Lacks in some areas </li></ul><ul><li>Extend the trial </li></ul><ul><li>Small scale digital pen trial (field and lab) </li></ul><ul><li>Confluence diagram plugin </li></ul>

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