Eln Jisc Mrc 18dec07 Nsb
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Eln Jisc Mrc 18dec07 Nsb

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Presentation to IT managers from MRC Dec 2007

Presentation to IT managers from MRC Dec 2007

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Transcript

  • 1. Electronic Lab Notebooks at the Centre for Ecology & Hydrology Nicolas Bertrand, Environmental Informatics e-Science Consultant
  • 2. Overview • Centre for Ecology and Hydrology • Lab books • Issues • Opportunities • Trial • Lessons learned • Future Direction
  • 3. Centre for Ecology & Hydrology
  • 4. CEH Large-scale Long-term Data CEH Monitoring Networks e.g. • National River Flow Archive Location of CEH Sites • Heavy Metals Monitoring Network • Biological Records Centre • Environmental Change Network • Predatory Birds Monitoring Scheme
  • 5. National River Flow Archive • Network for 1300 gauging stations • Provides monthly summaries of hydrological trends • Provides a baseline for comparison for ‘extreme events’ UK annual runoff trends, 1972 - 1999
  • 6. Heavy Metals Monitoring Network • Site network collecting data on 5 heavy metals weekly or monthly • Data modelled to provide national-scale results • Results disseminated for UK Government monitoring
  • 7. Biological Record Centre • Records of species occurrence across UK collected since 1964 • Over 15 million records for over 12000 species • Support for UK National Biodiversity Network
  • 8. Scientific Lab books • Day to day account of scientific research • Essential information about planning, designing and running of scientific experiments • A component of Quality Assurance • Communication tool between project leader and scientist
  • 9. What is a lab book? • Hard bound • Diary • (Index) • Page numbers • Chronological • (Carbon copies) • Sketches / diagrams • Text • Raw data • Counter signature
  • 10. Issues • Not readily accessible • Not searchable • (Not readable) • Easy to loose • Most data is digital • Much effort • At a corporate level, Archival, annotation, QA, review and referencing of lab book material has been inconsistent
  • 11. Examples
  • 12. Opportunities • Searching • Archival • Sharing • Openness • Auditing • Version Control • Accessibility • Data integration / analysis • Compliance • Data reuse
  • 13. Context Knowledge People and Context Information Rules and Context Data
  • 14. Electronic lab notebook trial: call for volunteers • Maintain in parallel a paper based lab notebook and a personal web-based lab book for a period of 3 Weeks. • Provide regular feedback to build a desired feature list to define requirements for an electronic lab notebook system for CEH.
  • 15. The Trial • Web diary (a.k.a. Blog or weblog) • Confluence (wiki & blog)
  • 16. More about Confluence • Commercial Java-based blog + wiki • Open API for extension and integration • Source code available for developers • Built on Open source technologies • Enterprise security • Attractive, user-friendly interface • Powerful tools for structuring and searching your labbook • Professional features such as PDF export
  • 17. Confluence Features (continued)
  • 18. Confluence at CEH • Environmental Informatics • Countryside Survey • Countryside Survey Steering group • Countryside Survey Surveyors • High Performance Computing and e-Science Technical Advisory Group • Trobit • CCS • EHFI Bids • Informatics Liaison Network 400 Users • ISFG ~50% users are external Growth by word of mouth • Mixture Toxicity • edcat • Electronic lab book trials • Electronic lab book discussion wiki
  • 19. Volunteers Microbiologist Chemist (x3) QA Manager Head of site Virologist Hydrologist (x2) Lanscape Ecologist GIS Climate Modeller (x2) Long term monitoring Field site
  • 20. Issues with the trial • Lack of support for sketching / diagrams • Not quite there as a replacement for a paper lab book (lab environment / field work) • No offline editing
  • 21. In the lab Digital Pens upload Digital lab book
  • 22. Diagrams Gliffy Confluence plugin (http://www.gliffy.com/)
  • 23. Benefits of using wiki & blog • Most of the benefits sought at inception were achieved • Data sharing • Rich access control (closed, completely to groups, individuals) • Version control • Searchable • Attach diagrams, documents • Add semantics (tags/labels) • Can “subscribe” to lab books (via RSS or email notification) • Others can comment (effective peer review) • Ability to structure Lab book information (in addition to provision of diary function) • Content can be locked, exported (archival)
  • 24. What's next? • wiki & blog represent a good generic lab notebook • Electronic lab notebooks are the missing link in an informatics / information management strategy • Proper project to evaluate and decide on way forward • Bring analysis and data integration within Lab book environment • Project and change management key to sucess
  • 25. Questions?