Eln Jisc Mrc 18dec07 Nsb

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Presentation to IT managers from MRC Dec 2007

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  • Eln Jisc Mrc 18dec07 Nsb

    1. 1. Electronic Lab Notebooks at the Centre for Ecology & Hydrology Nicolas Bertrand, Environmental Informatics e-Science Consultant
    2. 2. Overview • Centre for Ecology and Hydrology • Lab books • Issues • Opportunities • Trial • Lessons learned • Future Direction
    3. 3. Centre for Ecology & Hydrology
    4. 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. 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. 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. 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. 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. 9. What is a lab book? • Hard bound • Diary • (Index) • Page numbers • Chronological • (Carbon copies) • Sketches / diagrams • Text • Raw data • Counter signature
    10. 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. 11. Examples
    12. 12. Opportunities • Searching • Archival • Sharing • Openness • Auditing • Version Control • Accessibility • Data integration / analysis • Compliance • Data reuse
    13. 13. Context Knowledge People and Context Information Rules and Context Data
    14. 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. 15. The Trial • Web diary (a.k.a. Blog or weblog) • Confluence (wiki & blog)
    16. 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. 17. Confluence Features (continued)
    18. 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. 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. 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. 21. In the lab Digital Pens upload Digital lab book
    22. 22. Diagrams Gliffy Confluence plugin (http://www.gliffy.com/)
    23. 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. 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. 25. Questions?

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