Presentation to IT managers from MRC Dec 2007

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?