Electronic Lab Books Nicolas Bertrand, Environmental Informatics e-Science Consultant

Overview Lab books in Science Issues Opportunities Trial Lessons learned Future Direction

Lab books in Science

Issues

Opportunities

Trial

Lessons learned

Future Direction

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

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

What is a lab book? Hard bound Diary (Index) Page numbers Chronological (Carbon copies) Sketches / diagrams Text Raw data Counter signature

Hard bound

Diary

(Index)

Page numbers

Chronological

(Carbon copies)

Sketches / diagrams

Text

Raw data

Counter signature

Issues Not readily accessible Not searchable (Not readable) Easy to loose Archival, annotation, QA, reviewal and referencing of lab book material is at the very least inconsistent

Not readily accessible

Not searchable

(Not readable)

Easy to loose

Archival, annotation, QA, reviewal and referencing of lab book material is at the very least inconsistent

Examples

Opportunities Searching Archival Sharing Openness Auditing Version Control Accessibility

Searching

Archival

Sharing

Openness

Auditing

Version Control

Accessibility

Electronic lab notebook: 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.

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.

The Trial Web diary (a.k.a. Blog or weblog) Confluence (wiki & blog)

Web diary

(a.k.a. Blog or

weblog)

Confluence (wiki & blog)

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 WYSIWYG interface Powerful tools for structuring and searching your wiki Professional features such as PDF export

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 WYSIWYG interface

Powerful tools for structuring and searching your wiki

Professional features such as PDF export

Confluence Features (continued)

Confluence at CEH Environmental Informatics Countryside Survey Countryside Survey Steering group Countryside Survey Surveyors NERC Strategy Group High Performance Computing and e-Science Technical Advisory Group Trobit CCS EHFI Bids Informatics Liaison Network ISFG Mixture Toxicity edcat Electronic lab book trial Electronic lab book discussion wiki STATISTICS 701 pages 5447 versions 249 pages with attachments 1347 pages with attachments 1555 attachment versions 41 pages with comments 123 comments 52 Authors

Environmental Informatics

Countryside Survey

Countryside Survey Steering group

Countryside Survey Surveyors

NERC Strategy Group

High Performance Computing and e-Science Technical Advisory Group

Trobit

CCS

EHFI Bids

Informatics Liaison Network

ISFG

Mixture Toxicity

edcat

Electronic lab book trial

Electronic lab book discussion wiki

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

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

Lack of support for sketching / diagrams

Not quite there as a replacement for a paper lab book (lab environment / field work)

No offline editing

In the lab Digital Pens Digital lab book upload

Diagrams Gliffy Confluence plugin (http://www.gliffy.com/)

Benefits of using Confluence 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)

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)

What's next? Confluence has the potential to be fulfill many of the requirements Lacks in some areas Extend the trial Small scale digital pen trial (field and lab) Confluence diagram plugin

Confluence has the potential to be fulfill many of the requirements

Lacks in some areas

Extend the trial

Small scale digital pen trial (field and lab)

Confluence diagram plugin