Introducing an Electronic Lab Notebook (ELN)

Dave Mason

Slidedeck @ http://pcwww.liv.ac.uk/~dnmason/eln.html
(Use 'm' for menu and arrow keys to navigate)

  • Why use an ELN?
  • Wordpress
  • Live Demo
  • Easily Searchable
  • Fewer books / folders to store
  • Can be backed-up
  • Legible and standardised
  • Media are embedded (cf. printed, cut, glued)
  • Collaboration / Surveillance / Protocol Sharing
  • Less work to implement best practice (sign-off, edits, version control &c)

Image credit: Steve Royle

  • Paid Commercial solutions (eg. Evernote, LabFolder, LabGuru, Studies)
  • Free Commercial solutions (eg. Shared Dropbox)
  • Bespoke Open Source solutions (eg. Wiki, Blog, custom platform)

Lots of considerations: Cost (finance and time), IT support, learning curve, backups, hackability, data access, data ownership

Steve Royle's Blog detailing his move to an ELN:

https://quantixed.wordpress.com/2017/04/25/the-soft-bulletin-electronic-lab-notebooks

Follow up with the technical details:

https://quantixed.wordpress.com/2017/04/27/notes-to-the-future

Documenting our setup:

https://postacquisition.wordpress.com/2017/10/17/more-notes-to-the-future

Links available on menu (hit 'm')

Big advantages of WordPress as an ELN

  • Established platform
  • Open Source: can be installed locally (as many times as you like)
  • Highly modular: themes, plugins, hooks
  • No more page budgeting for multi-day experiments
  • Integrated Comment System
  • Built in Version Control
  • Embed or attach media (jpg,pdf,doc,xls, OMERO iFrame?). Hyperlinks!
  • Record experimental metadata at the equipment and access in the office (no cross-contamination!)
Three main types of page:
  1. Static pages
  2. List pages
  3. Content pages
Three main types of page:
  1. Static pages
  2. List pages
  3. Content pages
Three main types of page:
  1. Static pages
  2. List pages
  3. Content pages

Categories and tags help to bring together related posts.

Typeface, font style, colour, lists and formatting are available, plus pre-formatted styles


  • Easy Footnotes:
    [note]This is the text to appear in the footnote[/note]
  • MathJax-LaTeX (LangRef):
    [latex]c=\sqrt{a^2+b^2}[/latex]

Content Templates

  • Allow discussion of experiments and protocols
  • Can link to other posts ("I tried this and found something different / a better way / new antibody etc")
  • Kudos!
  • Supervisor sign-off (esp wrt project students as comments are date stamped)

Authentication is controlled through the University active directory (MWS).

Each group has a separate site on the multisite network.

Access to each site is controlled though AD security groups
(Administered through a web browser)

Group leaders can administer their own groups

Most users will be 'Authors' with the following permissions:

You can:

  • Write posts
  • Edit posts
  • Upload media
  • View and comment on other posts
  • Fully manage tags
  • Add posts to categories

You cannot:

  • Delete posts
  • Edit others' posts
  • Edit or delete Categories
  • Administer the platform
    (eg. change themes, plugins &c)

Group leaders are 'Editors' with some additional roles (eg. category management, editing the welcome page).

Wordpress has built-in version control. All revisions are saved

  • Data Loss/Hardware failure
    - VM platform /w Daily backups (and testing!)
  • Access
    - Onsite only (or via Apps Anywhere)
  • Mobility
    - Migrate database / PDF of user's entire 'lab book'
  • Trust Issues
    - Multisite superadmin has global access
  • You tell me???

Discussion points from presentation 2017-09-29
(Sée / Lévy Groups)

  • Users should have the ability to create categories
    - Split opinions as to whether this is a good idea. One option is to include a SuperAuthor role that can manage categories.
  • Policy for titles
    - Coded titles (eg. DNM2017_001) are good for labelling physical media, but user-friendly titles make finding pages easier. Left to the individual lab to implement rules.
  • Double work if your notebook is lab-resident?
    - Fair point: if your notebook is lab-resident you will end up having to transcribe notes twice (what about a lab-resident tablet/workstation?). Alternative solution is to use both systems. Lab notes then analysis/opinion/quants recorded in ELN.
  • Better Search
    - The default search doesn't let you specifically search Author, Cat, Tag, Date, text, although this is bound to exist as a plugin.