It’s been a long time since I wrote about electronic laboratory notebooks (ELNs). My set up has changed significantly and I now use Notion, so I thought I’d describe why and how. Firstly, some things I know about notebooks:

1. There are both commercial science ELN solutions, and more cutting edge general software
2. Free solutions do not have a good business model and may disappear
3. Nothing is more important than a good exit strategy
4. Different people want very different things, I only speak for me

What is important for me?

I want to enjoy my experience and I want to be able to collaborate. Old-fashioned software is ugly, feature-poor, and frustrating. I want a better experience. Secondly, I want the people working with me to be able to easily share their lab book with me, that is an important part of supervision and collaboration.

I have chosen Notion, here’s why

Easy to use modern wiki

• I want a wiki based documentation system and looked around very extensively including at a lot of specific ELN software. I often found specific ELN software to be 10 years out of date (old and ugly) or else to follow a specific architecture not fitting well with how I wanted to work (constrained).
• Notion is free for small use and charges for larger teams, meaning I have been able to battle test it before committing. If you sign up with an academic email address you get most things for free.
• Notion allows use of templates for different types of entry, and sharing of entries with other users. It is based around databases (tables) with markdown pages as text entry. I really like working in markdown, allowing me to do everything at the keyboard. You don’t have to use markdown, it looks like any word processor. The powerful database architecture has been a revelation, and I can’t imagine using a file and folder system again.
• In Notion search actually works. I’m looking at you Microsoft.

Very powerful features and likely to persist

• I really value that Notion is cutting edge software with incredibly powerful features. I can’t do justice to the features here, but YouTube is full of explainer videos. I like documenting research in my ELN, its a modern work environment.
• Notion is available on most platforms including mobile and web, and synchronises very well.
• Sharing is possible with others and generally works well
• Databases for ELNs are more useful and transformative than you think they are. I was once an unbeliever, but I will never go back to a system that is not organised around databases
• Persistence. Notion is one of the most modern and powerful wiki knowledge management systems. It is very popular with the business community and has a very large user base with a clear financial model (meaning it is likely to persist). Persistence is important to avoid software decay and disappearance.

Data export is possible

All software has problems with it’s exit strategy in my experience. I chose Evernote years ago because it promised a great exit strategy to take my notes anywhere. That never transpired in practice, it’s very clunky. Notion will export in many different file formats which preserves the record (essential), but this isn’t well tested by me yet.
Data is stored in the cloud, not locally, which is both good and bad. I would recommend a strategy to export and archive completed projects

Very briefly, how I use Notion

• I have a main ELN database of my entries, each having metadata such as creation date and modification date. Entries are annotated with tags such as “PCR” or “blast” or “pipelines”.
• Each also has a project assignment (eg “NERC grant X”). I can of course filter and search appropriately.
• The entries themselves are markdown documents based on an ELN template I created. This includes overall aim, methods, results, next actions. You can of course have different templates for different types of work or just use a blank page. Doing a PCR, choose your PCR template, add sample and primer names into a pre-filled PCR recipe, later insert the gel photo and link to the next ELN entry “Sequencing”.
• My students have similar systems but their databases are shared with me so that I can browse their work, and comment if needed.
• My strategy is that an entry is one chunk of work and Projects link them. So my entries might only be one hour to one day of work, not a large experiment. Large experiments are projects, or named parts of projects.

Projects, Categories and Tags

Each distinct work topic is a Project. These could be general and exploratory “battle-testing database scripts” or a funded project “NERC root-knot nematodes” or small and specific “assembly of student E.coli minION data”. Any topic with an end is a Project. My ELN template has a field to associate it with a Project. Projects can have their own ELN landing pages and templates.
Categories are more general than projects and include areas like “sequencing” or “metagenomics”, “C. elegans” or “workflows”. They help if you want to find entries taking an approach used across projects.
Tags are for small specific things used across projects: PCR, blast, python, conda. These are useful for finding recent entries.

The database of all ELN entries can be filtered to show views of projects categories and tags. Saved filters (e.g. ‘installation’) are useful to pull up key areas, and then the number of entries is small enough to see the thing I want. Saved filters, very usefully, can be tabs in your table view of the database. This could be “2023 records” or “ongoing” or “paused waiting input” for example.

Organisation using “Projects” is very useful

• A Projects page is a landing page for information on all aspects of a particular research project
• It usually contains a database of all ELN entries assigned to that project. Assign ELN items to Projects to see only those entries on the Project page.
• Papers, videos, software, documents can be tagged as part of this project and appear in a project resources database, on the main Project page
• I label Projects as in progress, paused, completed, archived so that only those currently in progress come to the foreground. I also have a “crazy ideas I just thought of” category, populating a database of Projects that will likely never work.

Links

Notion main page https://www.notion.so/product

Notion ELN example page, yes you can publish to the web for collaborators https://davelunt.notion.site/Database-2023-test-150e057046438025aa35f98c29f13276