The Soft Bulletin: Electronic Lab Notebooks

We finally took the plunge and adopted electronic lab notebook (ELNs) for the lab. This short post describes our choice of software. I will write another post about how it’s going, how I set it up and other technical details.

tl;dr we are using WordPress as our ELN.

First, so you can understand my wishlist of requirements for the perfect ELN.

1. Easy-to-use. Allow adding pictures and notes easily.
2. Versioning (ability to check edits and audit changes)
3. Backup and data security
4. Ability to export and go elsewhere if required
5. Free or low cost
6. Integration with existing lab systems if possible
7. Open software, future development
8. Clarity over who owns the software, who owns the data, and where the information is stored
9. Can be deployed for the entire lab

There are many ELN software solutions available, but actually very few fulfil all of those requirements. So narrowing down the options was quite straightforward in the end. Here is the path I went down.

Evernote

I have used Evernote as my ELN for over a year. I don’t do labwork these days, but I make notes when doing computer programming, data analysis and writing papers. I also use it for personal stuff. I like it a lot, but Evernote is not an ELN solution for a whole lab. First, there is an issue over people using it for work and for personal stuff. How do we archive their lab documents without accessing other data? How do we pay for it? What happens when they leave? These sorts of issues prevent the use of many of the available ELN software packages, for a whole lab. I think many ELN software packages would work well for individuals, but I wanted something to deploy for the whole lab. For example, so that I can easily search and find stuff long after the lab member has left and not have to go into different packages to do this.

OneNote

The next most obvious solution is OneNote from Microsoft. Our University provides free access to this package and so using it would get around any pricing problems. Each lab member could use it with their University identity, separating any problems with work/life. It has some nice features (shared by Evernote) such as photographing documents/whiteboards etc and saving them straight to notes. I know several individuals (not whole labs) using this as their ELN. I’m not a big fan of running Microsoft software on Macs and we are completely Apple native in the lab. Even so, OneNote was a promising solution.

I also looked into several other software packages:

• RSpace (Research Space)
• Benchling
• Findings
• DEVONthink
• Apple’s own Notes feature
• A few other things, including ELNs that are packaged as part of lab databasing (e.g. LabCollector).

I liked the sound of RSpace, but it wasn’t clear to me who they were, why they wanted to offer a free ELN service and where they would store our data and what they might want to do with it. Last year, the scare that Evernote were going to snoop on users’ data made me realise that when it came to our ELNs – we had to host the data. I didn’t want to trust a company to do this. I also didn’t want to rely on a company to:

• continue to do what we sign up for, e.g. provide a free software
• keep updating the software, e.g.  so that macOS updates don’t kill it
• not sell up to an evil company
• do something else that I didn’t agree with.

As I saw it, this left one option: self-hosting and not only that, there were only two possibilities.

Use a wiki

This is – in many ways – my preferred solution. Wikis have been going for years and they are widely used. I set one up and made a lab notebook entry. It was great. I could edit it and edits were timestamped. It looked OK (but not amazing). There were possibilities to add tables, links etc. However, I thought that doing the code to make an entry would be a challenge for some people in the lab. I know that wikis are everywhere and that editing them is simple, but I kept thinking of the project student that comes to the lab for a short project. They need to read papers to figure out their project, they have to learn to clone/run gels/image cells/whatever AND then they also have to learn to write in a wiki? Just to keep a log of what they are doing? For just a short stay? I could see this meaning that the ELN gets neglected and things didn’t get documented.

I know other labs are using a wiki as an ELN and they do it successfully. It is possible, but I don’t think it would work for us. I also needed to entice people in the lab to convert them from using paper lab notebooks. This meant something that looked nice.

Use WordPress

This option I did not take seriously at first. A colleague told me two years ago that WordPress would be the best platform for an ELN, and I smiled politely. I write this blog on a wordpress dot com platform, but somehow didn’t consider it as an ELN option. After looking for alternatives that we could self-host, it slowly dawned on me that WordPress (a self-hosted installation) actually meets all of the requirements for an ELN.

1. It’s easy-to-use. My father, who is in his 70s, edits a website using WordPress as a platform. So any person working in the lab should be able to do it.
2. Versioning. You can see edits and roll back changes if required. Not as granular as wiki but still good.
3. Backup and data security. I will cover our exact specification in a future post. Our ELN is internal and can’t be accessed from outside the University. We have backup and it is pretty secure. Obviously, self-hosting means that if we have a technical problem, we have to fix it. Although I could move it to new hardware very quickly.
4. Ability to export and go elsewhere if required. It is simple to pack up an xml and move to another platform. The ubiquity of WordPress means that this will always be the case.
5. Free or low cost. WordPress is free and you can have as many users as you like! The hardware has a cost, but we have that hardware anyway.
6. Integration with existing lab systems if possible. We use naming conventions for people’s lab book entries and experiments. Moving to WordPress makes this more formal. Direct links to the primary data on our lab server are possible (not necessarily true of other ELN software).
7. Open software, future development. Again WordPress is ubiquitous and so there are options for themes and plugins to help make it a good ELN. We can also do some development if needed. There is a large community, meaning tweaking the installation is easy to do.
8. Clarity over who owns the software, who owns the data, and where the information is stored. It’s installed on our machines and so we don’t have to worry about this.
9. It can be deployed for the whole lab. Details in the follow-up post.

It also looks good and has a more up-to-date feel to it than a wiki. A screenshot of an innocuous lab notebook entry is shown to the right. I’ve blurred out some details of our more exciting experiments.

It’s early days. I started by getting the newer people in the lab to convert. Anyone who had only a few months left in the lab was excused from using the new system. I’m happy with the way it looks and how it works. We’ll see how it works out.

The main benefits for me are readability and being able to look at what people are doing. I’m looking forward to being able to search back through the entries, as this can be a serious timesuck with paper lab notebooks.

Edit 2017-04-26T07:28:43Z After posting this yesterday a few other suggestions came through that you might want to consider.

Labfolder, I had actually looked at this and it seems good but at 10 euros per user per month, I thought it was too expensive. I get that good software solutions have a cost and am not against paying for good software. I’d prefer a one-off cost (well, of course I’d prefer free!).

Mary Elting alerted me to Shawn Douglas’s lektor-based ELN. Again this ticks all of the boxes I mentioned above.

Manuel Théry suggested ELab. Again, I hadn’t seen this and it looks like it meets the criteria.

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The Soft Bulletin is an occasional series of posts about software choices in research. The name comes from The Flaming Lips LP of the same name.