Electronic Lab Notebooks: Hope or Hype?

The lab notebook has long been hallowed as the fundamental unit of scientific research. From the cuneiform tablets to meticulous scrolls, written records of scientific discoveries have played a key role in human innovation. Because of this importance, before I switched to an electronic lab notebook, I would often wake up in a cold sweat, dreaming that fire, flood, or calamity had befallen the lab overnight and all of my treasured data and lab notebook had been forever lost. But in the wonderful age of cloud computing and digital documents, my fears are assuaged. In case of emergency, my trusty electronic lab notebook has my back.

What is an electronic lab notebook?

An electronic lab notebook is a complete and semi-digital set of documents that are stored on a device and often also in the cloud. Entries could be entirely stored in an app (either made for lab notebooks or a generic note-taking app) or exported in a generic file format (i.e. .pdf) and stored in your normal file system (i.e. Finder/Documents). These files, whether in an app or in your own filing system, are typically backed up in the cloud. This increases security (in case of loss/destruction/theft of your device) and also allows you to access your entries from other devices (such as at home or on the go from your phone). I will go into detail about how I manage each of these aspects in this blog post.

I use my iPad with an Apple Pencil as my electronic lab notebook. I keep my lab notebook entries in Microsoft OneNote. I export completed entries as PDFs and save them on my computer in a Box Sync folder, which saves them on the cloud. When I am doing sterile lab work, I store my iPad and Apple Pencil in Ziplock freezer/sandwich bags that I spray with ethanol.

Figure 1: My iPad and Apple Pencil in bags that can be sterilized with ethanol. You can write on the iPad with the Pencil when both are in bags!

Why keep an electronic lab notebook?

• Easy sharing between lab members and teams:
  • I am working with close collaborator who is based in New Zealand. It was very useful that they could reference my lab notebook as needed.
  • This is also helpful when overseeing undergraduate researchers. Most of my undergrads keep a semi-electronic lab notebook. In the lab, they write in a paper lab notebook and upload scanned copies to our shared Google Drive (thanks @Meg Duffy for sharing her lab’s management system in this Dynamic Ecology post). This way, I can see their progress. I add them to view my electronic lab notebook through Microsoft OneNote folder sharing so they can see my progress on the project in real time and can download relevant protocols on their own.
• Better back-up and accessibility. No more concerns about the building burning down or flooding and losing all of your data or notes–the notebook is always backed up the cloud and is accessible on any device. This has saved me a few times when my advisor emailed/texted me a quick question while I’m away from the lab and I could quickly send them a screenshot of the relevant results from my lab notebook.
• Notebook can be encrypted and password protected (if necessary): I’ll discuss security with electronic lab notebooks at length below, but with PDFs and especially in Microsoft OneNote, it’s easy to protect your work with a password, or encrypt your documents (such as with an app like Encrypto). Besides keeping my work on an encrypted server, I don’t individually lock or password protect my lab notebook because most of my lab notebooks are accessible by members on various collaborative teams.
• More features: Unlike paper lab notebooks, it’s easy to add a lot of different unique features to an electronic lab notebook. For example, I can easily embed (and write in) photos in my entries that I take as I complete an experiment. With a click of a button, I can paste plots from R, as well as link to my RMarkdown/Rproject files. I can insert PDFs and documents into my entries, as well as insert tables that auto-update from linked Excel spreadsheets. I can also search all of the text in my lab notebooks, which is nice when I’m trying to find something and forgot which entry contains the experiment.

Because everything is already online, I can easily attach lab notebook entries (and their names) to emails, calendar invites, and other project management apps I use like Todoist, Trello, and Toggl (see this blog post I wrote last year about how I use these apps to streamline my project management workflow). Because my figures and conclusions are all in one place (and digital), I can easily drag and drop figures from my lab notebook into presentations for my advisor, lab meetings, or meetings for collaborators.

I use a tablet for my electronic lab notebook, and it’s nice to have a timer, calculator, a web browser, and music source nearby.

Do I need a tablet?

No, you do NOT need a tablet to keep an electronic lab notebook. You can use all of the functionality of an electronic lab notebook by simply writing in it on your computer. However, it’s much easier to write notes in your notebook while you are doing experiments (assuming you are doing experimental work) if you have a device close to you. If you’re not into keeping your computer near you in lab, or if this isn’t safe, then scanning a paper lab notebook may be a better option.

I use a tablet for my lab notebook. I purchased a used Apple iPad with an Apple Pencil on Ebay and has been working well for the past three years. When I am wearing nitrile gloves in the lab, especially if I am working in a Biosafety Cabinet, I put my iPad in a gallon Ziplock freezer bag and my Apple Pencil in a Ziplock sandwich bag and spray both down with ethanol (see picture above). That way, I can touch them with gloves on and everything stays sterile. This seems more sterile than a paper lab notebook, I’d say! Also, music from the iPad seems louder when it is in the bag, bizarrely.

Besides tablets, a PLOS paper on electronic lab notebooks describes how some researchers have been using Apple Watches to read protocols and keep time. This seems better for biochemists and molecular biologists who are frequently using highly repetitive, timed protocols. Right now, this is too much for me, but others in my lab have an Apple Watch (although not for lab notebooks) and seem to like them. I worry about touching an Apple Watch with gloves on.

Apps for electronic lab notebooks:

There are a lot of paid options, but if you’re looking for free options here are my top suggestions (in no particular order):

1. Microsoft Word: This means saving documents on your computer as PDFs, printing them off, and signing and dating them as experiments are completed OR saving them as secure PDFs and using Adobe Acrobat Pro to sign them. It works but isn’t efficient, hard to search, and it is easy to become disorganized. I’m switching away from this. Recently, you can annotate Microsoft Word documents with an Apple Pencil, but it’s still clunky and I think that Microsoft OneNote (described in detail later) is better.
2. Google Docs: You can write and update all of your lab notebook entries in Google Docs. A nice benefit is that you can track changes easily, but I worry about how to sign and verify lab notebook entries in Google Docs. I would imagine this would work well if you’re doing highly collaborative work and for some reason don’t want to share a OneNote notebook.
3. Evernote: This free program with an optional paid subscription service has, until about 2017, was a favorite for electronic lab notebooks. It has great features like inserting documents, tables, pictures, writing in line with text, screenshots, handwriting searching (via iPad app Penultimate), and tagging for easy searching through entries.
4. Microsoft OneNote: This is what I use. OneNote is a free program if you have Microsoft 365 and has lots of great features, including allowing handwritten observations side-by-side of typed notes and protocols. You can also insert and edit Excel spreadsheets directly from within OneNote entries, which is very helpful when wrangling datasets, and OneNote has all of the features (and more) Evernote has. OneNote also has an excellent iPad app. You can see below for pictures of how I set up my lab notebook in OneNote.
5. Benchling: This is new software, free for academics, which has become increasingly popular with molecular biologists because it has some really nice native features for cloning and bioinformatics. I decided not to use this because it is web based, so I couldn’t use it in the field. It’s new and pretty buggy. Not recommended for ecologists.
6. Notability: If you’re planning on handwriting the majority of your lab notebook entries and want easily printable PDFs that auto-upload to the cloud, I’d suggest using Notability. I’m a big fan of OneNote and avoid paid apps, but several of my colleagues are big Notability fans and I wanted to include it here.

There’s a nice Nature Toolbox article outlining other considerations for choosing an electronic lab notebook here and a comparison of ELN options from Harvard Medical School here.

Backing up to the cloud:

Saving documents in most of the apps I listed above will automatically back up your digital lab notebook entries to the cloud. I would encourage you to turn on version control so you and others can track when changes are made and protect yourself against any fraud accusations. In addition to keeping version control tracking on my lab notebook entries, once an entry is finished for the day, I export it as a PDF and upload it to the cloud (in my case, a Box Sync folder), which also maintains version control on the PDF. Box is supported by my university, but any other cloud provider such as Dropbox and Google Drive work just as well.

Electronic Lab Notebook security:

As mentioned above, electronic lab notebooks have pros and cons with security. A big pro is back-up to the cloud and version control. However, in some ways, an electronic lab notebook is not as secure as a paper one. Most academic labs that don’t need to meet FDA regulations or might file for a patent don’t need this level of security, but I’ll briefly outline some additional security measures.

• Not all apps support version control: With a digital document, how do you know that an entry, note, or picture was actually taken on the day that you say and not added after the fact? The gold standard is to use version control on your lab notebook, but this is challenging for many apps that don’t have built-in version control. You can bypass this by exporting each entry to a Cloud service that has built-in version control or using Git (if you’re that kind of person).
• Getting digital signature are hard: There is a lot of different expensive electronic lab notebook software available for purchase from companies like Perkin Elmer. They are quite expensive, almost always require an internet connection for use (which makes them useless in the field), and are primarily used by companies with many employees and have patent/FDA regulations that require all lab entries be electronically signed off by a supervisor and stored on a secure server. These systems are good for large companies who have hundreds of people working on projects and need to coordinate ordering large quantities of chemicals, etc. I don’t think this is necessary for a relatively small, academic lab like ours. It’s possible that you can get one using Adobe Acrobat, but I’m not sure how this works.
• Federal reporting requirements: The FDA outlines specific lab notebook requirements (21 CFR Section 11) which are required for using lab notebooks as evidence in a patent application for “first-to-discover,” which is the new standard for US patents (this new rule is what caused the recent CRISPR patent battle). I believe that some Microsoft 365 accounts can be configured to be 21 CFR Section 11 compliant, but the entire lab needs special (and expensive) licenses. If you have to be 21 CFR Section 11 compliant, I’d recommend using a corporate lab notebook software.

How do I organize my ELN?

1. Each lab notebook entry: I write the protocol for the experiment in Microsoft Word (or sometimes directly into OneNote). Then as the experiment progresses, I write in the app (just like how you would with a paper lab notebook) with pictures and notes about the experiment. In OneNote, you can also insert PDFs, Microsoft Word, PowerPoint, and Excel documents.

Figure 2: Example lab notebook entry with photos and annotations

2. Within the app: Within the app (I use Microsoft OneNote), I organize projects into notebooks (NXX), then projects (NXX-PXX), then specific experiments (NXX-PXX-EXX) (Figure 1).

Figure 3: Electronic lab notebook organization within an app (Microsoft OneNote)

3. On my computer/cloud: I export PDFs of each lab notebook page and store them in a folder on my Box Sync folder on my computer, which automatically backs up to the cloud using version control.

Figure 4: File organization on my computer

Concluding thoughts:

Based on my experiences having used a semi-electronic lab notebook for the past three years, a tablet-based electronic lab notebook is my preferred option. However, although ELNs have lots of benefits, I don’t think an ELN is for everyone so I certainly wouldn’t recommend requiring everyone to use one.

Additional References:

1. Guerrero, S. et al. A quick guide for using Microsoft OneNote as an electronic laboratory notebook. PLOS Computational Biology 15, e1006918 (2019).
2. Guerrero, S. et al. Analysis and Implementation of an Electronic Laboratory Notebook in a Biomedical Research Institute. PLOS ONE 11, e0160428 (2016).
3. Kanza, S. et al. Electronic lab notebooks: can they replace paper? Journal of Cheminformatics 9, 31 (2017).