Electronic Lab Notebooks

The search for the perfect ELN

01/15/16: Views on this post are increasing lately. Please note that this article was written in 2013 and things have surely changed. My previous lab has settled on LabGuru + Benchling. In my current lab I’m writing my notes in OneNote and using Benchling for plasmid.
Feel free to drop a comment here for requesting testing of ELNs not listed here.

I study on my iPad, I take notes on my Mac. I hardly ever needed pen and paper. When I first started doing something close to research last year, I didn’t even think of using a notebook to keep record of what I was doing.

But many people do. In my group everyone had their personal notebook. When someone leaves, the book stays in the lab for future reference so nothing is lost.
Imagine having to go through someone else’s handwritten notes to find out what the concentration of that reagent was. Many researchers probably did multiple times. Today it feels like an unnecessary hassle.
There are now services that try to make the researcher’s life easier, very originally called Electronic Lab Notebooks (ELNs).

In our lab, we use a wiki as the knowledge base, so we already had an electronic foundation. Our boss decided to take this a step further, and to make the jump to a full-fledged ELN, assigning me the task to find some good candidates. In this post I’m sharing my thoughts during the process and I hope it could be of help to others looking for the same stuff.
(Updated to Nov 2013. As of Mar 2015 many products have matured. I will update this post when I have some time)

What I was looking for

First thing first. My naive idea of a good ELN was that of a service that:
(i) would allow me to organize research stuff based on projects, (ii) to log experiments and data files, (iii) to share commonly used knowledge-base info and (iv) to reference “stuff” from other pages from a page. It would have a simple text editor with basic features (à-la Wordpress) and a task manager. Plasmid creation tools and inventory support would also be mandatory.

I started digging.

Legacy Players

The likes of Perkin-Elmer and Agilent offer ELNs. I’ll call them legacy players. Actually, I didn’t even bother to look at them. Just by looking at their websites you can understand they’re not serious about this. It’s 2013: if you’re not offering me a free-trial — he**, even some decent screenshots — how am I going to understand what your product is? You actually need to call their representatives to have the products shown. And there’s no mention about pricing. The worst thing is that if you look at that tiney-tiny screenshots, the actual software looks like 1998 Windows — it most likely is.
There might be some serious power underneath, but this stuff would have been ok 10 years ago. Don’t bother.
(UPDATE: Perkin-Elmer aquired a service called Elements. This is now their ELN. I was contacted by them and offered a tour and trial of the service. I would file it under the cool players. It’s easy to use, give it a look.)

Me-Too Players

There’s a whole another class of ELN services trying to take it a step above the legacy players. And oh boy, we have free trials! We have nice websites! We have actual feature lists! It feels like being out of the Dark Age again.
I liked eCAT and LabArchives.

eCAT lets you keep notebooks, inventory, everything else you might need, but I found the interface a bit confusing. I have to admit that sometimes I care too much about the interface and the design of a piece of software. Still, I’m getting more and more convinced that — especially in a work-related situation — the software has to be clean, simple (but powerful) and hassle-free, otherwise you’ll just get frustrated. If this is the case, one should just stick to the classic paper notebook. I’m not saying I didn’t like eCAT, it just didn’t click for me.

LabArchives is basically a folder in the cloud (just like Dropbox) with an “inline” text-editor that supports some science-related widgets (and custom widgets) and a permission manager for the folders themselves. It’s really simple, but I think it might serve the purpose if the folder hierarchy, the files and the permission system is well organized. Unfortunately, it lacks inventory support. LabArchives would substitute our Wiki, but wouldn’t add much to it. Nice, but not what we’re looking for.

Cool Players

Now we get to the cool stuff. These services take some cues from social networks, sport a nice design and feature powerful tools. We’re looking at Quartzy, Colwiz and LabGuru. Plus I added Evernote Business.

Quartzy is a popular service, but there’s no notebook section (they say it will be added in some future update). It also lacks a good way to enter plasmid information, and that’s a deal breaker for us. Just for inventory.

Colwiz, developed from some Oxford guys, stands for Collective Wisdom. It’s a good tool to organize research life, but it’s more a GTD system with literature support than a ELN.

LabGuru is the most forward looking service. It boasts a ton of features, and it’s been built to be a complete all-around tool for a scientific research group. You can create Projects, set milestones, record experiments, assign tasks to people. There’s a very detailed inventory section, there’s plasmid support. It’s surely the most promising. At first glance, LabGuru seems like a no-brainer, but I’m not without reserves. There are some flaws here and there; the design is inconsistent, confusing and cluttered especially in the typography department.

Evernote is a great service. It’s a throw-in-everything bucket we all know and love. There’s a Business version of Evernote, allowing for shared notebooks and many other features. I had two main issues: (i) you cannot nest notebook more than one level down (meaning you cannot have a folder inside another folder, basically), and (ii) the text editor doesn’t allow for image resizing (you put an image in and it goes automatically to it’s actual size in pixels –you can resize it before uploading, but that’s not ideal). The latter could be solved by importing formatted pdf files made with a word processor –or using Markdown, as I prefer– but that’s inconvenient.

There’s still not a completely mature service. Labguru is one that comes very close to it, but it needs some refinement.
Its feature list is impressing, but I feel like there’s a decent learning curve to master it. However, I have to admit the support is great, and being Nature Group behind the project, one can rest assured it will be further developed –but you never know these days.

Team Management Tools

As none of the services I listed completely satisfied me, I started looking into the team management tools department. My rationale was that maybe a good team management/GTD service, combined with some other service for inventory purposes (like Quartzy), a tool for plasmids (take a look at Benchling), and a system to keep the notebooks online (we could use LabArchives just for notebooks, or a Dropbox folder, or even a Wordpress or Tumblr website) would suffice for our needs.
A single service that does everything kind-of-well or a couple of different services that do only some things, but do what they do better? That’s not so easy to answer, it comes down to convenience versus functionality.
The ones I selected here were Basecamp, TeamBox 4, Asana and Apollo.

Basecamp is probably the most well known. Everyone in the software development world uses Basecamp, it seems. It’s clean, pretty straightforward, but I find the latest version to be pretty scarce in the feature list. There are more powerful alternatives.

Asana is built by two Facebook founders. It’s minimal and clean –a very promising service– but again, it’s not much more than a group task manager. (UPDATE: Asana is now a full-fledge team management solution, and it’s free.)

Apollo and Teambox 4 are very similar. They are more powerful than the others, but they still manage to keep clean design –usally, more features mean more clutter. Being complete GTD tools, you’ll find everything you might need.
Teambox looked and felt better to me. In a way, task lists and task comments reminded the Project/Milestones/Experiments hierarchy of LabGuru, which I really liked. There’s also Dropbox and Google Drive integration for common files, a Message board, a Notes section. All this features might make this the ideal tool for the hybrid solution I was mentioning before. To make things even more interesting, you can add any external service to the Teambox interface (it basically embeds another web page in the interface). This feature is still in beta, but I could add Quartzy and Benchling to our Teambox dashboard, letting us keep everything we need into the same system. It was not all bells and whistles, though. This features employs — I believe — AJAX to load the pages, and it’s sloooow.

A Word on Pricing and Backup

I never mentioned pricing. I didn’t really look into pricing when trying to find the best solution.
LabArchives, LabGuru and Teambox 4 were the only three that passed my initial review, so let’s look at the pricing of those.
LabArchives comes at $99 per user per year; LabGuru comes at $120 per user per year; Teambox is $60 per user per year.
I think LabArchives is priced too high for what it offers. The other two seem fair to me.

Another important consideration is data backup and portability.
Since the idea is to put (important) lab data into these services, it’s best to not take any chances. In case of company failure or, Galaxy forbid, disaster, what happens to the data? The best services would allow us to download all the data from their service, preferably in a readable format (I mean, not in some encoded wtf way), and then eventually reupload it to the service if needed (just like Wordpress, for example).
Our current lab website is a Doku wiki, so we can simply download the root folder to a local machine and have a secure backup (A backup is never secure enough) a hand. Teambox offers these functionalities, but using it in a hybrid system, we would be relying to other companies too. It’s not so simple.
Labguru allows to export each page in printable way (.pdf) or in .csv format, which is not readable. Also, you can’t automatically import it back.
None of them completely satisfied me.

The Winner Is

All things considered, I failed in my search. I did not find the perfect ELN. Between Teambox and LabGuru, I was really split. Teambox is beautiful: it makes me want to use it. But using it is not so streamlined. LabGuru is ugly instead, but it’s built for research.
In the end we went with LabGuru. Honestly, considering what I originally wanted from an ELN, it’s the one that comes closer. I believe ELNs will be a hit in the near future, and LabGuru –right now– is the best choice.

(UPDATE: As of March 2015 we’re still using LabGuru. The interface is improved, as well as stability. They constantly add new features. For plasmids we use Benchling.)