Moving from Paper to Electronic Lab Notebooks

By jeltsch on Tue, 07/26/2016 - 13:16
Paper or Pad?

Electronic lab notebooks (ELN) are the future. While this statement appears self-evident, it is not clear what software will establish itself and which ones will disappear. When I first checked the ELN market about three years ago, there were only a handful of solutions. Now there are already maybe about a hundred different software companies that try to cash in on the trend. And what is even more worrisome is the fact that the list of vendors contains already about 20 abandoned products...

Thus, settling on a software is a serious decision for a lab and even more so for a whole institute. Many points need to be taken into consideration. Just to mention a few of them:

- How sure is it, that the software is available and supported in 10 years? If the company disappears, your data might as well. All vendors will claim that your data is safe. You should be realistic given the widespread deception of customers and authorities by companies. Just think about VW...

- What is the upfront investment and what are the running costs? If they charge you for storage space, the price might initially be low, but don't underestimate how much data you will accumulate with all the new high res imaging and sequencing technologies. Once you are doing superresolution, you easily can gather a many GB each week. E.g. SciNote includes 100 GB of storage for 2 teams, which can fill up within a few weeks depending what type of research you are doing. I was trying to figure out how to buy storage beyond 100 GB, but I could not figure out how. I hope that the usability of their ELN is not on the same level...

- How free is your data? Can you easily (and in an automated fashion in regular intervals) pull out your data if you need to? In what format can you get your data? If it is only PDF or Word files, just forget about it. You should get a real database dump that can be used to populate other systems. I would not trust any company to tell me ahead of time that they will go belly-up soon and that I should rescue my data...

- Where are the data stored physically? This determines e.g. what law the data falls under and who has access to it. How much can you trust a small company overseas to keep your data private and secure? Let's remind everybody of the data breaches that affected Sony, Linkedin, IRS, T Mobile, UPS, JP Morgan Chase... Some vendors offer in-house hosting, but the pricing seems to be too high for many academic labs to make this a viable alternative.

- Open Source seems to be a solution to may of these problems. However, with diminishing computing infrastructure support from the university, the maintenance requirements of such a system need to be very low in order to make this feasible.

- If it is marketed as "free", what do they mean with free? Often, the "free" offering is not sufficient for any serious work and hence misleading. "Free" as in "free beer" is also not enough... Many labs need also the freedom to adapt the software to their specific needs, which excludes proprietary solutions without public APIs.

In my lab we have been testing a few of the available solutions. Our emphasis was on open source solutions since only Open Source solutions make it easy to test the software extensively. So far we have tried:

  • LabGuru (http://www.labguru.com/electronic-lab-notebook): We tried LabGuru two years ago and it was not yet fully usable. However, LabGuru has improved their offerings by quite a bit since then. At the time, we also did not like that the service was not located on-site. We are still not sure about the long-term viability of the company. In-house hosting inside the University of Helsinki network would have been possible, but out of the question due to financial reasons (I wonder why? It should be cheaper since the vendor doesn't need to provide the hardware. Obviously, there are lots of problems with this setup due to the proprietary nature of the software). Considering that there are also anecdotal reports about data loss ("I would give it a qualified thumbs up, as long as you are willing to suffer with occasional data loss.") and the less than transparent marketing behavior (no info about the costs on their website), we probably will again pass.
  • SciNote (http://scinote.net/): This was a kick-starter project. I liked it but the other lab members didn't so much. Since they will use it much more often then me, they get to decide. However, I still think that it has potential and is constantly improving. Developed with Ruby on Rails. UPDATE (October 9th, 2016): There are still many problems with SciNote, including the inability to upload images and other files (version 1.3, tested with up-to-date Firefox). These problems concern the very basic functionality of an ELN and I am wondering how well and robustly written the code is because it takes so long to fix them. We will test SciNote again after the 1.4 update, but in the good tradition of open source, software versions with that much work ahead should have a zero in front of the point and not a one.
  • ELabFTW (http://www.elabftw.net/): This is a very neat one. Easy to install, easy to use. In addition, it is programmed in php/mysql and hence I do understand its inner workings and can fix problems easily. However, it has one drawback: Collaborative editing is not possible. This was by design according to its lead developer, but imho, there needs to be more flexibility. We often share the responsibility in one experiment among several people and all of them need "edit" access to the relevant experimental description. The development team is also quite small and hence its future development difficult to predict. UPDATE (November 5th, 2016): According to its lead developer, INRIA (the French computer science research department) and the Institut Curie (a cancer research institute and hospital) have chosen this one for their researchers and others will probably follow. INRIA will also fund a full-time developer, which lessens our worries about its future development.
  • OpenBIS LIMS/ELN (https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+ELN-LIMS): This is my favorite despite it being written in Java and uses postgresql (neither of which I know, hence my inital reservation). It's a very extensive and extensible suite and the Electronic Lab Notebook/Laboratory Information Management System (ELN/LIMS) is just one of its plugins (the others being High Content Screening, Proteomics, Metabolomics and Deep Sequencing). It's developed by a team at the ETH Zürich. I tried the Virtualbox image, which the developers provide and then decided to attempt a real install (details of this experience will be the topic of a future post). UPDATE (November 5th, 2016): My people do not like this one because of its steep learning curve and it being not so much geared towards small laboratories.

Needless to say, a few other ELN software solutions have appeared since we decided to move from paper notebook to an ELN. Some look promising (below a list of examples). However, while they all solve the problem of information retrieval, none handles well the information entry. In this respect, the paper notebook is still infinitely more flexible and straightforward.

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