9 minutes reading time (1706 words)

Electronic Lab Notebooks - should you go “e”?

Authors: Paula Maria Martinez Lavanchy (ORCID), Technical University of Denmark and Asger Væring Larsen (ORCID), University Library of Southern Denmark

A lab notebook is one of the most elementary records of research – at least in some disciplines. In a lab notebook, the researcher records all kinds of project related information – from hypothesis to results of experiments. The way a paper lab notebook is structured differs from discipline to discipline and from lab to lab. But, it often serves as the most important piece of documentation of the researchers’ work. It means that lab notebooks are crucial for ensuring accountability and reproducibility of research, and they are often needed to enable the re-usability of data.

As more and more research is based on digital data, a digital or electronic lab notebook (ELN) is often preferred. Methods for creating a digital version of a lab notebook includes a multitude of tools that have been developed for this specific purpose, but according to Santiago Schnell, some labs are just using Word or WordPress.

So, what’s all the hubbub about? Should a researcher switch from paper to electronic lab notebooks (ELN’s)? Why? And where to get started? This blogpost intends to highlight the advantages of switching from paper notebooks to an electronic version of it, and to point researchers towards different initiatives and case studies that can facilitate the decision of adopting an ELN.

The switch from an analogue to a digital technology is not always easy. Think about everything else that has seen a digital counterpart suddenly appear – cameras, storage media, typewriters and so on. There are many advantages to digital technology in general and some specific for this particular purpose – but also downsides. We will touch upon some of them in this post.

Additionally, choosing the right ELN can be difficult and time-consuming as they differ in features and price, but there is a lot of published advice that you can turn to. This Nature article by Roberta Kwok is the latest piece of advice about how to choose a suitable tool.
Foto: Neil Conway, https://flic.kr/p/9z8dWi, CC–BY

Pros & Cons

Generally speaking, tools for research need to support the increased volume of data being collected in digital form and the growing trends in research collaboration. When using an ELN, features like findability, sharing, legibility of writing (part of the basic interoperability of data) and archiving are obvious, making them useful tools for implementing some of the key elements of the FAIR data principles into your research workflows.

ELN’s can ease the recording of the experimental procedures since they provide the possibility to use templates and facilitate reusing your own or others’ protocols, which can save you a lot of time. They also help you to have a better overview of your experiments and projects.

When you have learned how to use an ELN, it is relatively fast and easy to use, and the possibility to share and reuse content makes it an attractive alternative to paper notebooks. It is also possible to link from the ELN to relevant data files and external resources related to your experiments, improving the reproducibility, transparency and collaboration within research. An electronic notebook can thus be an important part of conducting transparent and reproducible research, because edits to the content are logged and time-stamped. The research process is also easier to record in an ELN compared to a paper log.

There are disadvantages though. An ELN does not allow for hand–written notes or drawings, which are necessary in some research. You would need to take a picture of those and upload an image file. Many of the available ELN’s are commercial products, which means an additional cost for a research group or institution. In some cases, commercial providers offer free versions, but with reduced functionalities like limited number of users, storage space or file size. Most commercial ELN’s offer the possibility to extract data but only in PDF format, which does not allow you to move your data to another product. Normally, Open Source ELN’s can help to solve issues of cost and extractability of data, but they might offer less features (e.g. ELOG, eLABFTW) than some commercial solutions and you should make sure that there is a strong community supporting the development and updates of the software.
Foto: Tony Hirst, https://flic.kr/p/8G78CK, CC–BY

Which tool to choose?

A number of institutions have done comparison tests of different tools. In 2017, the Gurdon Institute tested 30 different tools and compared features – see their conclusions here. They have listed a number of relevant questions to consider when choosing an ELN.

Also in 2017, Harvard conducted a comprehensive study into ELN’s and have created a matrix comparing 29 tools on 50 different parameters. Their results can be seen here.

In 2018, the University of Delft held a workshop on Digital Notebooks. Presentations from that workshop are available in Zenodo and a report on the workshop can be found here. All of these investigations offer their experience openly for everyone to use, and share potential pros and cons of the available tools. It is apparent that the choice of tool depends on several different user needs like: ability to share protocols, compatibility with other tools, cloud storage, cost reduction, an Open Source solution, or capability of dictation/voice input.

The Technical University of Denmark (DTU) – lessons learned from ELN pilot cases

In 2015, the RDM group at DTU Library established the DTU ELN–network. The purposes of this network are: to provide information about available ELN’s tools, facilitate the exchange of experiences between those already using an ELN and newcomers, and investigate and evaluate relevant ELN software together with research groups. For the latter, three pilot projects were established: the radioecology group from DTU Nutech, the polymer group from DTU Chemical Engineering and the Centre for Oil and Gas – DTU who was looking for an ELN solution for the whole department. There were several and diverse motivations for these groups to join the pilot, but three of them were shared among them: prevent the loss of documentation and data, keep track of the progress of projects and a have better overview of experimental data, and finally, increase and facilitate collaborations within the group or the department.

At the beginning of the project, the three pilot groups were presented with a list of common features that ELN’s can provide and they were asked to classify them as ‘must have’, ‘nice to have’ and ‘not needed’. This exercise helped them to focus their evaluation on those features that were relevant to their workflows to avoid getting lost in too many choices. There were differences between the three pilots along the whole process. The number of ELN’s tested varied from one ELN tool to three. Only two groups selected an ELN tool and decided to move forward to the implementation phase. Interestingly, they chose different ELN’s even though their main research activities are both within the field of chemistry.

There are several lessons learned from these pilots. First, different research groups can have very different needs for the documentation of experimental data. Therefore, taking the time to investigate the research workflows is very important in deciding if an ELN can meet those needs before entering into a trial phase. Secondly, the selection and implementation process of an ELN can be very different even among groups with similar research activities. The sentence ‘one size does not fit all’ becomes especially true when talking about ELN’s. For example, from the two groups that selected an ELN, one required an integration with a sample management system to link their experiments to specific samples, while the other group considered it more important to get an ELN with a feature that allowed them to draw chemical structures.

Thirdly, the central RDM support at DTU are far from being able to recommend one single solution to all researchers. However, researchers greatly appreciated the guidance on what to consider when selecting an ELN. So providing support in the selection and implementation process and facilitating the exchange of knowledge between research groups using an ELN, is equally important. The DTU pilot cases were part of the ‘eLabBook’ project funded by the Danish National RDM forum (in Danish). The University of Copenhagen and Aarhus University also participated. You can find a detailed description of all the cases part of the ‘eLabBook’project on the eScience – vidensportalen website.

The openness of research

Due to the digital nature of ELN’s, they are an obvious choice of tool to be used for conducting Open Science. Open Science is all about sharing – not only the more traditional products of science and research like publications, but also research (data) documentation. Opening up science has many benefits: increasing collaborations, improving transparency, honesty and accountability, improving reproducibility of research (good documentation is crucial for this) which results in increase of impact of research for both science and society. Transparency and honesty are prerequisites for building and improving societal trust in science and research.

There is a growing trend for institutions, funders and publishers to include more and more requirements regarding Open Science (e.g. Open Access and Open Data/FAIR data) in their policies. And, although this carries a price of investment and it requires some cultural changes, there are more benefits than downsides.

An ELN can be a powerful tool to accomplish a more open way of doing science and research, and researchers from different fields are starting to share their laboratory notebooks online. An example is  Dr. Rachel Harding who does research in Huntington’s disease and shares real-time experimental data in its rawest form. Also, the Structural Genomics Consortium (SGC), as part of its ‘Extreme Open Science Initiative’ has shared the laboratory notebooks of researchers from different SGC labs aiming at reducing the duplication of work, improving collaborations and to accelerate the discovery of new medicines.

Additional web resources

Simon Bongers: The Electronic Lab Notebook in 2018: A comprehensive guide

Yasemin Velden: “Digital Notebooks – Productivity Tools for Researchers”


Valerie McCutcheon: “Research Notebooks”


Acknowledgements:

A huge thank you to The RDM Task Force in OpenAIRE and especially to Valerie McCutcheon, University of Glasgow for valuable input to this post. Greatly appreciated.

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Tuesday, 22 October 2019

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