The Electronic Lab Notebook: Am I going have one?

Submitted by redoxoma on Thu, 02/28/2019 - 18:06
The electronic lab notebook

Main Article by Percíllia Oliveira and Patricia Nolasco

Communication is at the heart of science throughout all stages of work development. Ideas, evidences, experimental findings have to be shared and discussed among students or post-docs themselves and with their supervisors, as well among collaborating groups, funding agencies and in some cases the industry, long before they are externally communicated to the public. Paper laboratory notebooks have been at center stage of this scientific communication. Science starts and gains life in those pages. Science starts and gains life in those pages What is written there is fundamental documentation to provide a safe basis for assessing at any time the collection of observations, accompanied by crucial experimental details, which underlie the rite of passage of a hypothesis to results that are negative or positive, failed or successful, correctly or incorrectly interpreted, etc. But the essential element in the lab notebook is the data. Immutable and solid as they should be. From there, the results are assembled into scientific papers, go to meeting presentations, construct scientific contributions and in some cases serve as the basis for patents and turn into applications. It runs between the naïve and ironic to consider that vast implications ranging from novel worldwide research avenues to drug developments that cost millions — and directly reflect in the lives of many patients and the public in general — are based solely on the good faith that experiments in fact occurred as they are written in a lab notebook.

Thus, the lab notebook remains the crucial depository of raw scientific advances. However, human writing is not always easy to understand/interpret, the paper media is slow to write, its information is tedious to retrieve, it is environmentally unfriendly and very hard to store on a large scale basis for prolonged periods of time. Moreover, it is always possible to forget documenting crucial information. And the physical media has its intrinsic fragility. Moreover, as scientists deal with increasing volumes of data, such as in Systems Biology or Big Data, paper notebooks have indeed become inefficient and can be viewed as archaic. In addition, the increasing concerns over reproducibility of scientific experiments, as well as data manipulation, have promoted a significant upscaling in the documentation standards required from funding agencies and publications.

Can you easily find the previous data?Furthermore, from a practical standpoint, let's put ourselves into the skin of a young student or post-doc. The first thing that happens when you join a lab is to receive a book which you should take care as much as your own life, because all your work during graduation and ensuing years will be on those sheets. In the beginning, keeping the lab notebook is relatively effortless and it even seems simple. Until time starts to pass faster and faster and, maybe in one week or in 3 years, you need to replicate some experiment. Can you easily find the previous data? Are you sure this will be possible using just lab your notebook notes? Can you decipher all notes and drafts? And if something happens with your lab notebook? And why did you forget to write that small detail that has now become critical? In many cases you start to wish you were that kind of person who would take organized notes of everything at the very moment they happen. And then you may remember that everybody told you that — today more than ever — we must be quite focused to be organized and document everything we did in the lab using precise rules. And you might feel guilty and more than ever part of a huge party named… human beings.

Thus, further solutions to the lab notebook are a logical and needed step to improve the accuracy, accessibility and ability to reproduce raw scientific results. In a logical sequence of events, electronic lab notebooks (ELNs) have come up to fulfill this gap and are growing steadily. Historically, the idea of a paperless lab has been a promising development since the early 1990s.ELN will replace the way scientific information is kept It is expected that ELN will replace the way scientific information is kept, facilitating reproducibility, long-term storage and availability of experimental records across multiple devices (e.g. phones, computer, tablets) and also providing interfaces to instrumentations through integration with all digital data and images. In particular, ELNs may logically facilitate investigator adherence to best practices in data documentation. Other relevant aspects of ELN include easy data sharing and backups, search algorithms, enhanced transparency and a way to protect intellectual property by ensuring that records are properly dated and maintained. Indeed, ELNs can be very useful for knowledge management, by housing all raw research-related files (notes, data, results, graphs, images, etc) in a unique local; this provide an easy tool to browse and search through these experiments as a whole, up to years later.

Currently there is a wide range of ELNs in the market (ca.72 versions available among free and paid to use), covering different areas within Chemistry and Biology within most active knowledge domains. Furthermore, there are generic note-taking products, which have been evaluated for use as ELNs such as Evernote and Onenote. In addition, several investigators have been using cloud storage such Dropbox and GoogleDrive as well, which are reasonable options depending on the type of laboratory and data to be stored or exchanged. The best-rated ELNs available, according to a systematic search by a Life Sciences news website (Splice [7]) include SciNote, Benchling, RSpace, Docollab, LabFolder, LabArchives, Mbook Labguru and Hivebench. Also, many universities and research institutes have started to provide ELNs to their investigators, for example VIB Institute in Belgium [8]. Each lab has its own set of expectations, intentions, needs and capabilities, which will most likely never be fulfilled by a single universal ELN but may be satisfactorily addressed by one of these possibilities.

Despite the large ELN portfolio and their advantages, a number of scientific labs still prefer paper over digital technology and the majority of them are likely still handwriting on paper notebooks and continue to paste tables and gel figures on them. In some other cases, research labs are still struggling with mixed success to introduce ELNs or digital data management into their teams. These difficulties can be accounted for by a number of reasons, including: resistance or fear to give up the security blanket of paper lab notebooks; inertia to change established practices (i.e. documentation, storage data), especially in the middle of an ongoing research project; lack of information about how ELNs work; extra time needed to start learning to use ELNs; lack of encouragement and support from supervisors to the use of ELNs by their students; finally, the feeling that all is well, why change it? — even if all is not well, as we will see in the next paragraph. These points highlight the main issues about widespread adoption of ELNs. However, each lab has its own issues and challenges to introduce ELNs in the routine. In this way, there is no best preferred approach to get started. In general, however, it would be great to start addressing this issue and instigate students and post-docs to get involved in ELN practices as soon as possible. Today’s early-career researchers, undergraduates and PhD students who have grown up with digital technology, preferentially tend to embrace electronic solutions. However, adoption of ELNs demands more than just a fine technology but a change of attitude and organization. For beginning students, it would be great to adopt ELNs from the start of their projects. Nevertheless, a parallel structure to support the old ones who have to do the transition appears essential. Also, it seems important to encourage new students to try distinct ELNs to find one that better suits the needs of the lab. Another alternative is to have one person in the lab designated to set up the best tool and then introduce it to the whole team. It is important to realize that the transition from paper to ELNs is not going to happen overnight: each lab needs to establish a model. In this process, adopting a balanced integration between electronic and paper format has been considered a better approach than the sudden replacement of paper by ELNs. Perhaps, adopting cloud storage may be a useful first approach to a number of labs. Overall, some companies marketing ELNs advertise that about 15-20% working time could be saved by adoption of ELNs. This number, as far as we know, has not been validated, but could be encouraging.

During the first entrepreneurship course developed in University of São Paulo School of Medicine (September to November/2018, Prof. Flávio Grynszpan) we focused into ‘ELN world’ and, in this process, we interviewed 31 science-related individuals including PIs, post-docs, PhD and master students, technicians and associated researchers. Surprisingly, most of them (>90%) did not even know about ELNs. Even more surprisingly, contrarily to the best investigative practices, the vast majority of interviewed investigators (excluding the PIs in this case) use scratch-paper notes to record their experiments and their processes and organizational structures for these notes are quite different. They usually update their lab notebooks daily (37%) or at least once a week (29%) and the others (34%) do not write up their experiments frequently, in some cases possibly not at all (our guess…). Almost uniformly, they were very interested in the idea of getting into the ‘ELN world’. Thus, a striking conclusion from this small sample is that in parallel with best ways to record experimental results, one has to struggle to implant good practices in data recording. We expect that ELNs will be of great help also along this direction.

sometimes some disruption is necessary to achieve progressOverall, the trend towards the ELN is taking force: it is an exciting time to try these tools in research and to get involved into a new era of information and science propagation. ELN implantation has a clear potential to address several questions related to improve accuracy and possibly reproducibility of science. In parallel, we acknowledge it is not so easy to move away from ingrained habits, but sometimes some disruption is necessary to achieve progress. Along this line, the most effective way to adopt ELNs may be… just do it !! …and then harvest the rewards of an improved work.


References and additional information

  1. J. Giles. Going paperless: The digital lab Nature, 481(7382): 430–1, 2012 | doi: 10.1038/481430a
  2. D. Butler. A new leaf Nature, 436(7047): 20–1, 2005 | doi: 10.1038/436020a
  3. H. K. Machina, D. J. Wild. Electronic Laboratory Notebooks Progress and Challenges in Implementation Journal of Laboratory Automation, 18(4): 264–8, 2013 | doi: 10.1177/2211068213484471
  4. R. Kwok. How to pick an electronic laboratory notebook Nature, 560(7717): 269–70, 2018 | doi: 10.1038/d41586-018-05895-3
  5. S. Guerrero, G. Dujardin, A. Cabrera-Andrade, C. Paz-y-Miño, A. Indacochea, M. Inglés-Ferrándiz, H. P. Nadimpalli, N. Collu, Y. Dublanche, I. De Mingo, D. Camargo. Analysis and Implementation of an Electronic Laboratory Notebook in a Biomedical Research Institute PLOS ONE, 11(8): e0160428, 2016 | doi: 10.1371/journal.pone.0160428
  6. S. Kanza, C. Willoughby, N. Gibbins, R. Whitby, J. G. Frey, J. Erjavec, K. Zupančič, M. Hren, K. Kovač. Electronic lab notebooks: can they replace paper? Journal of Cheminformatics, 9(1): , 2017 | doi: 10.1186/s13321-017-0221-3
  7. Splice website: splice-bio.com/the-7-best-electronic-lab-notebooks-eln-for-your-research/
  8. VIB Institute ELN webpage: www.vib.be/en/training/VIB%20Informatics/Pages/ELN.aspx
  9. Newsletter SciNote: scinote.net/blog/paper-and-electronic-lab-notebooks-can-work-together/

List of cited ELN websites

Percíllia Victória Santos de Oliveira (perc-I-am-here-illia.oliveira@hotmail.com@gmail.com) and
Patricia Nolasco Santos (pat-I-am-here-ty_ns8@@gmail.com@hotmail.com),
PhD students from the Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo, Brazil


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