Difference between revisions of "Journal:Institutional ELN-LIMS deployment: Highly customizable ELN-LIMS platform as a cornerstone of digital transformation for life sciences research institutes"

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==Introduction==
==Introduction==
Research tools in the life sciences are continuously evolving and improving, and scientists have always been eager to use the latest equipment. Ironically though, their main method of recording and managing experimental data has remained largely the same for centuries, with the paper-based [[laboratory notebook]] still the main method of record‐keeping. (Fig. 1) The adoption of [[electronic laboratory notebook]]s (ELNs) in academic laboratories has been slow, if laboratories have actually shown any interest at all. Their implementation necessitates institutional support 1, and despite much discussion of ELNs in the literature 2, 3, success stories and recipes for their deployment remain scarce. 4-6 Moreover, although ELNs can improve efficiency in data capturing and reuse, they lack the features to rigorously document data critical for experimental reproducibility, such as sample traceability data and standard operating procedures (SOP). These features are, however, part of another tool for data management called the [[laboratory information management system]] (LIMS). (See Table 1 for a comparison of the two.)
Research tools in the life sciences are continuously evolving and improving, and scientists have always been eager to use the latest equipment. Ironically though, their main method of recording and managing experimental data has remained largely the same for centuries, with the paper-based [[laboratory notebook]] still the main method of record‐keeping. (Fig. 1) The adoption of [[electronic laboratory notebook]]s (ELNs) in academic laboratories has been slow, if laboratories have actually shown any interest at all. Their implementation necessitates institutional support<ref name="AshPeople08">{{cite journal |title=People and Organizational Issues in Research Systems Implementation |journal=JAMIA |author=Ash, J.S.; Anderson, N.R.; Tarczy-Hornoch, P. |volume=15 |issue=3 |pages=283–9 |year=2008 |doi=10.1197/jamia.M2582 |pmid=18308986 |pmc=PMC2410012}}</ref>, and despite much discussion of ELNs in the literature<ref name="KwokHow18">{{cite journal |title=How to Pick an Electronic Laboratory Notebook |journal=Nature |author=Kwok, R. |volume=560 |issue=7717 |pages=269-270 |year=2028 |doi=10.1038/d41586-018-05895-3 |pmid=30082695}}</ref><ref name="ManzelRequire13">{{cite journal |title=Requirement analysis for an electronic laboratory notebook for sustainable data management in biomedical research |journal=Studies in Health Technologies and Informatics |author=Menzel, J.; Weil, P.; Bittihn, P. et al. |volume=192 |page=1108 |year=2013 |doi=10.3233/978-1-61499-289-9-1108 |pmid=23920882}}</ref>, success stories and recipes for their deployment remain scarce.<ref name="GuerreroAnalysis16">{{cite journal |title=Analysis and Implementation of an Electronic Laboratory Notebook in a Biomedical Research Institute |journal=PLoS One |author=Guerrero, S.; Dujardin, G.; Cabrera-Andrade, A. et al. |volume=11 |issue=8 |pages=e0160428 |year=2016 |doi=10.1371/journal.pone.0160428 |pmid=27479083 |pmc=PMC4968837}}</ref><ref name="DirnaglAPocket16">{{cite journal |title=A pocket guide to electronic laboratory notebooks in the academic life sciences |journal=F1000Research |author=Dirnagl, U.; Przesdzing, I. |volume=5 |pages=2 |year=2016 |doi=10.12688/f1000research.7628.1 |pmid=26835004 |pmc=PMC4722687}}</ref><ref name="RileyImplement17">{{cite journal |title=Implementation and use of cloud-based electronic lab notebook in a bioprocess engineering teaching laboratory |journal=Journal of Biological Engineering |author=Riley, E.M.; Hattaway, H.Z.; Felse, P.A. |volume=11 |pages=40 |year=2017 |doi=10.1186/s13036-017-0083-2 |pmid=29201138 |pmc=PMC5701295}}</ref> Moreover, although ELNs can improve efficiency in data capturing and reuse, they lack the features to rigorously document data critical for experimental reproducibility, such as sample traceability data and standard operating procedures (SOP). These features are, however, part of another tool for data management called the [[laboratory information management system]] (LIMS). (See Table 1 for a comparison of the two.)





Revision as of 20:47, 26 May 2020

Full article title Institutional ELN-LIMS deployment: Highly customizable ELN-LIMS platform as a
cornerstone of digital transformation for life sciences research institutes
Journal EMBO Reports
Author(s) Argento, Nicolas
Author affiliation(s) École Polytechnique Fédérale de Lausanne
Year published 2020
Volume and issue 21(3)
Article # e49862
DOI 10.15252/embr.201949862
ISSN 1469-3178
Distribution license Creative Commons Attribution 4.0 International
Website https://www.embopress.org/doi/full/10.15252/embr.201949862
Download https://www.embopress.org/doi/epdf/10.15252/embr.201949862

Abstract

The systematic recording and management of experimental data in academic life science research remains an open problem. École Polytechnique Fédérale de Lausanne (EPFL) engaged in a program of deploying both an electronic laboratory notebook (ELN) and a laboratory information management system (LIMS) six years ago, encountering a host of fundamental questions at the institutional level and within each laboratory. Here, based on our experience, we aim to share with research institute managers, prinicpal investigators (PIs), and any scientists involved in a combined ELN-LIMS deployment helpful tips and tools, with a focus on surrounding yourself with the right people and the right software at the right time. In this article we describe the resources used, the challenges encountered, key success factors, and the results obtained at each phase of our project. Finally, we discuss the current and next challenges we face, as well as how our experience leads us to support the creation of a new position in the research group: the laboratory data manager.

Keywords: electronic laboratory notebook, laboratory information management system, life sciences, research, laboratory data management

Introduction

Research tools in the life sciences are continuously evolving and improving, and scientists have always been eager to use the latest equipment. Ironically though, their main method of recording and managing experimental data has remained largely the same for centuries, with the paper-based laboratory notebook still the main method of record‐keeping. (Fig. 1) The adoption of electronic laboratory notebooks (ELNs) in academic laboratories has been slow, if laboratories have actually shown any interest at all. Their implementation necessitates institutional support[1], and despite much discussion of ELNs in the literature[2][3], success stories and recipes for their deployment remain scarce.[4][5][6] Moreover, although ELNs can improve efficiency in data capturing and reuse, they lack the features to rigorously document data critical for experimental reproducibility, such as sample traceability data and standard operating procedures (SOP). These features are, however, part of another tool for data management called the laboratory information management system (LIMS). (See Table 1 for a comparison of the two.)


Fig1 Argento EMBOReports2020 21-3.jpg

Figure 1. Challenges of traditional record‐keeping in modern science. (A) Comparison of research instruments and laboratory records from the 1700s and 2000s. While the development of research instruments has driven progress, laboratory record‐keeping is almost unchanged. (B) Data are distributed across multiple locations and media, including notebooks, printed material, physical samples, disks, hard drives, servers and cloud storage. (C) Locating specific data is difficult as the location may be unknown, and the media may be difficult to search.

Table 1. ELN and LIMS main benefits in research institutions
ELN benefits LIMS benefits
  • Provides research work traceability
  • Enhances knowledge transmission
  • Protects intellectual property and patents
  • Supports sample management (plasmids, virus, antibodies, chemicals databases)
  • Provides stock management
  • Improves workflows, typically with templates
  • Improves management of SOPs
  • Tracks laboratory equipment usage and inventory
  • Offers equipment integration for direct data acquisition


Acknowledgements

I acknowledge Gaël Anex and all the School of Life Sciences and EPFL directors for creating this favorable environment, improving laboratory data management; Pr. Andy Oates and Pierig Le Pottier for their strong support and help in writing the article; my colleagues from the IT department, in particular Paul Schalbetter, for the scripting of the figures, as well as Philippe Borel, Peter Hliva, and Christopher Tremblay who ensure the continuity of ELN-LIMS deployments; and finally all the scientific staff who actively fostered and participated in the ELN and LIMS deployments in their laboratory.

Funding

The EPFL, School of Life Sciences provided funding for this research.

References

  1. Ash, J.S.; Anderson, N.R.; Tarczy-Hornoch, P. (2008). "People and Organizational Issues in Research Systems Implementation". JAMIA 15 (3): 283–9. doi:10.1197/jamia.M2582. PMC PMC2410012. PMID 18308986. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2410012. 
  2. Kwok, R. (2028). "How to Pick an Electronic Laboratory Notebook". Nature 560 (7717): 269-270. doi:10.1038/d41586-018-05895-3. PMID 30082695. 
  3. Menzel, J.; Weil, P.; Bittihn, P. et al. (2013). "Requirement analysis for an electronic laboratory notebook for sustainable data management in biomedical research". Studies in Health Technologies and Informatics 192: 1108. doi:10.3233/978-1-61499-289-9-1108. PMID 23920882. 
  4. Guerrero, S.; Dujardin, G.; Cabrera-Andrade, A. et al. (2016). "Analysis and Implementation of an Electronic Laboratory Notebook in a Biomedical Research Institute". PLoS One 11 (8): e0160428. doi:10.1371/journal.pone.0160428. PMC PMC4968837. PMID 27479083. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968837. 
  5. Dirnagl, U.; Przesdzing, I. (2016). "A pocket guide to electronic laboratory notebooks in the academic life sciences". F1000Research 5: 2. doi:10.12688/f1000research.7628.1. PMC PMC4722687. PMID 26835004. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722687. 
  6. Riley, E.M.; Hattaway, H.Z.; Felse, P.A. (2017). "Implementation and use of cloud-based electronic lab notebook in a bioprocess engineering teaching laboratory". Journal of Biological Engineering 11: 40. doi:10.1186/s13036-017-0083-2. PMC PMC5701295. PMID 29201138. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701295. 

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. Grammar was cleaned up for smoother reading. In some cases important information was missing from the references, and that information was added.