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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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, principal 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

In order to encourage adoption of ELNs at the institutional level, École Polytechnique Fédérale de Lausanne (EPFL) started a dedicated program for ELN-LIMS deployment six years ago that involved research institute managers, principal investigators (PIs), and scientists at all levels. Here, we share the challenges, key success factors, and the results obtained at each phase of our project. Afterwards, we discuss the current and upcoming challenges and how our experience led us to support the creation of a new position in research groups: the laboratory data manager.

The project

Our efforts towards ELN-LIMS deployment began in March 2012 and has run through five distinct phases, as shown in Fig. 2.


Fig2 Argento EMBOReports2020 21-3.jpg

Figure 2. Institutional ELN-LIMS project macro‐planning. Project phases are indicated in blue underneath a timeline from March 2012, and associated human resources in FTE (full‐time equivalent) for each period are indicated in green (see text for details).

In the following sections, we present the step‐by‐step approach to deploy the platform in a laboratory. From our experience, each step contributed to successful and sustained ELN-LIMS adoption and use.

Initiating the project

By definition, an institutional ELN and LIMS project involves management, PIs, scientists at all levels, and the institute's IT department. As such, the steering committee for our project therefore included the Vice President of Research, who is responsible for scientific information, and the Vice President of Information Systems, who is responsible for IT governance and IT core services on campus. Representing the main users, the Life Sciences Faculty's Dean chaired the committee. This executive body defined the overall goals: to rationalize laboratories’ efforts, reduce waste of time and money, reduce loss and enable reuse of data, improve the reproducibility of experiments, and facilitate data sharing for collaborative projects.

The steering committee hired a project manager to coordinate the interests and requirements of the multiple stakeholders from distant fields, which made this project as complex as it was fascinating. To ensure the introduction of an ELN-LIMS service was suitable for those affected, we involved a panel of scientists. The project manager also played the role of a “business analyst” by meeting and surveying 25 laboratories whose needs and demands were synthesized in a weighted wish list that, along with legal requirements, helped to choose the ELN-LIMS solution. For instance, our institutional rules and laws about privacy and the use of human data prevented us from using a cloud‐based solution.

Identification of a suitable ELN-LIMS platform

The initiation phase revealed that the project required more than just picking a commercial off‐the‐shelf (COTS) ELN. Our key users were active in bioengineering, immunology, neurology, and oncology, with correspondingly diverse approaches and demands, though developers of technology platforms also showed a strong interest (Fig 3). Those stakeholders' routine workflows required additional functionality and administrative support. An analysis of those needs highlighted difficulties in managing data related to laboratory SOPs and samples, which are crucial for data reusability and experimental reproducibility in biomedical research.[7] Samples and experiments with human data require more sophisticated privacy management, a requirement that is increasing with the rise of personalized medicine. Feedback from laboratory staff also indicated that integration with third‐party information systems would be of added value for everyday work. For example, importing data from an animal facility was relevant to the experimental laboratories, while integration with work request forms and integration with the billing system were key features for technology platforms. The issue of authentication was also raised by laboratories and IT staff, for ease of use for the first group and security for the second group.


Fig3 Argento EMBOReports2020 21-3.jpg

Figure 3. Laboratory participation by institute. Number of laboratories participating in the ELN/LIMS project at EPFL from each Institute in the School of Life Sciences listed since the project's inception in 2019. Others refers to laboratories at EPFL, but outside life sciences. Note the largest increase in laboratory participation in 2018 (see text for details).

Involving the IT department from the beginning prevented us from taking obvious wrong directions in terms of technical choice. A striking example of their input was highlighting the heterogeneity of the scientists’ personal computers in the research institute, which made the choice of a web‐based solution almost mandatory, rather than installing software on each computer. However, the most interesting technical question was how to manage the diversity of needs. And the most important question for scientists was how to preserve creativity and freedom of research without introducing new technological burdens and hassles.

It was important that individual laboratories using our services remain architects of their own information system so as to preserve and maintain freedom and creativity. An ELN typically has highly standardized features, but new software technologies allow the creation of highly customizable databases and graphical user interfaces. The software we chose uses visual, declarative techniques instead of programming to enable fast, iterative, collaborative, and tailored implementation. Applications can be rapidly modified and maintained centrally.

Mastering such a powerful toolbox required the appointment of skilled people and best practices of implementation. This investment was counterbalanced by the possibility of the inclusion of a wide range of data, development of home-made features (e.g., financial management, work request forms), and integration with other information systems. It also opened the possibility for compliance with ISO 9001 or 21 CFR Part 11 standards that are required by some technology platforms. Those standards' quality assurance and data privacy concerns affect many industries and can also help to foster reproducibility in the life sciences.[8][9]

Pilot and full deployment

To accurately assess the personnel and skills needed to install and configure the platform, and then train the staff, a dedicated budget to run a pilot phase was required. This budget covered a six‐month license fee for the ELN-LIMS platform and a system administrator along with training and support. Through this pilot, five volunteer laboratories began to configure and use the ELN-LIMS platform. At the end, all stakeholders validated the choice of the solution over the short and long term, and the steering committee approved deployment at a larger scale.

The same staff then organized the full deployment. A dedicated ELN-LIMS platform engineer was hired to help laboratories to get the most from the customizable platform (Fig 2). Such an ELN-LIMS expert needed to have strong IT competencies, project management skills, and good general knowledge in research to efficiently communicate with the scientific staff. More specifically, the engineer developed and optimized the work methodology to ensure sustainable growth from a technical and scientific point of view. The announcement of the Swiss National Science Foundation (SNSF) to make a data management plan mandatory for all grant applications from October 2017[10] created a peak of demand for our services in 2018, when 10 laboratories voluntarily started ELN-LIMS deployment (Fig 3). Nonetheless, laboratories were not forced to use the ELN-LIMS, and it still remains a PI's decision to use the platform. Fig. 4 shows examples of the current typical usage of the ELN-LIMS platform.


Fig4 Argento EMBOReports2020 21-3.jpg

Figure 4. Typical usage of the ELN /LIMS platform. (A) ELN with scientist's notes, samples linked to the laboratory inventories, files, and procedures showing how we solved the initial issue illustrated in Fig 1C. (B) Laboratory sample inventories viewed with associated physical storage locations and links to ELN entries. (C) Example of a biopsy biobank and list of all derived crypts, organoids, and cryovial samples from one single biopsy.

Each ELN-LIMS platform deployment is managed as a separate sub‐project, since the information systems are tailor‐made for each laboratory. The deployment phase starts with informal discussions between the ELN-LIMS application expert and the laboratory's management to demonstrate the offered services. This introduction aims to confirm that the tool could support the laboratory's objectives. If so, the list of objectives is formalized and validated by the project sponsor, the PI in this case. Objectives are prioritized (Box 1) and have an appointed reference person. Roles and responsibilities must be clarified.

Box 1. Example of research laboratory requirements, sorted by decreasing priority
  • Configure and adopt ELN/LIMS for all laboratory members
  • Create a standard operating procedure (SOP) and simple operating procedure library accessible for everyone
  • Centralize antibody database
  • Centralize plasmid database
  • Centralize chemical database
  • Manage the laboratory storage location (freezer, cabinet, etc.)
  • Define uniform identification of locations and sample thanks to label printers


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. 
  7. Freedman, L.P.; Cockburn, I.M.; Simcoe, T.S. (2015). "The Economics of Reproducibility in Preclinical Research". PLoS Biology 13 (6): e1002165. doi:10.1371/journal.pbio.1002165. PMC PMC4461318. PMID 26057340. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461318. 
  8. Dirngal, U.; Kurreck, C.; Castaños-Vélez, E. et al. (2018). "Quality Management for Academic Laboratories: Burden or Boon? Professional Quality Management Could Be Very Beneficial for Academic Research but Needs to Overcome Specific Caveats". EMBO Reports 19 (11): e47143. doi:10.15252/embr.201847143. PMC PMC6216282. PMID 30341068. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6216282. 
  9. Riedl, D.H.; Dunn, M.K. (2013). "Quality Assurance Mechanisms for the Unregulated Research Environment". Trends in Biotechnology 31 (10): 552-4. doi:10.1016/j.tibtech.2013.06.007. PMID 24054820. 
  10. Swiss National Science Foundation (6 March 2017). "Open Research Data: Data management plans will be introduced in project funding". http://www.snf.ch/en/researchinFocus/newsroom/Pages/news-170306-towards-open-research-data.aspx. 

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. The inline link to the SNSF article was turned into a formal citation for this version.