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[[File:|right|350px]] Title: Is there a benefit to utilizing both a LIMS and an ELN in the lab?

Author for citation: Shawn E. Douglas

License for content: Creative Commons Attribution-ShareAlike 4.0 International

Publication date: March 2023

Introduction

The ELN and what it does outside the scope of a LIMS

To answer the question, knowledge of what an ELN does and what it addresses outside of a LIMS is important. An ELN is a modern electronic equivalent of the traditional paper-based laboratory notebook, which historically has served as a collection of scribblings—often with individual, regional, or temporal idiosyncratic styles of "subjectivity, unruliness, and privacy"[1]—concerning the notes and protocols of one or more particular scientific research endeavors.[1][2] In recent times, these scribblings have become more recognizably organized and thorough as a necessary part of presenting all the details of experiments, observations, and analyses such that the results can be reproduced and verified by peers in the scientific community (often referred to as part of a broader "reproducibility crisis").[2][3][4] As laboratory research has increasingly incorporated more digital sources of data and information from instruments and other sources, labs conducting laboratory notebook-assisted research today—in both academic and industrial environments—have had to necessarily look at old paper notebook formats as antiquated and incompatible with modern research methods and increasingly digitalized workflows.[2][3]

As a modern substitute for the paper-based laboratory notebook, the ELN at its core intends to similarly provide a means to document experiments, observations, and analyses but in a more organized, consistent, readable, searchable, and shareable way. Because it is software, additional thought has gone into the development of an ELN to allow users to do their research more effectively while integrating with other digital instruments and software solutions to capture and manage data and information closer to real-time. As a result, today's ELNs take many shapes and forms, many of them being developed to address the needs of specific research activities, such as biology and DNA sequencing[5][6] or chemical analysis.[6][7] However, the sheer number of research use cases and workflows across numerous disciplines and experiment types, as well as varying vendor approaches to ELN development, can lead to difficulty in finding the right ELN for a given lab[8][9], even leading some to develop their own custom ELNs[10], often as an extension of some other piece of software like a knowledge management system[11], course management system[12], or note-taking application.[13]

Despite the diverse needs of a wide variety of academic and industrial research labs in regards to ELNs, there are some functional aspects that stand out as being somewhat unique to the software, even when compared to common laboratory informatics solutions like a LIMS or laboratory information system (LIS). This includes[2][3][6][8][9][14][15][16][17]:

  • direct real-time recording of data and information in various (standard) formats like text, images, tables, chromatograms, and raw data files;
  • robust support for tagging, searching, and reusing data, information, files, etc.;
  • support for standard vocabularies and metadata schemes, including semantic enrichment schemes[18];
  • lending of structure to data and information through the use of preformatted or customizable templates with drag-and-drop support;
  • flexible creation of links between records, including reference managers and other notebooks;
  • group, project, and experiment management;
  • import and export functionality, particularly in standard, portable file formats;
  • storage of fully searchable records in a secure database format, with automatic backup;
  • inclusion of messaging and commenting functionality for better collaboration;
  • inclusion of safety data, including flags for dangerous chemicals;
  • data integrity and security tools like electronic signatures, time-stamped audit logs, controlled access levels, version control, automated import of instrument data, and archiving capabilities;
  • generation of secure forms that accept laboratory data input real-time via a computing device and/or laboratory equipment (i.e., integration);
  • accommodation of a scheduling option for routine procedures such as equipment qualification and study-related timelines;
  • support for standard chemical, genetic, and other molecular libraries, visualization, and nomenclature formats, e.g., LaTeX; and
  • inventory management of instruments, reagents, samples, etc. (usually associated with a LIMS or separate system, but useful as an integrated option within an ELN[3][6][9]).

Note that the more functionality bolted on to an ELN, the greater chance of overall cost and complexity of use increasing, in turn negatively impacting overall adoption of the ELN by laboratorians.[3] The ELN also needs to be intuitive, easy-to-learn, and well-documented in order to better ensure full adoption.[8]

Pairing a LIMS and ELN together

After browsing some of the ELN functionality listed above, comparisons to some types of LIMS functionality become easier. From instrument integration and data integrity mechanisms to equipment scheduling and inventory management, the LIMS and ELN can most certainly share functionality.[3][6][8][9][17][19] This can be viewed as highly desirable by some organizations[9], while others may be frustrated by the introduction of a similar standalone system and an impediment to the original desire for the time-saving benefits of digitizing and integrating workflows and systems with a LIMS.[8] After all, it's even more work to learn how to effectively use another system like an ELN after spending time and energy on learning to use a LIMS.[3][9]

So why would a lab pair an ELN with a LIMS? Is there a benefit to utilizing both? First, as noted prior, both academic and industrial research laboratories are the typical users of an ELN, with adoption by academic research labs slightly lagging industrial research labs.[14] The ELN is a replacement for the laboratory notebook, typically used in research settings to document research workflows. (While there may be legitimate non-research use cases for an ELN, it is beyond the scope of this article to address them, and thus this article assumes research-based use.) Use cases of an ELN include[20][21][22]:

  1. those working strictly in R&D, focusing on innovation and proof-of-concept delivery as easily and efficiently as possible in order to get to market faster;
  2. those working beyond strict innovation and proof-of-concept, taking those ideas into more demanding production-based experimentation, where processes and procedures must strictly be followed; and
  3. advanced, multi-department research and production environments where integrated systems management is essential to ensuring a clean continuum of data and information across an entire product lifecycle, as well as more timely and efficient workflows.

In the first case, a LIMS is most likely not necessary, with the ELN providing the most benefit. It's only with perhaps the second case and often the third case that pairing an ELN with a LIMS begins to make some sense, particularly if there's a greater need for sample traceability and management/enforcement of standard operating procedures and/or test methods.[17] And even then multiple considerations need to be made. Additionally, these considerations may vary based upon the existing technology environment at the lab, e.g., if the lab is moving in full from a completely paper-based workflow to an electronic workflow that intends to incorporate both systems, or if the lab has one system and wants to add the other. Is there a definitive need for both systems? If so, does it make sense to acquire them separately, or are purpose-built solutions that combine LIMS functionality with ELN functionality a viable solution? What are the cost, vendor lock-in, data and information export, maintenance, IT, integration, data cleansing, change management, and workflow considerations to be made? Do proposed solutions manage both structured and unstructured data well? If two separate solutions (rather than a single combined solution) are being considered, will they both not only integrate well with the labs' instruments and software, but also with each other?[8][15][20][21]

Those considerations made, there indeed can be some benefit to using both a LIMS and an ELN in the lab. Many of these benefits are assumed upon two different programs working together without sharing much of the same functionality; however, a single solution that incorporates both LIMS and ELN functionality[5][6] could also provide these benefits but differently. Examples of benefits to using both systems include[6][17][20][21][22]:

  • Adding one of the two to the other provides a necessary and informative opportunity to reflect upon, update, and consolidate existing workflows, as well as any new ones to potentially be introduced down the line. Will adding an ELN or LIMS to the total mix duplicate functionality, or will it be complementary? How will workflows change for the better, and what new challenges may emerge as a result? Look to this as an opportunity to ask these and other questions not only as part of the acquisition process but also as part of maintaining and updating any relevant quality management system (QMS) or continual improvement processes.[8]
  • When interfaced well, using the same standard vocabularies and metadata schemes, the duo would allow for greater findability, accessibility, interoperability, and reusability (FAIR) of data and information across a research-driven academic or industrial enterprise.[6][17] This in turn can lend to more rapid innovation and discovery, as well as time-to-market.[22]

Conclusion

References

  1. ↑ 1.0 1.1 Holmes, F.L.; Renn, J.; Rheinberger, H.-J., ed. (2003). "Introduction". Reworking the Bench - Research Notebooks in the History of Science. Archimedes - New Studies in the History and Philosophy of Science and Technology. 7. Kluwer Academic Publishers. pp. vii–xv. doi:10.1007/0-306-48152-9. ISBN 9780306481529. 
  2. ↑ 2.0 2.1 2.2 2.3 Nussbeck, Sara Y; Weil, Philipp; Menzel, Julia; Marzec, Bartlomiej; Lorberg, Kai; Schwappach, Blanche (2014). "The laboratory notebook in the 21 st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity" (in en). EMBO reports 15 (6): 631–634. doi:10.15252/embr.201338358. ISSN 1469-221X. PMC PMC4197872. PMID 24833749. https://www.embopress.org/doi/10.15252/embr.201338358. 
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 Dirnagl, Ulrich; Przesdzing, Ingo (4 January 2016). "A pocket guide to electronic laboratory notebooks in the academic life sciences" (in en). F1000Research 5: 2. doi:10.12688/f1000research.7628.1. ISSN 2046-1402. PMC PMC4722687. PMID 26835004. https://f1000research.com/articles/5-2/v1. 
  4. ↑ Hunter, Philip (1 September 2017). "The reproducibility “crisis”: Reaction to replication crisis should not stifle innovation" (in en). EMBO reports 18 (9): 1493–1496. doi:10.15252/embr.201744876. ISSN 1469-221X. PMC PMC5579390. PMID 28794201. https://www.embopress.org/doi/10.15252/embr.201744876. 
  5. ↑ 5.0 5.1 Barillari, Caterina; Ottoz, Diana S. M.; Fuentes-Serna, Juan Mariano; Ramakrishnan, Chandrasekhar; Rinn, Bernd; Rudolf, Fabian (15 February 2016). "openBIS ELN-LIMS: an open-source database for academic laboratories" (in en). Bioinformatics 32 (4): 638–640. doi:10.1093/bioinformatics/btv606. ISSN 1367-4811. PMC PMC4743625. PMID 26508761. https://academic.oup.com/bioinformatics/article/32/4/638/1743839. 
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 Plass, Fabian; Englisch, Silvan; Apeleo Zubiri, Benjamin; Pflug, Lukas; Spiecker, Erdmann; Stingl, Michael (22 November 2023). "Using OpenBIS as Virtual Research Environment: An ELN-LIMS Open-Source Database Tool as a Framework within the CRC 1411 Design of Particulate Products". Data Science Journal 22: 44. doi:10.5334/dsj-2023-044. ISSN 1683-1470. https://account.datascience.codata.org/index.php/up-j-dsj/article/view/1500. 
  7. ↑ Tremouilhac, Pierre; Nguyen, An; Huang, Yu-Chieh; Kotov, Serhii; Lütjohann, Dominic Sebastian; Hübsch, Florian; Jung, Nicole; Bräse, Stefan (1 December 2017). "Chemotion ELN: an Open Source electronic lab notebook for chemists in academia" (in en). Journal of Cheminformatics 9 (1): 54. doi:10.1186/s13321-017-0240-0. ISSN 1758-2946. PMC PMC5612905. PMID 29086216. https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0240-0. 
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 Higgins, Stuart G.; Nogiwa-Valdez, Akemi A.; Stevens, Molly M. (1 February 2022). "Considerations for implementing electronic laboratory notebooks in an academic research environment" (in en). Nature Protocols 17 (2): 179–189. doi:10.1038/s41596-021-00645-8. ISSN 1754-2189. https://www.nature.com/articles/s41596-021-00645-8. 
  9. ↑ 9.0 9.1 9.2 9.3 9.4 9.5 Loveluck, J. (8 October 2020). "Finding the Right Electronic Lab Notebook with the Corey Lab". Harvard Research Data Management. Harvard Medical School. https://datamanagement.hms.harvard.edu/news/finding-right-electronic-lab-notebook-corey-lab. Retrieved 05 March 2024. 
  10. ↑ Liscouski, J. (April 2021). "LII:The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies". In Douglas, S.E.. LIMSwiki. https://www.limswiki.org/index.php/LII:The_Application_of_Informatics_to_Scientific_Work:_Laboratory_Informatics_for_Newbies#Expanding_the_research_team. Retrieved 05 March 2024. 
  11. ↑ Khan, Arshad M.; Hahn, Joel D.; Cheng, Wei-Cheng; Watts, Alan G.; Burns, Gully A. P. C. (2006). "NeuroScholar\'s Electronic Laboratory Notebook and Its Application to Neuroendocrinology" (in en). Neuroinformatics 4 (2): 139–162. doi:10.1385/NI:4:2:139. ISSN 1539-2791. PMC PMC4476904. PMID 16845166. http://link.springer.com/10.1385/NI:4:2:139. 
  12. ↑ Cardenas, M. (2014). "An Implementation of Electronic Laboratory Notebooks (ELN) Using a Learning Management System Platform in an Undergraduate Experimental Engineering Course" (PDF). Proceedings of the 121st ASEE Annual Conference & Exposition: 24.164.1–16. https://peer.asee.org/an-implementation-of-electronic-laboratory-notebooks-eln-using-a-learning-management-system-platform-in-an-undergraduate-experimental-engineering-course.pdf. 
  13. ↑ Guerrero, Santiago; López-Cortés, Andrés; García-Cárdenas, Jennyfer M.; Saa, Pablo; Indacochea, Alberto; Armendáriz-Castillo, Isaac; Zambrano, Ana Karina; Yumiceba, Verónica et al. (9 May 2019). Ouellette, Francis. ed. "A quick guide for using Microsoft OneNote as an electronic laboratory notebook" (in en). PLOS Computational Biology 15 (5): e1006918. doi:10.1371/journal.pcbi.1006918. ISSN 1553-7358. PMC PMC6508581. PMID 31071077. https://dx.plos.org/10.1371/journal.pcbi.1006918. 
  14. ↑ 14.0 14.1 Kanza, Samantha; Willoughby, Cerys; Gibbins, Nicholas; Whitby, Richard; Frey, Jeremy Graham; Erjavec, Jana; Zupančič, Klemen; Hren, Matjaž et al. (1 December 2017). "Electronic lab notebooks: can they replace paper?" (in en). Journal of Cheminformatics 9 (1): 31. doi:10.1186/s13321-017-0221-3. ISSN 1758-2946. PMC PMC5443717. PMID 29086051. https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0221-3. 
  15. ↑ 15.0 15.1 Knippenberg, R. (30 June 2018). "Best Practices for Electronic Laboratory Notebook Implementation in R&D Labs". Astrix Insights. Astrix, Inc. Archived from the original on 08 December 2023. https://web.archive.org/web/20231208184311/https://astrixinc.com/best-practices-for-electronic-laboratory-notebook-implementation-in-rd-labs/. Retrieved 05 March 2024. 
  16. ↑ Covey, M.; Goto, R.; Ceglia, I. (May 2019). "Electronic Lab Notebooks: From paper to screen, keeping track of your research" (PDF). Rita and Frits Markus Library, Rockefeller University. https://www.rockefeller.edu/markus-library/uploads/www.rockefeller.edu/sites/207/2019/05/Electronic-Notebooks-CCTS.pdf. Retrieved 05 March 2024. 
  17. ↑ 17.0 17.1 17.2 17.3 17.4 Argento, Nicolas (4 March 2020). "Institutional ELN/LIMS deployment: Highly customizable ELN/LIMS platform as a cornerstone of digital transformation for life sciences research institutes" (in en). EMBO reports 21 (3): e49862. doi:10.15252/embr.201949862. ISSN 1469-221X. PMC PMC7054672. PMID 32129000. https://www.embopress.org/doi/10.15252/embr.201949862. 
  18. ↑ Prior, D. (21 January 2024). "Semantic Enrichment of Electronic Lab Notebook Data". Pistoia Alliance. https://www.pistoiaalliance.org/projects/current-projects/semantic-enrichment-of-eln-data/. Retrieved 06 March 2024. 
  19. ↑ Douglas, S.E. (December 2022). "LIMSpec 2022 R2". LIMSwiki. https://www.limswiki.org/index.php/LII:LIMSpec_2022_R2. Retrieved 06 March 2024. 
  20. ↑ 20.0 20.1 20.2 DePalma, A. (6 September 2012). "A Close Look at LIMS and ELNs". Lab Manager. https://www.labmanager.com/a-close-look-at-lims-and-elns-16191. Retrieved 06 March 2024. 
  21. ↑ 21.0 21.1 21.2 Wu, Y. (27 June 2022). "Barrier Busting: Bringing ELN and LIMS Scientific Data Together". TetraScience Blog. https://www.tetrascience.com/blog/barrier-busting-bringing-eln-and-lims-scientific-data-together. Retrieved 06 March 2024. 
  22. ↑ 22.0 22.1 22.2 "The Potent Combination of ELN and LIMS: The Fast-Track from Ideation to Commercialization". STARLIMS Corporation. 3 November 2023. https://www.starlims.com/resources/the-potent-combination-of-eln-and-lims-the-fast-track-from-ideation-to-commercialization/. Retrieved 06 March 2023. 


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