|
|
| Line 8: |
Line 8: |
| ==Sandbox begins below== | | ==Sandbox begins below== |
| <div class="nonumtoc">__TOC__</div> | | <div class="nonumtoc">__TOC__</div> |
| [[File:ТНМУ - Лабораторія клініко-експериментальних досліджень - Степан Подобівський - 17071680.jpg|right|400px]]
| |
| '''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''': [https://creativecommons.org/licenses/by-sa/4.0/ 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"<ref name="HolmesArchRework03">{{cite book |title=Reworking the Bench - Research Notebooks in the History of Science |chapter=Introduction |series=Archimedes - New Studies in the History and Philosophy of Science and Technology |editor=Holmes, F.L.; Renn, J.; Rheinberger, H.-J. |publisher=Kluwer Academic Publishers |volume=7 |pages=vii–xv |year=2003 |isbn=9780306481529 |doi=10.1007/0-306-48152-9}}</ref>—concerning the notes and protocols of one or more particular scientific research endeavors.<ref name="HolmesArchRework03" /><ref name="NussbeckTheLab14">{{cite journal |last=Nussbeck |first=Sara Y |last2=Weil |first2=Philipp |last3=Menzel |first3=Julia |last4=Marzec |first4=Bartlomiej |last5=Lorberg |first5=Kai |last6=Schwappach |first6=Blanche |year=2014 |title=The laboratory notebook in the 21 st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity |url=https://www.embopress.org/doi/10.15252/embr.201338358 |journal=EMBO reports |language=en |volume=15 |issue=6 |pages=631–634 |doi=10.15252/embr.201338358 |issn=1469-221X |pmc=PMC4197872 |pmid=24833749}}</ref> 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").<ref name="NussbeckTheLab14" /><ref name="DirnaglAPocket16">{{cite journal |last=Dirnagl |first=Ulrich |last2=Przesdzing |first2=Ingo |date=2016-01-04 |title=A pocket guide to electronic laboratory notebooks in the academic life sciences |url=https://f1000research.com/articles/5-2/v1 |journal=F1000Research |language=en |volume=5 |pages=2 |doi=10.12688/f1000research.7628.1 |issn=2046-1402 |pmc=PMC4722687 |pmid=26835004}}</ref><ref>{{Cite journal |last=Hunter |first=Philip |date=2017-09 |title=The reproducibility “crisis”: Reaction to replication crisis should not stifle innovation |url=https://www.embopress.org/doi/10.15252/embr.201744876 |journal=EMBO reports |language=en |volume=18 |issue=9 |pages=1493–1496 |doi=10.15252/embr.201744876 |issn=1469-221X |pmc=PMC5579390 |pmid=28794201}}</ref> 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.<ref name="NussbeckTheLab14" /><ref name="DirnaglAPocket16" />
| |
|
| |
| 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]]<ref name="BarillariOpenBIS16">{{Cite journal |last=Barillari |first=Caterina |last2=Ottoz |first2=Diana S. M. |last3=Fuentes-Serna |first3=Juan Mariano |last4=Ramakrishnan |first4=Chandrasekhar |last5=Rinn |first5=Bernd |last6=Rudolf |first6=Fabian |date=2016-02-15 |title=openBIS ELN-LIMS: an open-source database for academic laboratories |url=https://academic.oup.com/bioinformatics/article/32/4/638/1743839 |journal=Bioinformatics |language=en |volume=32 |issue=4 |pages=638–640 |doi=10.1093/bioinformatics/btv606 |issn=1367-4811 |pmc=PMC4743625 |pmid=26508761}}</ref><ref name=":3">{{Cite journal |last=Plass |first=Fabian |last2=Englisch |first2=Silvan |last3=Apeleo Zubiri |first3=Benjamin |last4=Pflug |first4=Lukas |last5=Spiecker |first5=Erdmann |last6=Stingl |first6=Michael |date=2023-11-22 |title=Using OpenBIS as Virtual Research Environment: An ELN-LIMS Open-Source Database Tool as a Framework within the CRC 1411 Design of Particulate Products |url=https://account.datascience.codata.org/index.php/up-j-dsj/article/view/1500 |journal=Data Science Journal |volume=22 |pages=44 |doi=10.5334/dsj-2023-044 |issn=1683-1470}}</ref> or chemical analysis.<ref name=":3" /><ref>{{Cite journal |last=Tremouilhac |first=Pierre |last2=Nguyen |first2=An |last3=Huang |first3=Yu-Chieh |last4=Kotov |first4=Serhii |last5=Lütjohann |first5=Dominic Sebastian |last6=Hübsch |first6=Florian |last7=Jung |first7=Nicole |last8=Bräse |first8=Stefan |date=2017-12 |title=Chemotion ELN: an Open Source electronic lab notebook for chemists in academia |url=https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0240-0 |journal=Journal of Cheminformatics |language=en |volume=9 |issue=1 |pages=54 |doi=10.1186/s13321-017-0240-0 |issn=1758-2946 |pmc=PMC5612905 |pmid=29086216}}</ref> 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<ref name=":0">{{Cite journal |last=Higgins |first=Stuart G. |last2=Nogiwa-Valdez |first2=Akemi A. |last3=Stevens |first3=Molly M. |date=2022-02 |title=Considerations for implementing electronic laboratory notebooks in an academic research environment |url=https://www.nature.com/articles/s41596-021-00645-8 |journal=Nature Protocols |language=en |volume=17 |issue=2 |pages=179–189 |doi=10.1038/s41596-021-00645-8 |issn=1754-2189}}</ref><ref name=":1">{{Cite web |last=Loveluck, J. |date=08 October 2020 |title=Finding the Right Electronic Lab Notebook with the Corey Lab |work=Harvard Research Data Management |url=https://datamanagement.hms.harvard.edu/news/finding-right-electronic-lab-notebook-corey-lab |publisher=Harvard Medical School |accessdate=05 March 2024}}</ref>, even leading some to develop their own custom ELNs<ref name="LiscouskiTheApp21">{{cite web |url=https://www.limswiki.org/index.php/LII:The_Application_of_Informatics_to_Scientific_Work:_Laboratory_Informatics_for_Newbies#Expanding_the_research_team |title=LII:The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies |author=Liscouski, J. |editor=Douglas, S.E. |work=LIMSwiki |date=April 2021 |accessdate=05 March 2024}}</ref>, often as an extension of some other piece of software like a knowledge management system<ref>{{Cite journal |last=Khan |first=Arshad M. |last2=Hahn |first2=Joel D. |last3=Cheng |first3=Wei-Cheng |last4=Watts |first4=Alan G. |last5=Burns |first5=Gully A. P. C. |date=2006 |title=NeuroScholar\'s Electronic Laboratory Notebook and Its Application to Neuroendocrinology |url=http://link.springer.com/10.1385/NI:4:2:139 |journal=Neuroinformatics |language=en |volume=4 |issue=2 |pages=139–162 |doi=10.1385/NI:4:2:139 |issn=1539-2791 |pmc=PMC4476904 |pmid=16845166}}</ref>, course management system<ref>{{Cite journal |last=Cardenas, M. |year=2014 |title=An Implementation of Electronic Laboratory Notebooks (ELN) Using a Learning Management System Platform in an Undergraduate Experimental Engineering Course |url=https://peer.asee.org/an-implementation-of-electronic-laboratory-notebooks-eln-using-a-learning-management-system-platform-in-an-undergraduate-experimental-engineering-course.pdf |format=PDF |journal=Proceedings of the 121st ASEE Annual Conference & Exposition |pages=24.164.1–16 |at=9040}}</ref>, or note-taking application.<ref>{{Cite journal |last=Guerrero |first=Santiago |last2=López-Cortés |first2=Andrés |last3=García-Cárdenas |first3=Jennyfer M. |last4=Saa |first4=Pablo |last5=Indacochea |first5=Alberto |last6=Armendáriz-Castillo |first6=Isaac |last7=Zambrano |first7=Ana Karina |last8=Yumiceba |first8=Verónica |last9=Pérez-Villa |first9=Andy |last10=Guevara-Ramírez |first10=Patricia |last11=Moscoso-Zea |first11=Oswaldo |date=2019-05-09 |editor-last=Ouellette |editor-first=Francis |title=A quick guide for using Microsoft OneNote as an electronic laboratory notebook |url=https://dx.plos.org/10.1371/journal.pcbi.1006918 |journal=PLOS Computational Biology |language=en |volume=15 |issue=5 |pages=e1006918 |doi=10.1371/journal.pcbi.1006918 |issn=1553-7358 |pmc=PMC6508581 |pmid=31071077}}</ref>
| |
|
| |
| 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<ref name="NussbeckTheLab14" /><ref name="DirnaglAPocket16" /><ref name=":3" /><ref name=":0" /><ref name=":1" /><ref name="KanzaElect17">{{Cite journal |last=Kanza |first=Samantha |last2=Willoughby |first2=Cerys |last3=Gibbins |first3=Nicholas |last4=Whitby |first4=Richard |last5=Frey |first5=Jeremy Graham |last6=Erjavec |first6=Jana |last7=Zupančič |first7=Klemen |last8=Hren |first8=Matjaž |last9=Kovač |first9=Katarina |date=2017-12 |title=Electronic lab notebooks: can they replace paper? |url=https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0221-3 |journal=Journal of Cheminformatics |language=en |volume=9 |issue=1 |pages=31 |doi=10.1186/s13321-017-0221-3 |issn=1758-2946 |pmc=PMC5443717 |pmid=29086051}}</ref><ref name="KnippenbergBest18">{{Cite web |last=Knippenberg, R. |title=Best Practices for Electronic Laboratory Notebook Implementation in R&D Labs |work=Astrix Insights |url=https://astrixinc.com/best-practices-for-electronic-laboratory-notebook-implementation-in-rd-labs/ |publisher=Astrix, Inc |archiveurl=https://web.archive.org/web/20231208184311/https://astrixinc.com/best-practices-for-electronic-laboratory-notebook-implementation-in-rd-labs/ |archivedate=08 December 2023 |date=30 June 2018 |accessdate=05 March 2024}}</ref><ref name="CoveyElectronic19">{{cite web |url=https://www.rockefeller.edu/markus-library/uploads/www.rockefeller.edu/sites/207/2019/05/Electronic-Notebooks-CCTS.pdf |format=PDF |title=Electronic Lab Notebooks: From paper to screen, keeping track of your research |author=Covey, M.; Goto, R.; Ceglia, I. |publisher=Rita and Frits Markus Library, Rockefeller University |date=May 2019 |accessdate=05 March 2024}}</ref><ref name=":2">{{Cite journal |last=Argento |first=Nicolas |date=2020-03-04 |title=Institutional ELN/LIMS deployment: Highly customizable ELN/LIMS platform as a cornerstone of digital transformation for life sciences research institutes |url=https://www.embopress.org/doi/10.15252/embr.201949862 |journal=EMBO reports |language=en |volume=21 |issue=3 |pages=e49862 |doi=10.15252/embr.201949862 |issn=1469-221X |pmc=PMC7054672 |pmid=32129000}}</ref>:
| |
|
| |
| *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<ref name="PASemantic24">{{cite web |url=https://www.pistoiaalliance.org/projects/current-projects/semantic-enrichment-of-eln-data/ |title=Semantic Enrichment of Electronic Lab Notebook Data |author=Prior, D. |publisher=Pistoia Alliance |date=21 January 2024 |accessdate=06 March 2024}}</ref>;
| |
| *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<ref name="DirnaglAPocket16" /><ref name=":3" /><ref name=":1" />).
| |
|
| |
| 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.<ref name="DirnaglAPocket16" /> The ELN also needs to be intuitive, easy-to-learn, and well-documented in order to better ensure full adoption.<ref name=":0" />
| |
|
| |
| ==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.<ref name="DirnaglAPocket16" /><ref name=":3" /><ref name=":0" /><ref name=":1" /><ref name=":2" /><ref name="DouglasLIMSpec22">{{cite web |url=https://www.limswiki.org/index.php/LII:LIMSpec_2022_R2 |title=LIMSpec 2022 R2 |author=Douglas, S.E. |work=LIMSwiki |date=December 2022 |accessdate=06 March 2024}}</ref> This can be viewed as highly desirable by some organizations<ref name=":1" />, 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.<ref name=":0" /> 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.<ref name="DirnaglAPocket16" /><ref name=":1" />
| |
|
| |
| 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.<ref name="KanzaElect17" /> 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<ref name="DePalmaAClose12">{{cite web |url=https://www.labmanager.com/a-close-look-at-lims-and-elns-16191 |title=A Close Look at LIMS and ELNs |author=DePalma, A. |work=Lab Manager |date=06 September 2012 |accessdate=06 March 2024}}</ref><ref name="WuBarrier22">{{cite web |url=https://www.tetrascience.com/blog/barrier-busting-bringing-eln-and-lims-scientific-data-together |title=Barrier Busting: Bringing ELN and LIMS Scientific Data Together |author=Wu, Y. |work=TetraScience Blog |date=27 June 2022 |accessdate=06 March 2024}}</ref><ref name="SLThePotent23">{{cite web |url=https://www.starlims.com/resources/the-potent-combination-of-eln-and-lims-the-fast-track-from-ideation-to-commercialization/ |title=The Potent Combination of ELN and LIMS: The Fast-Track from Ideation to Commercialization |publisher=STARLIMS Corporation |date=03 November 2023 |accessdate=06 March 2023}}</ref>:
| |
|
| |
| #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;
| |
| #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
| |
| #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.<ref name=":2" /> 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?<ref name=":0" /><ref name="KnippenbergBest18" /><ref name="DePalmaAClose12" /><ref name="WuBarrier22" />
| |
|
| |
| 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<ref name="BarillariOpenBIS16" /><ref name=":3" /> could also provide these benefits but differently. Examples of benefits to using both systems—whether stand-alone or integrated—include:
| |
|
| |
| *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 process]]es.<ref name=":0" />
| |
| *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.<ref name=":3" /><ref name=":2" /> This in turn can lend to more rapid innovation and discovery, as well as time-to-market.<ref name="SLThePotent23" />
| |
| *When combined into a single system, a LIMS+ELN can reduce software management, IT, and licensing costs; reduce the complexity of instrument and system integration; reduce the overall burden of learning how to effectively use multiple systems; improve overall throughput throughout the research and/or product lifecycle; and maximize regulatory compliance.<ref name="DePalmaAClose12" /><ref name="WuBarrier22" />
| |
| *In settings where sample or specimen tracking ties readily to the research side, as with bioanalytical labs assisting with toxicological and pharmacological research studies, data and information management is much more cohesive and efficient with a LIMS + ELN pairing. This in turn allows for quicker clinical and preclinical reporting, as well as more streamlined and maximized regulatory compliance and reporting. (The level of regulatory compliance needed with these labs can vary with the type of workflow, however.)<ref name="DePalmaAClose12" /><ref>{{Citation |last=Bennett |first=Patrick |last2=LeLacheur |first2=Richard M. |date=2017 |editor-last=Rocci |editor-first=Mario L. |editor2-last=Lowes |editor2-first=Stephen |title=Logistical and Operational Practice in the Regulated Bioanalysis Laboratory |url=http://link.springer.com/10.1007/978-3-319-54802-9_3 |work=Regulated Bioanalysis: Fundamentals and Practice |language=en |publisher=Springer International Publishing |place=Cham |volume=26 |pages=39–62 |doi=10.1007/978-3-319-54802-9_3 |isbn=978-3-319-54800-5 |accessdate=2024-03-06}}</ref>
| |
| *Of course, the instrument management, inventory control, data analysis, data visualization, and stability management functionality of a LIMS (the "laboratory control" portion of a lab implementing laboratory informatics solutions) can pair nicely with the experimental work and protocols maintained in the ELN (the "experiment and process control" portion). For example, the David Corey Lab of Harvard Medical School identified a strong need for integrated inventory management among it and its companion labs, which wasn't readily offered in many ELNs. The lab noted: "By integrating protocols and experiments with inventories of reagents and samples, researchers could work more efficiently, keeping track of samples, and knowing when to make orders. The inventory system also allows users to keep track of equipment, or even mice!"<ref name=":1" /> While they ultimately found an ELN that had this functionality, one can imagine a scenario where a lab has additional requirement found in a LIMS and lands on a LIMS + ELN combined solution that not only meets their needs but saves them money and training headaches, while improving overall research efficiencies.<ref name=":1" /><ref name="WuBarrier22" /><ref name="SLThePotent23" />
| |
|
| |
| ==Conclusion==
| |
| This brief Q&A article attempted to address the potential benefits of using both a LIMS and an ELN in the same laboratory. From the start, the importance of defining what an ELN is and what it can do outside of a LIMS and its functionality was identified and followed through. An ELN takes the place of paper-based laboratory notebooks, which are increasingly incompatible with the modern digital workflows of today's laboratories. In particular, academic and industrial research labs are the most likely to use notebooks, though finding the right ELN for the job can be difficult thanks to a number of factors, including vast differences in research workflows and ELN options. However, a base set of functionality for the ELN was identified as important to research labs, with some of that functionality sharing similarities to that of a LIMS. Yet not all LIMS and ELN are equal, and while the the two systems have their differences and similarities, pairing the two can make sense in certain contexts, especially if appropriate considerations are made. The pairing of the two in certain research environments can lead to valuable re-evaluation of laboratory workflows and processes, greater workflow efficiencies, improved regulatory compliance, more rapid discoveries and time-to-market, and improved reporting.
| |
|
| |
| ==References==
| |
| {{Reflist|colwidth=30em}}
| |
|
| |
| <!---Place all category tags here-->
| |
