Difference between revisions of "User:Shawndouglas/sandbox/sublevel12"

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* direct real-time recording of data and information in various (standard) formats like text, images, tables, chromatograms, and raw data files
* 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.
* robust support for tagging, searching, and reusing data, information, files, etc.
* support for standard vocabularies and [[metadata]] management
* support for standard vocabularies and [[metadata]] schemes
* lending of structure to data and information through the use of preformatted or customizable templates with drag-and-drop support
* 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
* flexible creation of links between records, including reference managers and other notebooks
Line 38: Line 38:
* inclusion of messaging and commenting functionality for better collaboration
* inclusion of messaging and commenting functionality for better collaboration
* inclusion of safety data, including flags for dangerous chemicals
* inclusion of safety data, including flags for dangerous chemicals
* data integrity and security tools like electronic signatures, time-stamped audit logs, controlled access levels, automated import of instrument data, and archiving capabilities
* 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)
* 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
* accommodation of a scheduling option for routine procedures such as equipment qualification and study-related timelines
* support for chemical, genetic, and other molecular libraries and visualization
* support for standard chemical, genetic, and other molecular libraries and visualization formats, e.g., LaTeX
* inventory management of instruments, reagents, samples, etc. (usually associated with a LIMS, but useful as a standalone option within an ELN<ref name="DirnaglAPocket16" /><ref name=":1" />)
* inventory management of instruments, reagents, samples, etc. (usually associated with a LIMS, but useful as a standalone option within an ELN<ref name="DirnaglAPocket16" /><ref name=":1" />)


Revision as of 00:17, 6 March 2024

This is sublevel12 of my sandbox, where I play with features and test MediaWiki code. If you wish to leave a comment for me, please see my discussion page instead.

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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 research today 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 DNA sequencing[5] or chemical analysis.[6] 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[7][8], even leading some to develop their own custom ELNs, often as an extension of some other piece of software like a knowledge management system[9], course management system[10], or note-taking application.[11]

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][7][8][12][13]:


  • 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
  • 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 and visualization formats, e.g., LaTeX
  • inventory management of instruments, reagents, samples, etc. (usually associated with a LIMS, but useful as a standalone option within an ELN[3][8])

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]


Pairing a LIMS and ELN together

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 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. ↑ 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. ↑ 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. 
  7. ↑ 7.0 7.1 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. 
  8. ↑ 8.0 8.1 8.2 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. 
  9. ↑ 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. 
  10. ↑ 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. 
  11. ↑ 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. 
  12. ↑ 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. 
  13. ↑ 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. 
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