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

From LIMSWiki
Jump to navigationJump to search
Line 23: Line 23:
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 research today 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" />
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 research today 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 DNA [[sequencing]]<ref>{{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> or chemical analysis.<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>
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]]<ref>{{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> or chemical analysis.<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>{{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>{{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, 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>


*https://www.limswiki.org/index.php/LII:The_Application_of_Informatics_to_Scientific_Work:_Laboratory_Informatics_for_Newbies#Expanding_the_research_team
*https://www.limswiki.org/index.php/LII:The_Application_of_Informatics_to_Scientific_Work:_Laboratory_Informatics_for_Newbies#Expanding_the_research_team

Revision as of 23:25, 5 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.

Sandbox begins below

[[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]

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 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 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. ↑ 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. ↑ 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. 
Retrieved from "https://www.limswiki.org/index.php?title=User:Shawndouglas/sandbox/sublevel12&oldid=58698"