Difference between revisions of "OpenLabFramework"

From LIMSWiki
Jump to navigationJump to search
(Abandoned)
 
(2 intermediate revisions by the same user not shown)
Line 9: Line 9:
| developer              = Markus List and Jochen Thomas
| developer              = Markus List and Jochen Thomas
| released              = {{Start date|2010|06|21}} (0.1)<ref name="OLFStartArch">{{cite web |archiveurl=https://web.archive.org/web/20100821221354/http://sourceforge.net/projects/openlaboratory/files |url=http://sourceforge.net/projects/openlaboratory/files/ |title=Open Laboratory Framework - Files |publisher=SourceForge |archivedate=21 August 2010 |accessdate=25 January 2016}}</ref>
| released              = {{Start date|2010|06|21}} (0.1)<ref name="OLFStartArch">{{cite web |archiveurl=https://web.archive.org/web/20100821221354/http://sourceforge.net/projects/openlaboratory/files |url=http://sourceforge.net/projects/openlaboratory/files/ |title=Open Laboratory Framework - Files |publisher=SourceForge |archivedate=21 August 2010 |accessdate=25 January 2016}}</ref>
| discontinued          =  
| discontinued          = Yes
| frequently updated    = yes<!-- Release version update? Don't edit this page, just click on the version number! -->
| frequently updated    = yes<!-- Release version update? Don't edit this page, just click on the version number! -->
| programming language  = JavaScript, XML
| programming language  = JavaScript, XML
Line 22: Line 22:
}}
}}


'''OpenLabFramework''' (formerly '''Open Laboratory Framework''') is a web-based [[laboratory information management system]] (LIMS) front-end that provides an extensible framework for better laboratory functionality.
'''OpenLabFramework''' (formerly '''Open Laboratory Framework''') was a web-based [[laboratory information management system]] (LIMS) front-end—with additional [[electronic laboratory notebook]] (ELN) capabilities—that provided an extensible framework for better laboratory functionality.


==Product history==
==Product history==
The OpenLabFramework project appears to have began as the "Open Laboratory Framework" project, with it first being opened up on Sourceforge on February 15, 2010.<ref name="OLFHomeArch">{{cite web |archiveurl=https://web.archive.org/web/20100821221349/http://sourceforge.net/projects/openlaboratory |url=http://sourceforge.net/projects/openlaboratory/ |title=Open Laboratory Framework |publisher=SourceForge |archivedate=21 August 2010 |accessdate=25 January 2016}}</ref> by Jochen Thomas and Markus List, likely as part of a project through German software developer OSTHUS.<ref name="MListLinked">{{cite web |url=http://dk.linkedin.com/pub/markus-list/27/809/3ba |title=Markus List - Bioinformatics in Cancer Research |publisher=LinkedIn |accessdate=02 October 2012}}</ref><ref name="JThomasOhloh">{{cite web |url=http://www.ohloh.net/accounts/jochen-thomas |title=J. Thomas - Ohloh |publisher=Ohloh |accessdate=02 October 2012}}</ref> The last SourceForge-based file release was with version 0.7 on December 7, 2011<ref name="OLFStartArch" />. On January 7, 2014, the project moved from SourceForge to GitHub<ref name="OLFStartArch" />, with several updates to the software arriving in 2014 and 2015.<ref name="OLFGit">{{cite web |url=https://github.com/NanoCAN/OpenLabFramework/releases |title=NanoCAN/OpenLabFramework - Releases |publisher=GitHub |accessdate=15 June 2015}}</ref> This coincided with the 2014 publication of a research paper on the software by List et al., citing the following as reason for the software's creation<ref name="ListEff14">{{cite journal |title=Efficient sample tracking with OpenLabFramework |journal=Scientific Reports |author=List, Markus; Schmidt, Steffen; Trojnar, Jakub; Thomas, Jochen; Thomassen, Mads; Kruse, Torben A.; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan |volume=4 |pages=4278 |year=2014 |doi=10.1038/srep04278 |pmid=24589879 |pmc=PMC3940979 |accessdate=25 January 2016}}</ref>:
The OpenLabFramework project appears to have began as the "Open Laboratory Framework" project, with it first being opened up on Sourceforge on February 15, 2010.<ref name="OLFHomeArch">{{cite web |archiveurl=https://web.archive.org/web/20100821221349/http://sourceforge.net/projects/openlaboratory |url=http://sourceforge.net/projects/openlaboratory/ |title=Open Laboratory Framework |publisher=SourceForge |archivedate=21 August 2010 |accessdate=25 January 2016}}</ref> by Jochen Thomas and Markus List, likely as part of a project through German software developer OSTHUS.<ref name="MListLinked">{{cite web |url=http://dk.linkedin.com/pub/markus-list/27/809/3ba |title=Markus List - Bioinformatics in Cancer Research |publisher=LinkedIn |accessdate=02 October 2012}}</ref><ref name="JThomasOhloh">{{cite web |url=http://www.ohloh.net/accounts/jochen-thomas |title=J. Thomas - Ohloh |publisher=Ohloh |accessdate=02 October 2012}}</ref> The last SourceForge-based file release was with version 0.7 on December 7, 2011<ref name="OLFStartArch" />. On January 7, 2014, the project moved from SourceForge to GitHub<ref name="OLFStartArch" />, with several updates to the software arriving in 2014 and 2015.<ref name="OLFGit">{{cite web |url=https://github.com/NanoCAN/OpenLabFramework/releases |title=NanoCAN/OpenLabFramework - Releases |publisher=GitHub |accessdate=15 June 2015}}</ref> This coincided with the 2014 publication of a research paper on the software by List ''et al.'', citing the following as reason for the software's creation<ref name="ListEff14">{{cite journal |title=Efficient sample tracking with OpenLabFramework |journal=Scientific Reports |author=List, Markus; Schmidt, Steffen; Trojnar, Jakub; Thomas, Jochen; Thomassen, Mads; Kruse, Torben A.; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan |volume=4 |pages=4278 |year=2014 |doi=10.1038/srep04278 |pmid=24589879 |pmc=PMC3940979 |accessdate=25 January 2016}}</ref>:


<blockquote>There is, however, no dedicated LIMS for the management of large vector construct and cell line libraries. At our Lundbeck Foundation Center of Excellence in Nanomedicine (NanoCAN) at the University of Southern Denmark in Odense such large-scale libraries need to be handled efficiently ... This motivated us to develop a novel open-source LIMS platform: OpenLabFramework (OLF).</blockquote>
<blockquote>There is, however, no dedicated LIMS for the management of large vector construct and cell line libraries. At our Lundbeck Foundation Center of Excellence in Nanomedicine (NanoCAN) at the University of Southern Denmark in Odense such large-scale libraries need to be handled efficiently ... This motivated us to develop a novel open-source LIMS platform: OpenLabFramework (OLF).</blockquote>
In the fall of 2015, List ''et al.'' published another paper describing a new add-on to OpenLabFramework called "OpenLabNotes." Citing the benefits of integrating a home-grown ELN into the LIMS platform, the group stated: "OpenLabNotes effectively closes the gap between research documentation and sample management, thus making OpenLabFramework more attractive for laboratories that seek to increase productivity through electronic data management."<ref name="ListOpenLabNotes15">{{cite journal |title=OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework |journal=Journal of Integrative Bioinformatics |author=List, M.; Franz, M.; Tan, Q.; Mollenhauer, J.; Baumbach, J. |volume=12 |issue=3 |pages=274 |year=2015 |doi=10.2390/biecoll-jib-2015-274 |pmid=26673790}}</ref> OpenLabNotes was first introduced to the framework with version 1.3.0 in February 2015<ref name="OLF130">{{cite web |url=https://github.com/NanoCAN/OpenLabFramework/releases/tag/v1.3.0 |title=v.1.3.0 WAR file for server deployment |author=List, M. |publisher=GitHub, Inc |date=25 February 2015 |accessdate=21 July 2016}}</ref> and significantly improved with version 1.3.2 in May 2015.<ref name="OLF132">{{cite web |url=https://github.com/NanoCAN/OpenLabFramework/releases/tag/v.1.3.2 |title=v.1.3.2 WAR file for server deployment |author=List, M. |publisher=GitHub, Inc |date=04 May 2015 |accessdate=21 July 2016}}</ref>
As of May 2021, the demo site is no longer available, and updates haven't been made for over five years. The project is presumably abandoned.


==Features==
==Features==
Features of OpenLabFramework include<ref name="OLFHomeArch" />:
Features of OpenLabFramework included<ref name="OLFHomeArch" />:


* web-based front-end
* web-based front-end
Line 36: Line 40:
* experiment management
* experiment management
* inventory management
* inventory management
* [[electronic laboratory notebook]] capabilities<ref name="ListOpenLabNotes15" /><ref name="OLF132" />
* barcode and printing support
* barcode and printing support
* document management
* document management
Line 41: Line 46:


==Hardware/software requirements==
==Hardware/software requirements==
Installation requirements [https://github.com/NanoCAN/OpenLabFramework/wiki/Getting-Started include]:
Installation requirements [https://github.com/NanoCAN/OpenLabFramework/wiki/Getting-Started included]:


* Grails 2.2.x
* Grails 2.5.3
* a supported browser, including Chrome (31.0.1650.63) or Firefox (26.0)
* a supported browser, including Chrome (31.0.1650.63) or Firefox (26.0)


==Videos, screenshots, and other media==
==Videos, screenshots, and other media==
* A demo of OpenLabFramework can be found at [http://www.nanocan.dk/openlabframework/demo http://www.nanocan.dk/openlabframework/demo]. (user: admin, password: demo0815)  
* A demo of OpenLabFramework originally could be found at [http://www.nanocan.dk/openlabframework/demo http://www.nanocan.dk/openlabframework/demo]. (user: admin, password: demo0815)  


==Entities using OpenLabFramework==
==Entities using OpenLabFramework==
Line 54: Line 59:
==Further reading==
==Further reading==
* {{cite journal |title=Efficient sample tracking with OpenLabFramework |journal=Scientific Reports |author=List, Markus; Schmidt, Steffen; Trojnar, Jakub; Thomas, Jochen; Thomassen, Mads; Kruse, Torben A.; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan |volume=4 |pages=4278 |year=2014 |doi=10.1038/srep04278 |pmid=24589879 |pmc=PMC3940979}} (Alternatively, found on LIMSwiki [[Journal:Efficient sample tracking with OpenLabFramework|here]].)
* {{cite journal |title=Efficient sample tracking with OpenLabFramework |journal=Scientific Reports |author=List, Markus; Schmidt, Steffen; Trojnar, Jakub; Thomas, Jochen; Thomassen, Mads; Kruse, Torben A.; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan |volume=4 |pages=4278 |year=2014 |doi=10.1038/srep04278 |pmid=24589879 |pmc=PMC3940979}} (Alternatively, found on LIMSwiki [[Journal:Efficient sample tracking with OpenLabFramework|here]].)
* {{cite journal |title=OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework |journal=Journal of Integrative Bioinformatics |author=List, Markus; Franz, Michael; Tan, Qihua; Mollenhauer, Jan; Baumbach, Jan |volume=12 |issue=3 |pages=274 |year=2015 |doi=10.2390/biecoll-jib-2015-274 |pmid=26673790}}


==External links==
==External links==
Line 64: Line 71:


<!---Place all category tags here-->
<!---Place all category tags here-->
[[Category:Bioinformatics software (open source)]]
[[Category:Discontinued or abandoned software (open source)]]
[[Category:Laboratory informatics software (open source)]]
[[Category:Laboratory information management systems (open source)]]

Latest revision as of 17:41, 4 May 2021

OpenLabFramework
Developer(s) Markus List and Jochen Thomas
Initial release June 21, 2010 (2010-06-21) (0.1)[1]
Discontinued

1.4.1  (March 3, 2016; 8 years ago (2016-03-03))

[±]
Written in JavaScript, XML
Operating system platform-independent
Type Laboratory informatics software
License(s) GNU Public License v3.0[2]
Website github.com/NanoCAN/OpenLabFramework

OpenLabFramework (formerly Open Laboratory Framework) was a web-based laboratory information management system (LIMS) front-end—with additional electronic laboratory notebook (ELN) capabilities—that provided an extensible framework for better laboratory functionality.

Product history

The OpenLabFramework project appears to have began as the "Open Laboratory Framework" project, with it first being opened up on Sourceforge on February 15, 2010.[3] by Jochen Thomas and Markus List, likely as part of a project through German software developer OSTHUS.[4][5] The last SourceForge-based file release was with version 0.7 on December 7, 2011[1]. On January 7, 2014, the project moved from SourceForge to GitHub[1], with several updates to the software arriving in 2014 and 2015.[6] This coincided with the 2014 publication of a research paper on the software by List et al., citing the following as reason for the software's creation[7]:

There is, however, no dedicated LIMS for the management of large vector construct and cell line libraries. At our Lundbeck Foundation Center of Excellence in Nanomedicine (NanoCAN) at the University of Southern Denmark in Odense such large-scale libraries need to be handled efficiently ... This motivated us to develop a novel open-source LIMS platform: OpenLabFramework (OLF).

In the fall of 2015, List et al. published another paper describing a new add-on to OpenLabFramework called "OpenLabNotes." Citing the benefits of integrating a home-grown ELN into the LIMS platform, the group stated: "OpenLabNotes effectively closes the gap between research documentation and sample management, thus making OpenLabFramework more attractive for laboratories that seek to increase productivity through electronic data management."[8] OpenLabNotes was first introduced to the framework with version 1.3.0 in February 2015[9] and significantly improved with version 1.3.2 in May 2015.[10]

As of May 2021, the demo site is no longer available, and updates haven't been made for over five years. The project is presumably abandoned.

Features

Features of OpenLabFramework included[3]:

  • web-based front-end
  • extensible framework
  • experiment management
  • inventory management
  • electronic laboratory notebook capabilities[8][10]
  • barcode and printing support
  • document management
  • data analysis

Hardware/software requirements

Installation requirements included:

  • Grails 2.5.3
  • a supported browser, including Chrome (31.0.1650.63) or Firefox (26.0)

Videos, screenshots, and other media

Entities using OpenLabFramework

University of Southern Denmark in Odense

Further reading

(Alternatively, found on LIMSwiki here.)
  • List, Markus; Franz, Michael; Tan, Qihua; Mollenhauer, Jan; Baumbach, Jan (2015). "OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework". Journal of Integrative Bioinformatics 12 (3): 274. doi:10.2390/biecoll-jib-2015-274. PMID 26673790. 


External links

References

  1. ↑ 1.0 1.1 1.2 "Open Laboratory Framework - Files". SourceForge. Archived from the original on 21 August 2010. https://web.archive.org/web/20100821221354/http://sourceforge.net/projects/openlaboratory/files. Retrieved 25 January 2016. 
  2. ↑ "Open Laboratory Framework: Project Summary". Ohloh. http://www.ohloh.net/p/olf. Retrieved 02 October 2012. 
  3. ↑ 3.0 3.1 "Open Laboratory Framework". SourceForge. Archived from the original on 21 August 2010. https://web.archive.org/web/20100821221349/http://sourceforge.net/projects/openlaboratory. Retrieved 25 January 2016. 
  4. ↑ "Markus List - Bioinformatics in Cancer Research". LinkedIn. http://dk.linkedin.com/pub/markus-list/27/809/3ba. Retrieved 02 October 2012. 
  5. ↑ "J. Thomas - Ohloh". Ohloh. http://www.ohloh.net/accounts/jochen-thomas. Retrieved 02 October 2012. 
  6. ↑ "NanoCAN/OpenLabFramework - Releases". GitHub. https://github.com/NanoCAN/OpenLabFramework/releases. Retrieved 15 June 2015. 
  7. ↑ List, Markus; Schmidt, Steffen; Trojnar, Jakub; Thomas, Jochen; Thomassen, Mads; Kruse, Torben A.; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan (2014). "Efficient sample tracking with OpenLabFramework". Scientific Reports 4: 4278. doi:10.1038/srep04278. PMC PMC3940979. PMID 24589879. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940979. Retrieved 25 January 2016. 
  8. ↑ 8.0 8.1 List, M.; Franz, M.; Tan, Q.; Mollenhauer, J.; Baumbach, J. (2015). "OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework". Journal of Integrative Bioinformatics 12 (3): 274. doi:10.2390/biecoll-jib-2015-274. PMID 26673790. 
  9. ↑ List, M. (25 February 2015). "v.1.3.0 WAR file for server deployment". GitHub, Inc. https://github.com/NanoCAN/OpenLabFramework/releases/tag/v1.3.0. Retrieved 21 July 2016. 
  10. ↑ 10.0 10.1 List, M. (4 May 2015). "v.1.3.2 WAR file for server deployment". GitHub, Inc. https://github.com/NanoCAN/OpenLabFramework/releases/tag/v.1.3.2. Retrieved 21 July 2016. 
Retrieved from "https://www.limswiki.org/index.php?title=OpenLabFramework&oldid=42486"