Difference between revisions of "Ms-lims"

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| developer              = [http://code.google.com/p/ms-lims/people/list ms-lims development group]
| developer              = [http://code.google.com/p/ms-lims/people/list ms-lims development group]
| released              = Unknown
| released              = Unknown
| 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  = Java
| programming language  = Java
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}}
}}


'''ms-lims''' is free open-source [[laboratory informatics]] software that automates the processing, identification, quantification, and interpretation of [[mass spectrometry]]-based [[proteomics]] data.
'''ms-lims''' was a free open-source [[laboratory informatics]] software solution that automated the processing, identification, quantification, and interpretation of [[mass spectrometry]]-based [[proteomics]] data.


==Product history==
==Product history==
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! Version
! Version
! Release date
! Release date
|- valign="top"
| 7.7.7
| 18 October 2012
|- valign="top"
|- valign="top"
| 7.7.6
| 7.7.6
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| 05 May 2010
| 05 May 2010
|}
|}
The last appreciable update to the software came nearly 10 years ago, and as of August 2022, the software is considered discontinued or abandoned.


==Features==
==Features==


Features of ms-lims include<ref name="msguidePDF">{{cite web |url=http://ms-lims.googlecode.com/files/ms_lims_manual.pdf |title=ms-lims Manual |author=Helsens, Kenny; Colaert, Niklaas; Wortelkamp, Steffi; Barsnes, Harald; Vaudel, Marc; Martens, Lennart |publisher=Ghent University |accessdate=12 October 2012}}</ref>:
Features of ms-lims included<ref name="msguidePDF">{{cite web |url=http://ms-lims.googlecode.com/files/ms_lims_manual.pdf |title=ms-lims Manual |author=Helsens, Kenny; Colaert, Niklaas; Wortelkamp, Steffi; Barsnes, Harald; Vaudel, Marc; Martens, Lennart |publisher=Ghent University |accessdate=12 October 2012}}</ref>:


* project management
* project management
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* project analysis tools
* project analysis tools
* automated validation of quantitation files
* automated validation of quantitation files


==Hardware/software requirements==
==Hardware/software requirements==
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==Further reading==
==Further reading==
 
* {{cite journal |title=ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics |journal=Proteomics |author=Helsens, Kenny; Colaert, Niklaas; Barsnes, Harald; Muth, Thilo; Flikka, Kristian; Staes, An; Timmerman, Evy; Wortelkamp, Steffi; Sickmann, Albert; Vandekerckhove, Joël; Gevaert, Kris; Martens, Lennart |volume=6 |issue=10 |pages=1261–1264 |year=2010 |doi=10.1002/pmic.200900409 |pmid=20058248}}
* {{cite journal |journal=Proteomics |year=2010 |volume=6 |issue=10 |pages=1261–1264 |title=ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics |author=Helsens, Kenny; Colaert, Niklaas; Barsnes, Harald; Muth, Thilo; Flikka, Kristian; Staes, An; Timmerman, Evy; Wortelkamp, Steffi; Sickmann, Albert; Vandekerckhove, Joël; Gevaert, Kris; Martens, Lennart |url=http://onlinelibrary.wiley.com/doi/10.1002/pmic.200900409/full |doi=10.1002/pmic.200900409}}
 
* {{cite journal |journal=BMC Bioinformatics |year=2011 |volume=11 |pages=70 |title=compomics-utilities: an open-source Java library for computational proteomics |author=Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S.; Martens, Lennart |url=http://www.biomedcentral.com/1471-2105/12/70 |doi=10.1186/1471-2105-12-70}}
* {{cite journal |journal=BMC Bioinformatics |year=2011 |volume=11 |pages=70 |title=compomics-utilities: an open-source Java library for computational proteomics |author=Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S.; Martens, Lennart |url=http://www.biomedcentral.com/1471-2105/12/70 |doi=10.1186/1471-2105-12-70}}


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<!---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)]]

Latest revision as of 19:08, 19 August 2022

ms-lims
Ms-lims logo.jpg
Developer(s) ms-lims development group
Initial release Unknown
Discontinued

7.7.7  (October 18, 2012; 11 years ago (2012-10-18))

[±]
Preview release none [±]
Written in Java
Operating system Cross-platform
Type Laboratory informatics software
License(s) Apache License 2.0
Website code.google.com/p/ms-lims

ms-lims was a free open-source laboratory informatics software solution that automated the processing, identification, quantification, and interpretation of mass spectrometry-based proteomics data.

Product history

Development of ms-lims began in 2003 via the Department of Biochemistry – Ghent University and the Department of Medical Protein Research - VIB.[1] Development began out of a need for automation of mass spectrometer-related proteomics data management and processing within a dynamic client-server architecture.[2] At an unknown point, the ms-lims project moved to Google Project Hosting as a public open-source project.

The following table shows the dates of various releases, based on a listing of download files and release notes on the site.[3][4] Many releases were made before this (shown in this changelog), though release dates are not currently known:

Version Release date
7.7.7 18 October 2012
7.7.6 30 July 2012
7.7.5 23 May 2012
7.7.4 06 April 2012
7.7.3 28 March 2012
7.7.2 21 March 2012
7.7.1 12 March 2012
7.6.10 01 February 2012
7.6.9 01 February 2012
7.6.8 21 December 2011
7.6.7 20 December 2011
7.6.6 25 August 2011
7.6.5 11 August 2011
7.6.4 04 July 2011
7.6.3 01 July 2011
7.6.2 20 June 2011
7.6.1 03 May 2011
7.6.0 24 April 2011
7.5.5 24 March 2011
7.5.4 21 March 2011
7.5.2 03 November 2010
7.5.1 21 October 2010
7.5.0 08 October 2010
7.4.1 09 August 2010
7.4.0 23 June 2010
7.3.3 27 May 2010
7.3.2 21 May 2010
7.3.1 18 May 2010
7.3.0 05 May 2010

The last appreciable update to the software came nearly 10 years ago, and as of August 2022, the software is considered discontinued or abandoned.

Features

Features of ms-lims included[5]:

  • project management
  • mass spectra storage
  • spectra merging
  • extract identifications from dat-file
  • extract quantitations from quantitation files
  • manually validate with built-in peptizer
  • query support
  • binary file storage
  • project analysis tools
  • automated validation of quantitation files

Hardware/software requirements

Installation requirements for ms-lims include:

  • Java 5 or later
  • MySQL (latest)

More installation information can be found in the user manual.

Videos, screenshots, and other media

Entities using ms-lims

Further reading

  • Helsens, Kenny; Colaert, Niklaas; Barsnes, Harald; Muth, Thilo; Flikka, Kristian; Staes, An; Timmerman, Evy; Wortelkamp, Steffi; Sickmann, Albert; Vandekerckhove, Joël; Gevaert, Kris; Martens, Lennart (2010). "ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics". Proteomics 6 (10): 1261–1264. doi:10.1002/pmic.200900409. PMID 20058248. 


External links

References

  1. Helsens, Kenny (15 March 2009). "ms-lims and friends: Tools to store and analyze proteomics information". Ghent University. http://estrellapolar.cnb.csic.es/proteored/Biblioteca/Ficheros/91042909_8-MS-LIMS_and_friends_tools_to_store_and_analyze_large_scale_proteomics_data..pdf. Retrieved 12 October 2012. 
  2. Helsens, Kenny; Colaert, Niklaas; Barsnes, Harald; Muth, Thilo; Flikka, Kristian; Staes, An; Timmerman, Evy; Wortelkamp, Steffi; Sickmann, Albert; Vandekerckhove, Joël; Gevaert, Kris; Martens, Lennart (2010). "ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics". Proteomics 6 (10): 1261–1264. doi:10.1002/pmic.200900409. http://onlinelibrary.wiley.com/doi/10.1002/pmic.200900409/full. 
  3. "Downloads - ms-lims". Google Project Hosting. http://code.google.com/p/ms-lims/downloads/list?can=1&q=&colspec=Filename+Summary+Uploaded+ReleaseDate+Size+DownloadCount. Retrieved 12 October 2012. 
  4. "ReleaseNotes - ms-lims". Google Project Hosting. http://code.google.com/p/ms-lims/wiki/ReleaseNotes. Retrieved 12 October 2012. 
  5. Helsens, Kenny; Colaert, Niklaas; Wortelkamp, Steffi; Barsnes, Harald; Vaudel, Marc; Martens, Lennart. "ms-lims Manual". Ghent University. http://ms-lims.googlecode.com/files/ms_lims_manual.pdf. Retrieved 12 October 2012.