Ms-lims - Revision history

Shawndouglas: /* Further reading */ Spacing

2022-08-19T19:08:24Z

Shawndouglas: /* Product history */

2022-08-19T19:08:05Z

Product history

← Older revision		Revision as of 19:08, 19 August 2022
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	\|}		\|}

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

Shawndouglas: Updated to abandoned/discontinued

2022-08-19T19:07:27Z

Updated to abandoned/discontinued

← Older revision		Revision as of 19:07, 19 August 2022
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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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	\| 05 May 2010		\| 05 May 2010
	\|}		\|}

			The last appreciable update to the software came more than 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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	<!---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)]]

Shawndouglas: /* Further reading */ Updated ref

2016-01-11T22:16:30Z

Shawndouglas: /* Product history */ Added version.

2013-02-01T19:08:50Z

Product history: Added version.

← Older revision		Revision as of 19:08, 1 February 2013
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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

Shawndouglas: /* Features */ Spacing.

2012-10-12T21:27:58Z

Features: Spacing.

← Older revision		Revision as of 21:27, 12 October 2012
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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==

Shawndouglas: Updated.

2012-10-12T21:27:35Z

Updated.

← Older revision		Revision as of 21:27, 12 October 2012
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	==Features==		==Features==

	Features of ms-lims include:		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>:

			* 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==		==Hardware/software requirements==
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	Installation requirements for ms-lims include:		Installation requirements for ms-lims include:

	*		* Java 5 or later
			* [[MySQL]] (latest)

			More installation information can be found in the [http://ms-lims.googlecode.com/files/ms_lims_manual.pdf user manual].

	==Videos, screenshots, and other media==		==Videos, screenshots, and other media==

	*		* Screenshots can be found in the [http://ms-lims.googlecode.com/files/ms_lims_manual.pdf ms-lims user manual].

	==Entities using ms-lims==		==Entities using ms-lims==
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	* {{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=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}}

	==External links==		==External links==

	*		* [http://www.biochemicrofys.ugent.be/index2.html Department of Biochemistry – Ghent University]
			* [http://www.vib.be/en/research/departments/Pages/VIB-Department-of-Medical-Protein-Research-UGent.aspx Department of Medical Protein Research - VIB]

	==References==		==References==

Shawndouglas: Created article stub. More to come.

2012-10-12T20:48:44Z

Created article stub. More to come.

New page

{{lowercase title}}
{{Infobox software
| name = ms-lims
| title = ms-lims
| logo = [[File:Ms-lims_logo.jpg|200px]]
| screenshot = 
| caption =
| collapsible =
| author =
| developer = [http://code.google.com/p/ms-lims/people/list ms-lims development group]
| released = Unknown
| discontinued =
| frequently updated = yes
| programming language = Java
| operating system = Cross-platform
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = Apache License 2.0
| website = [http://code.google.com/p/ms-lims/ code.google.com/p/ms-lims]
}}

'''ms-lims''' is free open-source [[laboratory informatics]] software that automates 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.<ref name="ms_friendsPDF">{{cite web |url=http://estrellapolar.cnb.csic.es/proteored/Biblioteca/Ficheros/91042909_8-MS-LIMS_and_friends_tools_to_store_and_analyze_large_scale_proteomics_data..pdf |title=ms-lims and friends: Tools to store and analyze proteomics information |author=Helsens, Kenny |publisher=Ghent University |date=15 March 2009 |accessdate=12 October 2012}}</ref> Development began out of a need for automation of mass spectrometer-related proteomics data management and processing within a dynamic client-server architecture.<ref name="msTechBrief">{{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}}</ref> 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.<ref name="msDloadsAll">{{cite web |url=http://code.google.com/p/ms-lims/downloads/list?can=1&q=&colspec=Filename+Summary+Uploaded+ReleaseDate+Size+DownloadCount |title=Downloads - ms-lims |publisher=Google Project Hosting |accessdate=12 October 2012}}</ref><ref name="msWikiRN">{{cite web |url=http://code.google.com/p/ms-lims/wiki/ReleaseNotes |title=ReleaseNotes - ms-lims |publisher=Google Project Hosting |accessdate=12 October 2012}}</ref> Many releases were made before this (shown in [http://ms-lims.googlecode.com/svn/trunk/src/main/resources/about.txt this changelog]), though release dates are not currently known:

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

==Features==

Features of ms-lims include:

*

==Hardware/software requirements==

Installation requirements for ms-lims include:

*

==Videos, screenshots, and other media==

*

==Entities using ms-lims==

==Further reading==

* {{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}}

==External links==

*

==References==
<references />


[[Category:Bioinformatics software (open source)]]
[[Category:Laboratory informatics software (open source)]]

← Older revision		Revision as of 19:08, 19 August 2022
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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 \|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=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}}

← Older revision		Revision as of 22:16, 11 January 2016
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	==Further reading==		==Further reading==

	* {{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 \|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=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}}