Difference between revisions of "Ms-lims"
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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== | ||
| Line 131: | Line 142: | ||
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== | ||
| Line 146: | Line 158: | ||
* {{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== | ||
Revision as of 21:27, 12 October 2012
 | |
| Developer(s) | ms-lims development group |
|---|---|
| Initial release | Unknown |
| Stable release |
7.7.7 (October 18, 2012) [±] |
| 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 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.[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 |
|---|---|
| 7.7.6 | 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 |
Features
Features of ms-lims include[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
- Screenshots can be found in the ms-lims user manual.
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. http://onlinelibrary.wiley.com/doi/10.1002/pmic.200900409/full.
- Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S.; Martens, Lennart (2011). "compomics-utilities: an open-source Java library for computational proteomics". BMC Bioinformatics 11: 70. doi:10.1186/1471-2105-12-70. http://www.biomedcentral.com/1471-2105/12/70.
External links
References
- ↑ 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.
- ↑ 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.
- ↑ "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.
- ↑ "ReleaseNotes - ms-lims". Google Project Hosting. http://code.google.com/p/ms-lims/wiki/ReleaseNotes. Retrieved 12 October 2012.
- ↑ 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.
