Difference between revisions of "LabKey Server"

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As early beta versions of the program floated around the Research Center, popularity grew, necessitating more resources. With the help of the FHCRC, Janaury 2005 saw the creation of a new entity called LabKey Software to better focus on the development of the software and to better support other institutions that would go on to utilize it. Additionally, another cohort of three former Microsoft developers joined the team to aid with development: George Snelling, Peter Hussey and Brendan MacLean.<ref name="LKBlog_Jan11" /><ref name="FHCRC_NewsMar05" /> The first public release of the software came on November 23, 2005, in the form of CPAS 1.1.<ref name="CPASArchive" /><ref name="LKAnnounce" /> A few weeks later the team released the source code to coincide with the the January 1, 2006 print publication of the groups corresponding paper in the ''Journal of Proteome Research'', making it officially an open-source release.<ref>{{cite web |url=https://www.labkey.org/announcements/home/thread.view?rowId=35 |title=CPAS 1.1 Source Code Released |author=Snelling, George |publisher=LabKey Software Foundation |date=8 December 2005 |accessdate=20 April 2012}}</ref> At that time, key features of the application included multiple standard-file formats, protein database search functionality, comprehensive experiment annotation, data sharing, and several proteomic-friendly analytic tools.<ref>{{cite web |url=http://proteomics.fhcrc.org/CPL/_docs/CPAS_media_backgrounder.doc |title=Hutchinson Center and NCI launch open-source software for proteomics analysis |publisher=Fred Hutchinson Cancer Research Center |date=8 December 2005 |accessdate=20 April 2012 |format=DOC}}</ref>
As early beta versions of the program floated around the Research Center, popularity grew, necessitating more resources. With the help of the FHCRC, Janaury 2005 saw the creation of a new entity called LabKey Software to better focus on the development of the software and to better support other institutions that would go on to utilize it. Additionally, another cohort of three former Microsoft developers joined the team to aid with development: George Snelling, Peter Hussey and Brendan MacLean.<ref name="LKBlog_Jan11" /><ref name="FHCRC_NewsMar05" /> The first public release of the software came on November 23, 2005, in the form of CPAS 1.1.<ref name="CPASArchive" /><ref name="LKAnnounce" /> A few weeks later the team released the source code to coincide with the the January 1, 2006 print publication of the groups corresponding paper in the ''Journal of Proteome Research'', making it officially an open-source release.<ref>{{cite web |url=https://www.labkey.org/announcements/home/thread.view?rowId=35 |title=CPAS 1.1 Source Code Released |author=Snelling, George |publisher=LabKey Software Foundation |date=8 December 2005 |accessdate=20 April 2012}}</ref> At that time, key features of the application included multiple standard-file formats, protein database search functionality, comprehensive experiment annotation, data sharing, and several proteomic-friendly analytic tools.<ref>{{cite web |url=http://proteomics.fhcrc.org/CPL/_docs/CPAS_media_backgrounder.doc |title=Hutchinson Center and NCI launch open-source software for proteomics analysis |publisher=Fred Hutchinson Cancer Research Center |date=8 December 2005 |accessdate=20 April 2012 |format=DOC}}</ref>


Over the next year CPAS went through several iterations, including an update to a more specific name of Computational Proteomics Analysis System. The software held the name up to version 1.7, released in December 2006. With version 2.0, released on April 16, 2007, came a renaming of the product to what is still known today as LabKey Server.<ref name="LKAnnounce" /><ref name="CPASOver" /><ref>{{cite web |url=http://proteomics.fhcrc.org/CPL/home.html |title=Computational Proteomics Laboratory |publisher=Fred Hutchinson Cancer Research Center |accessdate=20 April 2012}}</ref> In May 2007, the Canary Foundation announced the fifteen grant recipients of their $225,000 Bioinformatics Platform Dissemination Award, all of which would go towards the future design, development, and support of LabKey's software.<ref>{{cite web |url=http://www.canaryfoundation.org/newsroom/press-releases/grant-awardees-standardize-software-platform-for-early-cancer-detection/ |title=Grant Awardees Standardize Software Platform for Early Cancer Detection |publisher=Canary Foundation |date=22 May 2007 |accessdate=20 April 2012}}</ref>
Over the next year CPAS went through several iterations, including an update to a more specific name of Computational Proteomics Analysis System. The software held the name up to version 1.7, released in December 2006. With version 2.0, released on April 16, 2007, came a renaming of the product to what is still known today as LabKey Server.<ref name="LKAnnounce" /><ref name="CPASOver" /><ref>{{cite web |url=http://proteomics.fhcrc.org/CPL/home.html |title=Computational Proteomics Laboratory |publisher=Fred Hutchinson Cancer Research Center |accessdate=20 April 2012}}</ref> In May 2007, the Canary Foundation announced the fifteen grant recipients of their $225,000 Bioinformatics Platform Dissemination Award, all of which would go towards the future design, development, and support of LabKey's software.<ref>{{cite web |url=http://www.canaryfoundation.org/newsroom/press-releases/grant-awardees-standardize-software-platform-for-early-cancer-detection/ |title=Grant Awardees Standardize Software Platform for Early Cancer Detection |publisher=Canary Foundation |date=22 May 2007 |accessdate=20 April 2012}}</ref> That set of grant funding brought new features to CPAS/LabKey Server, including: improved label-free comparisons; MS peptide intensity data modules; and a more central integration of MsInspect, the signal processing component for locating and quantitating peptides.<ref>{{cite journal |url=http://cairob.fhcrc.org/science/international_biomarker/news/2007/december.html |title=CPAS update |journal=International Cancer Biomarker Consortium Newsletter |date=December 2007 |volume=3 |issue=4 |publisher=Fred Hutchinson Cancer Research Center |accessdate=20 April 2012}}</ref>


The 2.x incrementation ended with version 2.3 in February 2008.<ref name="LKAnnounce" /> The subsequent release after version 2.3 was 8.1 on May 1, 2008, though the increment jump was never publicly explained.<ref>{{cite web |url=https://www.labkey.org/project/home/Documentation/Archive/8.1/begin.view? |title=Get Started With LabKey Server 8.1 |publisher=LabKey Software Foundation |date=1 May 2008 |accessdate=20 April 2012}}</ref>  
The 2.x incrementation ended with version 2.3 in February 2008.<ref name="LKAnnounce" /> The subsequent release after version 2.3 was 8.1 on May 1, 2008, though the increment jump was never publicly explained.<ref>{{cite web |url=https://www.labkey.org/project/home/Documentation/Archive/8.1/begin.view? |title=Get Started With LabKey Server 8.1 |publisher=LabKey Software Foundation |date=1 May 2008 |accessdate=20 April 2012}}</ref>  


Shortly after release of 8.1, several news releases indicated LabKey would be lending support to Seattle businesses Insilicos and the Institute for Systems Biology (ISB) in an effort port proteomics software tools like LabKey Server through Amazon's cloud servers, allowing potential research groups with IT budgets to utilize the proteomics applications, scaling up web service as demand grows.<ref>{{cite web |url=http://insilicos.com/news/insilicos-awarded-grant-for-life-science-computing |title=Insilicos Awarded Grant for Life Science Computing |publisher=Insilicos LLC |date=5 May 2008 |accessdate=20 April 2012}}</ref><ref>{{cite web |url=http://www.genomeweb.com/informatics/insilicos-partners-labkey-isb-port-proteomics-software-tools-amazon’s-cloud |title=Insilicos Partners with LabKey, ISB to Port Proteomics Software Tools to Amazon’s Cloud |author=Toner, Bernadette |publisher=Genomeweb LLC |date=9 May 2008 |accessdate=20 April 2012}}</ref>
Shortly after release of 8.1, several news releases indicated LabKey would be lending support to Seattle businesses Insilicos and the Institute for Systems Biology (ISB). The goal of the collaboration was to port proteomics software tools like LabKey Server through Amazon's cloud servers, allowing potential research groups with IT budgets to utilize the proteomics applications and scale up web service as demand grows.<ref>{{cite web |url=http://insilicos.com/news/insilicos-awarded-grant-for-life-science-computing |title=Insilicos Awarded Grant for Life Science Computing |publisher=Insilicos LLC |date=5 May 2008 |accessdate=20 April 2012}}</ref><ref>{{cite web |url=http://www.genomeweb.com/informatics/insilicos-partners-labkey-isb-port-proteomics-software-tools-amazon’s-cloud |title=Insilicos Partners with LabKey, ISB to Port Proteomics Software Tools to Amazon’s Cloud |author=Toner, Bernadette |publisher=Genomeweb LLC |date=9 May 2008 |accessdate=20 April 2012}}</ref> A few months later, LabKey announced another collaboration, this time with the Microsoft BioIT Alliance, an association of life science organizations and informatics companies focused on accelerating the pace of drug discovery and development.<ref>{{cite web |url=http://www.businesswire.com/news/google/20080918005145/en |title=LabKey Software Joins BioIT Alliance |publisher=Business Wire |date=18 September 2012 |accessdate=20 April 2012}}</ref>
 
Version 9.1 of LabKey was released on April 2, 2009<ref>{{cite web |url=https://www.labkey.org/project/home/Documentation/Archive/9.1/begin.view? |title=Get Started With LabKey Server 9.1 |publisher=LabKey Software Foundation |date=2 April 2009 |accessdate=20 April 2012}}</ref>, with 10.1 arriving in March 2010<ref>{{cite web |url=https://www.labkey.org/project/home/Documentation/Archive/10.1/begin.view? |title=Get Started With LabKey Server 10.1 |publisher=LabKey Software Foundation |date=10 March 2010 |accessdate=20 April 2012}}</ref> and 11.1 releasing in April 2011.<ref>{{cite web |url=https://www.labkey.org/project/home/Documentation/Archive/11.1/begin.view? |title=Get Started With LabKey Server v11.1 |publisher=LabKey Software Foundation |date=12 April 2011 |accessdate=20 April 2012}}</ref> The latest version, 11.3, went live in December 2011, featuring enhanced data management, data visualization, and security functions.


==Features==
==Features==

Revision as of 00:25, 21 April 2012

LabKey Server
Developer(s) LabKey Corporation and the LabKey Software Foundation
Initial release April 16, 2007 (2007-04-16)[1]
Stable release

24.3.0  (March 25, 2024; 7 months ago (2024-03-25))

[±]
Preview release 20.11 [±]
Written in Java
Operating system Cross-platform
Type Laboratory informatics software
License(s) Apache Software License[2]
Website LabKey.org

LabKey Server is a free open-source laboratory informatics solution released under an Apache license. LabKey acts primarily as a web-based data management platform, though through its use of application programming interfaces (APIs), the software remains highly extensible. LabKey has been adapted to a variety of disciplines, including proteomics, flow cytometry, and observational study management.[3]

LabKey Corporation, the company the develops the software, also sells a number of professional services, including installations and upgrade assistance, training programs, customization, consulting, and support.[4]

Product history

The origins of LabKey Server trace back to 2003, where at the Fred Hutchinson Cancer Research Center (FHCRC) (located in Seattle, Washington) Professor Martin McIntosh saw a need for robust software that would facilitate cooperative proteomics and cancer research, with projects such as the Human Genome Project and the National Cancer Institute's (NCI's) caBIG as inspiration.[5][6] By October 2003, McIntosh had recruited three former Microsoft programmers — Mark Igra, Matthew Bellew, and Adam Rauch — to begin development on the core of an open-source application that would later be called the Computational Portal and Analysis System or CPAS.[7][6][8] Initial development was funded by the NCI and the nonprofit organization Canary Foundation.[5][9]

As early beta versions of the program floated around the Research Center, popularity grew, necessitating more resources. With the help of the FHCRC, Janaury 2005 saw the creation of a new entity called LabKey Software to better focus on the development of the software and to better support other institutions that would go on to utilize it. Additionally, another cohort of three former Microsoft developers joined the team to aid with development: George Snelling, Peter Hussey and Brendan MacLean.[6][8] The first public release of the software came on November 23, 2005, in the form of CPAS 1.1.[7][1] A few weeks later the team released the source code to coincide with the the January 1, 2006 print publication of the groups corresponding paper in the Journal of Proteome Research, making it officially an open-source release.[10] At that time, key features of the application included multiple standard-file formats, protein database search functionality, comprehensive experiment annotation, data sharing, and several proteomic-friendly analytic tools.[11]

Over the next year CPAS went through several iterations, including an update to a more specific name of Computational Proteomics Analysis System. The software held the name up to version 1.7, released in December 2006. With version 2.0, released on April 16, 2007, came a renaming of the product to what is still known today as LabKey Server.[1][9][12] In May 2007, the Canary Foundation announced the fifteen grant recipients of their $225,000 Bioinformatics Platform Dissemination Award, all of which would go towards the future design, development, and support of LabKey's software.[13] That set of grant funding brought new features to CPAS/LabKey Server, including: improved label-free comparisons; MS peptide intensity data modules; and a more central integration of MsInspect, the signal processing component for locating and quantitating peptides.[14]

The 2.x incrementation ended with version 2.3 in February 2008.[1] The subsequent release after version 2.3 was 8.1 on May 1, 2008, though the increment jump was never publicly explained.[15]

Shortly after release of 8.1, several news releases indicated LabKey would be lending support to Seattle businesses Insilicos and the Institute for Systems Biology (ISB). The goal of the collaboration was to port proteomics software tools like LabKey Server through Amazon's cloud servers, allowing potential research groups with IT budgets to utilize the proteomics applications and scale up web service as demand grows.[16][17] A few months later, LabKey announced another collaboration, this time with the Microsoft BioIT Alliance, an association of life science organizations and informatics companies focused on accelerating the pace of drug discovery and development.[18]

Version 9.1 of LabKey was released on April 2, 2009[19], with 10.1 arriving in March 2010[20] and 11.1 releasing in April 2011.[21] The latest version, 11.3, went live in December 2011, featuring enhanced data management, data visualization, and security functions.

Features

Hardware/software requirements

Videos, screenshots, and other media

Entities using LabKey Server

See also

Further reading

External links

References

  1. ↑ 1.0 1.1 1.2 1.3 "LabKey Software Foundation - News". LabKey Software Foundation. https://www.labkey.org/announcements/home/begin.view. Retrieved 20 April 2012. 
  2. ↑ "LabKey Frequently Asked Questions". LabKey Software Foundation. https://www.labkey.org/wiki/home/page.view?name=HomeFAQ. Retrieved 20 April 2012. 
  3. ↑ "LabKey Server". LabKey Corporation. http://labkey.com/server/labkey-server. Retrieved 20 April 2012. 
  4. ↑
  5. ↑ 5.0 5.1 "Center, NCI launch open-source software for proteomics analysis". Fred Hutchinson Cancer Research Center. 5 January 2006. http://www.fhcrc.org/content/public/en/news/center-news/2006/01/proteomics-software.html. Retrieved 20 April 2012. 
  6. ↑ 6.0 6.1 6.2 Nelson, Elizabeth (2 January 2011). "A Seattle Version of the Silicon Valley Garage". LabKey Corporation. http://labkey.com/blog/2011/01/tools-%E2%80%B9-labkey-blog-%E2%80%94-wordpress. Retrieved 20 April 2012. 
  7. ↑ 7.0 7.1 "CPAS - Computational Portal and Analysis System". Fred Hutchinson Cancer Research Center. 23 November 2005. Archived from the original on 24 November 2005. http://web.archive.org/web/20051124131402/http://cpas.fhcrc.org/Project/home/home.view. Retrieved 20 April 2012. 
  8. ↑ 8.0 8.1 Berg, Barbara (17 March 2005). "'Wizards' of computational science". Fred Hutchinson Cancer Research Center. http://www.fhcrc.org/content/public/en/news/center-news/2005/03/wizards-computational-science.html. Retrieved 20 April 2012. 
  9. ↑ 9.0 9.1 "LabKey CPAS Overview". LabKey Software Foundation. https://www.labkey.org/Project/home/CPAS/begin.view. Retrieved 20 April 2012. 
  10. ↑ Snelling, George (8 December 2005). "CPAS 1.1 Source Code Released". LabKey Software Foundation. https://www.labkey.org/announcements/home/thread.view?rowId=35. Retrieved 20 April 2012. 
  11. ↑ "Hutchinson Center and NCI launch open-source software for proteomics analysis" (DOC). Fred Hutchinson Cancer Research Center. 8 December 2005. http://proteomics.fhcrc.org/CPL/_docs/CPAS_media_backgrounder.doc. Retrieved 20 April 2012. 
  12. ↑ "Computational Proteomics Laboratory". Fred Hutchinson Cancer Research Center. http://proteomics.fhcrc.org/CPL/home.html. Retrieved 20 April 2012. 
  13. ↑ "Grant Awardees Standardize Software Platform for Early Cancer Detection". Canary Foundation. 22 May 2007. http://www.canaryfoundation.org/newsroom/press-releases/grant-awardees-standardize-software-platform-for-early-cancer-detection/. Retrieved 20 April 2012. 
  14. ↑ "CPAS update". International Cancer Biomarker Consortium Newsletter (Fred Hutchinson Cancer Research Center) 3 (4). December 2007. http://cairob.fhcrc.org/science/international_biomarker/news/2007/december.html. Retrieved 20 April 2012. 
  15. ↑ "Get Started With LabKey Server 8.1". LabKey Software Foundation. 1 May 2008. https://www.labkey.org/project/home/Documentation/Archive/8.1/begin.view?. Retrieved 20 April 2012. 
  16. ↑ "Insilicos Awarded Grant for Life Science Computing". Insilicos LLC. 5 May 2008. http://insilicos.com/news/insilicos-awarded-grant-for-life-science-computing. Retrieved 20 April 2012. 
  17. ↑ Toner, Bernadette (9 May 2008). "Insilicos Partners with LabKey, ISB to Port Proteomics Software Tools to Amazon’s Cloud". Genomeweb LLC. http://www.genomeweb.com/informatics/insilicos-partners-labkey-isb-port-proteomics-software-tools-amazon’s-cloud. Retrieved 20 April 2012. 
  18. ↑ "LabKey Software Joins BioIT Alliance". Business Wire. 18 September 2012. http://www.businesswire.com/news/google/20080918005145/en. Retrieved 20 April 2012. 
  19. ↑ "Get Started With LabKey Server 9.1". LabKey Software Foundation. 2 April 2009. https://www.labkey.org/project/home/Documentation/Archive/9.1/begin.view?. Retrieved 20 April 2012. 
  20. ↑ "Get Started With LabKey Server 10.1". LabKey Software Foundation. 10 March 2010. https://www.labkey.org/project/home/Documentation/Archive/10.1/begin.view?. Retrieved 20 April 2012. 
  21. ↑ "Get Started With LabKey Server v11.1". LabKey Software Foundation. 12 April 2011. https://www.labkey.org/project/home/Documentation/Archive/11.1/begin.view?. Retrieved 20 April 2012. 
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