Difference between revisions of "LabKey Server"

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| collapsible            =  
| collapsible            =  
| author                =  
| author                =  
| developer              = [[LabKey Corporation]] and the LabKey Software Foundation
| developer              = [[Vendor:LabKey Corporation|LabKey Corporation]]
| released              = {{Start date|2007|04|16}}<ref name="LKAnnounce">{{cite web |url=https://www.labkey.org/announcements/home/begin.view |title=LabKey Software Foundation - News |publisher=LabKey Software Foundation |accessdate=20 April 2012}}</ref>
| released              = {{Start date|2007|04|16}}<ref name="LKAnnounce">{{cite web |url=https://www.labkey.org/home/announcements-thread.view?rowId=1396 |title=LabKey / CPAS Version 2.0 Released |publisher=LabKey Corporation |date=16 April 2007 |accessdate=13 June 2019}}</ref>
| discontinued          =  
| discontinued          =  
| 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<ref name="LKInstall">{{cite web |url=https://www.labkey.org/wiki/home/Documentation/page.view?name=manualInstall |title=Install LabKey Manually |publisher=LabKey Software Foundation |accessdate=17 November 2012}}</ref>
| programming language  = Java<ref name="LKInstall">{{cite web |url=https://www.labkey.org/Documentation/wiki-page.view?name=manualInstall |title=Install LabKey Manually |publisher=LabKey Corporation |accessdate=13 June 2019}}</ref>
| operating system      = Cross-platform
| operating system      = Cross-platform
| platform              =  
| platform              =  
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| status                =  
| status                =  
| genre                  = [[Laboratory informatics]] software
| genre                  = [[Laboratory informatics]] software
| license                = Apache Software License<ref name="LKFAQ">{{cite web |url=https://www.labkey.org/wiki/home/page.view?name=HomeFAQ |title=LabKey Frequently Asked Questions |publisher=LabKey Software Foundation |accessdate=20 April 2012}}</ref>
| license                = Apache Software License<ref name="LKFAQ">{{cite web |url=https://www.labkey.org/Documentation/wiki-page.view?name=HomeFAQ |title==FAQ-Frequently Asked Questions |publisher=LabKey Corporation |accessdate=13 June 2019}}</ref>
| website                = [https://www.labkey.org/ LabKey.org]
| website                = [https://www.labkey.org/Documentation/wiki-page.view?name=lkserver labkey.org/Documentation]<br />[https://www.labkey.com/ LabKey.com]<br />[https://www.labkey.org/ LabKey.org]
}}
}}


'''LabKey Server''' is a free, open-source [[laboratory informatics]] solution released under an Apache license. LabKey Server is a web-based data management platform that helps scientists acquire, integrate, report, and securely share data from research studies conducted at distributed sites. It is customizable and extensible for particular scientific needs.  The platform supports a variety of applications, including high-throughput assays, [[flow cytometry]], genotyping/sequencing, [[proteomics]], specimen tracking, and observational study data management.<ref name="LK_Docs">{{cite web |url=https://www.labkey.org/project/home/Documentation/begin.view?|title=LabKey Server Documentation|author=|publisher=LabKey Software Foundation||accessdate=12 August 2014}}</ref><ref>{{cite web |url=http://labkey.com/server/labkey-server |title=LabKey Server |publisher=LabKey Corporation |accessdate=20 April 2012}}</ref>
'''LabKey Server''' is a free, open-source [[laboratory informatics]] solution released under an Apache license. LabKey Server is a web-based data management platform that helps scientists acquire, integrate, report, and securely share data from research studies conducted at distributed sites. It is customizable and extensible for particular scientific needs.  The platform supports a variety of applications, including high-throughput assays, [[flow cytometry]], genotyping/sequencing, [[proteomics]], specimen tracking, and observational study data management.<ref name="LK_Docs">{{cite web |url=https://www.labkey.org/Documentation/wiki-page.view?name=introLabKey |title=Introduction to LabKey Server |publisher=LabKey Corporation |accessdate=13 June 2019}}</ref><ref name="LSAbout">{{cite web |url=https://www.labkey.com/products-services/labkey-server/ |title=LabKey Server |publisher=LabKey Corporation |accessdate=13 June 2019}}</ref>


[[LabKey Corporation]] leads development and maintenance of the software for the LabKey Server user community. The company sells a number of professional services, including SaaS hosting, installation and upgrade assistance, training programs, customization, development, consulting, and support.<ref name="LKServ">{{cite web_short |url=http://labkey.com/services |title=LabKey Professional Services |publisher=LabKey Corporation |accessdate=20 April 2012}}</ref>
[[Vendor:LabKey Corporation|Labkey]] leads development and maintenance of the software for the LabKey Server user community. The company sells a number of professional services, including SaaS hosting, installation and upgrade assistance, training programs, customization, development, consulting, and support.<ref name="LKServ">{{cite web |url=https://www.labkey.com/products-services/ |title=Products and Services |publisher=LabKey Corporation |accessdate=13 June 2019}}</ref>


==Product history==
==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|National Cancer Institute's]] (NCI's) now retired [[caBIG]] program as inspiration.<ref name="FHCRC_NewsJan06">{{cite web |url=http://www.fhcrc.org/content/public/en/news/center-news/2006/01/proteomics-software.html |title=Center, NCI launch open-source software for proteomics analysis |publisher=Fred Hutchinson Cancer Research Center |date=5 January 2006 |accessdate=20 April 2012}}</ref><ref name="LKBlog_Jan11">{{cite web |url=http://labkey.com/blog/2011/01/tools-%E2%80%B9-labkey-blog-%E2%80%94-wordpress |title=A Seattle Version of the Silicon Valley Garage |author=Nelson, Elizabeth |publisher=LabKey Corporation |date=2 January 2011 |accessdate=20 April 2012}}</ref> 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.<ref name="CPASArchive">{{cite web |archiveurl=http://web.archive.org/web/20051124131402/http://cpas.fhcrc.org/Project/home/home.view |url=http://cpas.fhcrc.org/Project/home/home.view |title=CPAS - Computational Portal and Analysis System |publisher=Fred Hutchinson Cancer Research Center |archivedate=24 November 2005 |date=23 November 2005 |accessdate=20 April 2012}}</ref><ref name="LKBlog_Jan11" /><ref name="FHCRC_NewsMar05">{{cite web |url=http://www.fhcrc.org/content/public/en/news/center-news/2005/03/wizards-computational-science.html |title='Wizards' of computational science |author=Berg, Barbara |publisher=Fred Hutchinson Cancer Research Center |date=17 March 2005 |accessdate=20 April 2012}}</ref> Initial development was funded by the NCI and the nonprofit organization Canary Foundation.<ref name="FHCRC_NewsJan06" /><ref name="CPASOver">{{cite web |url=https://www.labkey.org/Project/home/CPAS/begin.view |title=LabKey CPAS Overview |publisher=LabKey Software Foundation |accessdate=20 April 2012}}</ref>
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|National Cancer Institute's]] (NCI's) now retired [[caBIG]] program as inspiration.<ref name="FHCRC_NewsJan06">{{cite web |url=http://www.fredhutch.org/en/news/center-news/2006/01/proteomics-software.html |title=Center, NCI launch open-source software for proteomics analysis |publisher=Fred Hutchinson Cancer Research Center |date=5 January 2006 |accessdate=20 April 2012}}</ref><ref name="LKBlog_Jan11">{{cite web |url=https://www.labkey.com/about/history/ |title=History |publisher=LabKey Corporation |accessdate=13 June 2019}}</ref> 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.<ref name="CPASArchive">{{cite web |archiveurl=http://web.archive.org/web/20051124131402/http://cpas.fhcrc.org/Project/home/home.view |url=http://cpas.fhcrc.org/Project/home/home.view |title=CPAS - Computational Portal and Analysis System |publisher=Fred Hutchinson Cancer Research Center |archivedate=24 November 2005 |date=23 November 2005 |accessdate=20 April 2012}}</ref><ref name="LKBlog_Jan11" /><ref name="FHCRC_NewsMar05">{{cite web |url=http://www.fhcrc.org/content/public/en/news/center-news/2005/03/wizards-computational-science.html |title='Wizards' of computational science |author=Berg, Barbara |publisher=Fred Hutchinson Cancer Research Center |date=17 March 2005 |accessdate=20 April 2012}}</ref> Initial development was funded by the NCI and the nonprofit organization Canary Foundation.<ref name="FHCRC_NewsJan06" /><ref name="CPASOver">{{cite web |url=https://www.labkey.org/Project/home/CPAS/begin.view |archiveurl=https://web.archive.org/web/20110411181815/https://www.labkey.org/Project/home/CPAS/begin.view |title=LabKey CPAS Overview |publisher=LabKey Software Foundation |archivedate=11 April 2011 |accessdate=13 June 2019}}</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" />  
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 the LabKey Software Foundation to better focus on the development of the software and to better support other institutions that would go on to utilize it.<ref name="GWCanary07">{{cite web |url=https://www.genomeweb.com/informatics/canary-awards-225k-help-15-labs-adopt-open-source-cpas-labkey-provide-support |archiveurl=https://web.archive.org/web/20090430150540/https://www.genomeweb.com/informatics/canary-awards-225k-help-15-labs-adopt-open-source-cpas-labkey-provide-support |title=Canary Awards $225K to help 15 Labs Adopt Open-Source CPAS; Labkey to Provide Support |work=GenomeWeb |date=25 May 2007 |archivedate=30 April 2009 |accessdate=13 June 2019}}</ref> 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.  
The first public release of the software came on November 23, 2005, in the form of CPAS 1.1.<ref name="CPASArchive" /><ref name="LKAnnounce05">{{cite web |url=https://www.labkey.org/home/announcements-thread.view?rowId=34 |title=CPAS 1.1 Ships |date=23 November 2005 |publisher=LabKey Corporation |accessdate=13 June 2019}}</ref> 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 |archiveurl=https://web.archive.org/web/20060430035736/http://proteomics.fhcrc.org/CPL/_docs/CPAS_media_backgrounder.doc |title=CPAS 1.1 Source Code Released |author=Snelling, George |publisher=LabKey Software Foundation |date=8 December 2005 |archivedate=30 April 2006 |accessdate=2 May 2016}}</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 the release of version 2.0 in April 2007, the team renamed CPAS to LabKey Server to reflect the growing use of the system beyond the [[proteomics]] research community; today, the platform includes tools useful across many kinds of biomedical research.<ref name="LKAnnounce">{{cite web |url=https://www.labkey.org/announcements/home/begin.view |title=LabKey Software Foundation - News |publisher=LabKey Software Foundation |accessdate=20 April 2012}}</ref>
With the release of version 2.0 in April 2007, the team renamed CPAS to LabKey Server to reflect the growing use of the system beyond the [[proteomics]] research community; today, the platform includes tools useful across many kinds of biomedical research.<ref name="LKAnnounce" /><ref name="CPASOver" /><ref name=FHCRCComp12>{{cite web |url=http://proteomics.fhcrc.org/CPL/home.html |archiveurl=https://web.archive.org/web/20120306030843/http://proteomics.fhcrc.org/CPL/home.html |title=Computational Proteomics Laboratory |publisher=Fred Hutchinson Cancer Research Center |archivedate=6 March 2012 |accessdate=2 May 2016}}</ref><ref name="LK_Docs"/> The 2.x incrementation ended with version 2.3 in February 2008.<ref name="LKAnnounce08">{{cite web |url=https://www.labkey.org/home/announcements-thread.view?rowId=2153 |title=LabKey Server Version 2.3 Now Available |date=11 February 2008 |publisher=LabKey Corporation |accessdate=13 June 2019}}</ref> The subsequent release after version 2.3 was 8.1 on May 1, 2008; from this point forward, releases were named after the year of release (2008, in this case) and the order of the release in that year (1 in this case).<ref>{{cite web |url=https://www.labkey.org/Documentation/Archive/8.1/project-begin.view? |title=Get Started With LabKey Server 8.1 |publisher=LabKey Corporation |date=1 May 2008 |accessdate=13 June 2019}}</ref> Version 9.1 of LabKey was released on April 2, 2009<ref>{{cite web |url=https://www.labkey.org/Documentation/Archive/9.1/project-begin.view? |title=Get Started With LabKey Server 9.1 |publisher=LabKey Corporation |date=2 April 2009 |accessdate=13 June 2019}}</ref>, with 10.1 arriving in March 2010<ref>{{cite web |url=https://www.labkey.org/Documentation/Archive/10.1/project-begin.view? |title=Get Started With LabKey Server 10.1 |publisher=LabKey Corporation |date=10 March 2010 |accessdate=13 June 2019}}</ref> and 11.1 releasing in April 2011.<ref>{{cite web |url=https://www.labkey.org/Documentation/Archive/11.1/project-begin.view? |title=Get Started With LabKey Server v11.1 |publisher=LabKey Corporation |date=12 April 2011 |accessdate=13 June 2019}}</ref> July 2014 saw the arrival of the 30th official, public release of the platform, v14.2.<ref>{{cite web |url=https://www.labkey.org/home/announcements-thread.view?rowId=9497 |title= LabKey Server v14.2 Now Available |accessdate=12 August 2014 |publisher=LabKey Corporation}}</ref>
<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>  
 
<ref name="LK_Docs"/> 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; from this point forward, releases were named after the year of release (2008, in this case) and the order of the release in that year (1 in this case).<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> 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> July 2014 saw the arrival of the 30th official, public release of the platform, v14.2. <ref>{{cite web|url=https://www.labkey.org/announcements/home/thread.view?rowId=9497|title= LabKey Server v14.2 Now Available|accessdate=12 August 2014|publisher=LabKey Software Foundation}}</ref>
At some point in 2022, Labkey Corporation began specifically referring to Labkey Server as a [[scientific data management system]] (SDMS) on its corporate website.


==Features==
==Features==


LabKey Server provides a secure, web-based repository for all types of biomedical data, including [[mass spectrometry]], [[flow cytometry]], microarray, [[Microtiter plate|microplate]], ELISpot, ELISA, NAb, and observational study information. A customizable data processing pipeline allows the upload and processing of the large data files common to biomedical research.<ref name="LK_Docs"/>
LabKey Server is an SDMS that provides a secure, web-based repository for all types of biomedical data, including [[mass spectrometry]], [[flow cytometry]], microarray, [[Microtiter plate|microplate]], ELISpot, ELISA, NAb, and observational study information. A customizable data processing pipeline allows the upload and processing of the large data files common to biomedical research.<ref name="LK_Docs"/>


The platform also provides domain-specific support for a variety of research areas, including:
The platform also provides domain-specific support for a variety of research areas, including:
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* '''flow cytometry''': supports automated quality control, centralized data management, and web-based data sharing; integrates with FlowJo
* '''flow cytometry''': supports automated quality control, centralized data management, and web-based data sharing; integrates with FlowJo
* '''data repository''': manages biomedical data, including raw data sets and spreadsheets; handles the data from built-in collaboration tools like the wiki and message board
* '''data repository''': manages biomedical data, including raw data sets and spreadsheets; handles the data from built-in collaboration tools like the wiki and message board
{{As of|2014}}, development of the platform is ongoing; for information on the most current release and associated features, visit the project's website. LabKey Server source code, compiled binaries, documentation, and tutorials are professionally maintained and freely available under the Apache 2.0 license at this site.
{{Ombox productfeature}}
{| class="wikitable collapsible" style="border-style:none;" background="#ffffff" border="0" cellpadding="0" cellspacing="0"
|-
  ! colspan="2"| Product: [http://www.labkey.com/server/labkey-server LabKey Server]
|-
  | style="background-color:white; border-style:none;"| {{Databox LIMSfeature
| sample_login_man  = Y<ref name="LKStudies">{{cite web |url=https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=study |title=LabKey Software Foundation - Studies |publisher=LabKey Corporation |accessdate=28 January 2012}}</ref>
| sample_track      = Y<ref name="LKStudies" />
| sample_batch      = Y<ref name="LKImport">{{cite web |url=https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=importSpecimenData |title=LabKey Software Foundation - Import a Specimen Archive |publisher=LabKey Corporation |accessdate=28 January 2012}}</ref>
| task_event_sched  = Y<ref name="LKStudies" />
| manual_entry      =
| multiple_view      = Y<ref name="LKStudies" />
| data_analysis      = Y<ref name="LKAbout">{{cite web |url=http://www.labkey.com/server/labkey-server |title=LabKey Server |publisher=LabKey Corporation |accessdate=28 January 2012}}</ref>
| data_sharing      = Y<ref name="LKAbout" />
| custom_fields      = Y<ref name="LKAdmin">{{cite web |url=https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=adminServer |title=LabKey Software Foundation - Administration |publisher=LabKey Corporation |accessdate=28 January 2012}}</ref>
| query              = Y<ref name="LKAbout" />
| import_data        = Y<ref name="LKAbout" />
| data_linking_int  =
| data_linking_ext  =
| eln_support        =
| export_msexcel    = Y<ref name="LKAbout" />
| export_raw        =
| data_warehouse    = Y<ref name="LKAbout" />
| deadline_control  =
| production_control =
| project_task_man  = Y<ref name="LKAdmin" />
| inventory_man      =
| document_man      = Y<ref name="LKStudies" />
| case_man          = Y<ref name="LKStudies" />
| workflow_man      =
| spec_man          =
| customer_man      =
| billing_man        =
| reg_compliance    =
| qa_qc              =
| performance_eval  =
| audit_trail        = Y<ref name="LKAbout" />
| chain_custody      =
| roles_security    = Y<ref name="LKAbout" />
| data_norm          =
| data_val          = Y<ref name="LKAbout" />
| data_encrypt      =
| version_control    =
| data_backup        = Y<ref name="LKBackup">{{cite web |url=https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=dbBackup |title=LabKey Software Foundation - Backup and Maintenance |publisher=LabKey Corporation |accessdate=28 January 2012}}</ref>
| enviro_monitoring  =
| custom_reporting  =
| report_printing    =
| label_support      =
| barcode_support    =
| export_pdf        =
| export_msword      =
| export_htmlxml    =
| fax_integration    =
| email_integration  = Y<ref name="LKAdmin" />
| admin_manage      = Y<ref name="LKAbout" />
| modular            =
| instrument_inter  =
| mobile_device      =
| alarms_alerts      =
| work_timetrack    =
| voice_rec          =
| external_monitor  =
| messaging          =
| multilingual      =
| network            =
| web_client        = Y<ref name="LKAbout" />
| online_help        =
| saas_model        = Y<ref name="LKSaaS">{{cite web |url=https://labkey.com/forms/try-labkey-server |title=Try LabKey Server |publisher=LabKey Corporation |accessdate=28 July 2014}}</ref>
| usage_cost        =
| industries        = biotechnology, clinical research, life sciences, pharmaceutical
}}
|-
|}


==Pricing==
==Pricing==
LabKey Server is free and open-source. For more about LabKey Server's license and free nature, please reference LabKey Server's [https://www.labkey.org/wiki/home/page.view?name=HomeFAQ FAQ].
LabKey Server is free and open-source. For more about LabKey Server's license and free nature, please reference LabKey Server's [https://www.labkey.org/wiki/home/page.view?name=HomeFAQ FAQ].


LabKey Software offers various professional services related to their product, including SaaS-based web hosting.<ref name="LKSaaS" /> However, only limited public pricing of its services is available at this time.
LabKey Corporation offers various professional services related to their product, including SaaS-based web hosting.<ref name="LKServ" /> However, only limited public pricing of its services is available at this time.<ref name="LSAbout" />


==Hardware/software requirements==
==Hardware/software requirements==
Components necessary for a Windows installation of LabKey Server are included in the binary Windows Installer. More complex installations may need to be done manually, which will require the separate installation of components.
Components necessary for a Windows installation of LabKey Server are included in the binary Windows Installer. More complex installations may need to be done manually, which will require the separate installation of components.


For all details concerning manual and automatic installation (and any necessary requirements), please consult the ''[https://www.labkey.org/wiki/home/Documentation/page.view?name=beforeInstall Before You Install]'' page of the software documentation.
For all details concerning manual and automatic installation (and any necessary requirements), please consult the ''[https://www.labkey.org/Documentation/wiki-page.view?name=config Install LabKey]'' page of the software documentation.


==Videos, screenshots, and other media==
==Videos, screenshots, and other media==
===Downloads===
Downloads of the free open-source community edition can be [https://www.labkey.org/Documentation/wiki-page.view?name=prevReleases found here].


===Videos===
===Videos===


The following demonstration videos are available for LabKey Server, listed by date with the most recent at the top. For a curated and sorted catalog, [https://www.labkey.org/wiki/home/Documentation/page.view?name=videos click here.]
The following demonstration videos are available for LabKey Server, listed by date with the most recent at the top. For a curated and sorted catalog, [https://www.labkey.org/Documentation/wiki-page.view?name=videos click here.]


* [http://labkey.wistia.com/medias/7pocihb7v1 LabKey Server Overview (March 2014)]
* [http://labkey.wistia.com/medias/7pocihb7v1 LabKey Server Overview (March 2014)]
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===Screenshots===
===Screenshots===
The following screenshots are available for LabKey Server:
The following screenshots are available for LabKey Server:


* [http://freecode.com/projects/labkey-server/screenshots All screenshots for LabKey Server on Freecode]
* [http://freecode.com/projects/labkey-server/screenshots All screenshots for LabKey Server on Freecode]


===Demos and live examples===
===Demos and case study examples===
 
* [https://www.labkey.org/Documentation/wiki-page.view?name=tutorials Live demos and tutorials]
* [https://www.labkey.org/wiki/home/Documentation/page.view?name=tutorials Live demos and tutorials]
* [https://www.labkey.com/case_study/ Case studies using LabKey Server]
* [https://www.labkey.org/wiki/home/Documentation/page.view?name=showcase Live examples of LabKey Server]


==Entities using LabKey Server==
==Entities using LabKey Server==
A sample of organizations using LabKey Server:  
A sample of organizations using LabKey Server:  


The Immune Tolerance Network (ITN), Fred Hutchinson Cancer Research Center, Statistical Center for HIV/AIDS Research & Prevention (SCHARP) at the FHCRC, HIV Vaccine Trials Network (HVTN), Collaboration for AIDS Vaccine Discovery (CAVD), Human Immunology Project Consortium (HIPC), Juvenile Diabetes Research Foundation (JDRF) Network for Pancreatic Organ Donors (nPOD), NWBioTrust, University of Washington, Duke University, Stanford Canary Center for Cancer Early Detection, Oregon National Primate Research Center, Wisconsin National Primate Research Center, Infectious Disease Research Institute, International Center of Excellence in Malaria Research (ICEMR) at the University of Washington, Seattle Children's Research Institute (SCRI), and University Hospital of Bern (Switzerland).
The Immune Tolerance Network (ITN), Fred Hutchinson Cancer Research Center, Statistical Center for HIV/AIDS Research & Prevention (SCHARP) at the FHCRC, HIV Vaccine Trials Network (HVTN), Collaboration for AIDS Vaccine Discovery (CAVD), Human Immunology Project Consortium (HIPC), Juvenile Diabetes Research Foundation (JDRF) Network for Pancreatic Organ Donors (nPOD), NWBioTrust, University of Washington, Duke University, Stanford Canary Center for Cancer Early Detection, Oregon National Primate Research Center, Wisconsin National Primate Research Center, Infectious Disease Research Institute, International Center of Excellence in Malaria Research (ICEMR) at the University of Washington, Seattle Children's Research Institute (SCRI), and University Hospital of Bern (Switzerland).


Sources: ''[https://www.labkey.org/wiki/home/Documentation/page.view?name=labkeyServerUsers LabKey Server Users]'', ''[https://www.labkey.org/wiki/home/Documentation/page.view?name=showcase Showcase of Live Sites]'', and ''[https://www.labkey.org LabKey Server Overview]''  pages
Sources: ''[https://www.labkey.com/resources/clients/ Representative LabKey Server Users]'', ''[https://www.labkey.com/products-services/labkey-server/ LabKey Server Overview]''  pages


==See also==
==See also==
 
* [[Vendor:LabKey Corporation|LabKey Corporation]]
* [[LabKey Corporation]]


==Further reading==
==Further reading==


* {{cite web |url=https://www.labkey.org/project/home/Documentation/begin.view? |title=LabKey Server documentation |publisher=LabKey Software Foundation}}
* {{cite web |url=https://www.labkey.org/Documentation/project-begin.view? |title=LabKey Server documentation |publisher=LabKey Corporation}}
* {{cite journal |journal=Journal of Proteome Research |year=January 2006 |volume=5 |issue=1 |pages=112–21 |title=Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments |author=Rauch, A.; M. Bellew; J. Eng; M. Fitzgibbon; T. Holzman; P. Hussey; M. Igra; B. Maclean; C. W. Lin; A. Detter; R. Fang; V. Faca; P. Gafken; H. Zhang; J. Whiteaker; D. States; S. Hanash; A. Paulovich; M. W. McIntosh |url=http://www.ncbi.nlm.nih.gov/pubmed/16396501 |pmid=16396501}}
* {{cite journal |journal=Journal of Proteome Research |year=January 2006 |volume=5 |issue=1 |pages=112–21 |title=Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments |author=Rauch, A.; M. Bellew; J. Eng; M. Fitzgibbon; T. Holzman; P. Hussey; M. Igra; B. Maclean; C. W. Lin; A. Detter; R. Fang; V. Faca; P. Gafken; H. Zhang; J. Whiteaker; D. States; S. Hanash; A. Paulovich; M. W. McIntosh |url=http://www.ncbi.nlm.nih.gov/pubmed/16396501 |pmid=16396501}}
* {{cite journal |title=LabKey Server: An open source platform for scientific data integration, analysis and collaboration |journal=BMC Bioinformatics |author=Nelson, Elizabeth K.; Britt Piehler; Josh Eckels; Adam Rauch; Matthew Bellew; Peter Hussey; Sarah Ramsay; Cory Nathe; Karl Lum; Kevin Krouse; David Stearns; Brian Connolly; Tom Skillman; Mark Igra |volume=12 |issue=71 |year=2011 |doi=10.1186/1471-2105-12-71 |pmid=21385461 |pmc=PMC3062597}}
* {{cite journal |title=LabKey Server: An open source platform for scientific data integration, analysis and collaboration |journal=BMC Bioinformatics |author=Nelson, Elizabeth K.; Britt Piehler; Josh Eckels; Adam Rauch; Matthew Bellew; Peter Hussey; Sarah Ramsay; Cory Nathe; Karl Lum; Kevin Krouse; David Stearns; Brian Connolly; Tom Skillman; Mark Igra |volume=12 |issue=71 |year=2011 |doi=10.1186/1471-2105-12-71 |pmid=21385461 |pmc=PMC3062597}}
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==External links==
==External links==


* [http://labkey.com/ LabKey Software] corporate site
* [https://www.labkey.com LabKey] corporate site
* [http://labkey.org LabKey Server] open source home
* [https://www.labkey.org/project/home/begin.view? LabKey Server] open source home
* [http://freecode.com/projects/labkey-server LabKey Server] at Freecode
* [https://www.labkey.org/Documentation/wiki-page.view?name=lkserver LabKey Server documentation]
* [https://www.labkey.org/project/home/Documentation/Archive/begin.view? LabKey Server and CPAS] archived documentation
* [https://www.labkey.com/blog/ LabKey blog]
* [https://www.labkey.org/announcements/home/begin.view LabKey Server and CPAS] archived news
* [http://freshmeat.sourceforge.net/projects/labkey-server LabKey Server] at Freecode
* [https://www.labkey.org/Documentation/Archive/project-begin.view? LabKey Server and CPAS] archived documentation
* [https://www.labkey.org/home/announcements-list.view?.lastFilter=true LabKey Server and CPAS] archived news


==References==
==References==
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[[Category:Bioinformatics software (open source)]]
[[Category:Bioinformatics software (open source)]]
[[Category:Laboratory informatics software (open source)]]
[[Category:Laboratory informatics software (open source)]]
[[Category:Laboratory information management systems (open source)]]
[[Category:Scientific data management systems (open source)]]

Latest revision as of 20:54, 31 May 2024

LabKey Server
Developer(s) LabKey Corporation
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[2]
Operating system Cross-platform
Type Laboratory informatics software
License(s) Apache Software License[3]
Website labkey.org/Documentation
LabKey.com
LabKey.org

LabKey Server is a free, open-source laboratory informatics solution released under an Apache license. LabKey Server is a web-based data management platform that helps scientists acquire, integrate, report, and securely share data from research studies conducted at distributed sites. It is customizable and extensible for particular scientific needs. The platform supports a variety of applications, including high-throughput assays, flow cytometry, genotyping/sequencing, proteomics, specimen tracking, and observational study data management.[4][5]

Labkey leads development and maintenance of the software for the LabKey Server user community. The company sells a number of professional services, including SaaS hosting, installation and upgrade assistance, training programs, customization, development, consulting, and support.[6]

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) now retired caBIG program as inspiration.[7][8] 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.[9][8][10] Initial development was funded by the NCI and the nonprofit organization Canary Foundation.[7][11]

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 the LabKey Software Foundation to better focus on the development of the software and to better support other institutions that would go on to utilize it.[12] Additionally, another cohort of three former Microsoft developers joined the team to aid with development: George Snelling, Peter Hussey and Brendan MacLean.[8][10]

The first public release of the software came on November 23, 2005, in the form of CPAS 1.1.[9][13] 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.[14] 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.[15] 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 the release of version 2.0 in April 2007, the team renamed CPAS to LabKey Server to reflect the growing use of the system beyond the proteomics research community; today, the platform includes tools useful across many kinds of biomedical research.[1][11][16][4] The 2.x incrementation ended with version 2.3 in February 2008.[17] The subsequent release after version 2.3 was 8.1 on May 1, 2008; from this point forward, releases were named after the year of release (2008, in this case) and the order of the release in that year (1 in this case).[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] July 2014 saw the arrival of the 30th official, public release of the platform, v14.2.[22]

At some point in 2022, Labkey Corporation began specifically referring to Labkey Server as a scientific data management system (SDMS) on its corporate website.

Features

LabKey Server is an SDMS that provides a secure, web-based repository for all types of biomedical data, including mass spectrometry, flow cytometry, microarray, microplate, ELISpot, ELISA, NAb, and observational study information. A customizable data processing pipeline allows the upload and processing of the large data files common to biomedical research.[4]

The platform also provides domain-specific support for a variety of research areas, including:

  • observational studies: supports management of longitudinal, large-scale studies of participants, subjects, or animals over time; allows the integration of clinical data with assay results
  • proteomics: allows the processing of high-throughput mass spectrometry data using tools such as the X! Tandem search engine, the Trans-Proteomic Pipeline, Mascot, and Sequest
  • flow cytometry: supports automated quality control, centralized data management, and web-based data sharing; integrates with FlowJo
  • data repository: manages biomedical data, including raw data sets and spreadsheets; handles the data from built-in collaboration tools like the wiki and message board

Pricing

LabKey Server is free and open-source. For more about LabKey Server's license and free nature, please reference LabKey Server's FAQ.

LabKey Corporation offers various professional services related to their product, including SaaS-based web hosting.[6] However, only limited public pricing of its services is available at this time.[5]

Hardware/software requirements

Components necessary for a Windows installation of LabKey Server are included in the binary Windows Installer. More complex installations may need to be done manually, which will require the separate installation of components.

For all details concerning manual and automatic installation (and any necessary requirements), please consult the Install LabKey page of the software documentation.

Videos, screenshots, and other media

Downloads

Downloads of the free open-source community edition can be found here.

Videos

The following demonstration videos are available for LabKey Server, listed by date with the most recent at the top. For a curated and sorted catalog, click here.

Screenshots

The following screenshots are available for LabKey Server:

Demos and case study examples

Entities using LabKey Server

A sample of organizations using LabKey Server:

The Immune Tolerance Network (ITN), Fred Hutchinson Cancer Research Center, Statistical Center for HIV/AIDS Research & Prevention (SCHARP) at the FHCRC, HIV Vaccine Trials Network (HVTN), Collaboration for AIDS Vaccine Discovery (CAVD), Human Immunology Project Consortium (HIPC), Juvenile Diabetes Research Foundation (JDRF) Network for Pancreatic Organ Donors (nPOD), NWBioTrust, University of Washington, Duke University, Stanford Canary Center for Cancer Early Detection, Oregon National Primate Research Center, Wisconsin National Primate Research Center, Infectious Disease Research Institute, International Center of Excellence in Malaria Research (ICEMR) at the University of Washington, Seattle Children's Research Institute (SCRI), and University Hospital of Bern (Switzerland).

Sources: Representative LabKey Server Users, LabKey Server Overview pages

See also

Further reading


External links

References

  1. ↑ 1.0 1.1 "LabKey / CPAS Version 2.0 Released". LabKey Corporation. 16 April 2007. https://www.labkey.org/home/announcements-thread.view?rowId=1396. Retrieved 13 June 2019. 
  2. ↑ "Install LabKey Manually". LabKey Corporation. https://www.labkey.org/Documentation/wiki-page.view?name=manualInstall. Retrieved 13 June 2019. 
  3. ↑ "=FAQ-Frequently Asked Questions". LabKey Corporation. https://www.labkey.org/Documentation/wiki-page.view?name=HomeFAQ. Retrieved 13 June 2019. 
  4. ↑ 4.0 4.1 4.2 "Introduction to LabKey Server". LabKey Corporation. https://www.labkey.org/Documentation/wiki-page.view?name=introLabKey. Retrieved 13 June 2019. 
  5. ↑ 5.0 5.1 "LabKey Server". LabKey Corporation. https://www.labkey.com/products-services/labkey-server/. Retrieved 13 June 2019. 
  6. ↑ 6.0 6.1 "Products and Services". LabKey Corporation. https://www.labkey.com/products-services/. Retrieved 13 June 2019. 
  7. ↑ 7.0 7.1 "Center, NCI launch open-source software for proteomics analysis". Fred Hutchinson Cancer Research Center. 5 January 2006. http://www.fredhutch.org/en/news/center-news/2006/01/proteomics-software.html. Retrieved 20 April 2012. 
  8. ↑ 8.0 8.1 8.2 "History". LabKey Corporation. https://www.labkey.com/about/history/. Retrieved 13 June 2019. 
  9. ↑ 9.0 9.1 "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. 
  10. ↑ 10.0 10.1 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. 
  11. ↑ 11.0 11.1 "LabKey CPAS Overview". LabKey Software Foundation. Archived from the original on 11 April 2011. https://web.archive.org/web/20110411181815/https://www.labkey.org/Project/home/CPAS/begin.view. Retrieved 13 June 2019. 
  12. ↑ "Canary Awards $225K to help 15 Labs Adopt Open-Source CPAS; Labkey to Provide Support". GenomeWeb. 25 May 2007. Archived from the original on 30 April 2009. https://web.archive.org/web/20090430150540/https://www.genomeweb.com/informatics/canary-awards-225k-help-15-labs-adopt-open-source-cpas-labkey-provide-support. Retrieved 13 June 2019. 
  13. ↑ "CPAS 1.1 Ships". LabKey Corporation. 23 November 2005. https://www.labkey.org/home/announcements-thread.view?rowId=34. Retrieved 13 June 2019. 
  14. ↑ Snelling, George (8 December 2005). "CPAS 1.1 Source Code Released". LabKey Software Foundation. Archived from the original on 30 April 2006. https://web.archive.org/web/20060430035736/http://proteomics.fhcrc.org/CPL/_docs/CPAS_media_backgrounder.doc. Retrieved 2 May 2016. 
  15. ↑ "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. 
  16. ↑ "Computational Proteomics Laboratory". Fred Hutchinson Cancer Research Center. Archived from the original on 6 March 2012. https://web.archive.org/web/20120306030843/http://proteomics.fhcrc.org/CPL/home.html. Retrieved 2 May 2016. 
  17. ↑ "LabKey Server Version 2.3 Now Available". LabKey Corporation. 11 February 2008. https://www.labkey.org/home/announcements-thread.view?rowId=2153. Retrieved 13 June 2019. 
  18. ↑ "Get Started With LabKey Server 8.1". LabKey Corporation. 1 May 2008. https://www.labkey.org/Documentation/Archive/8.1/project-begin.view?. Retrieved 13 June 2019. 
  19. ↑ "Get Started With LabKey Server 9.1". LabKey Corporation. 2 April 2009. https://www.labkey.org/Documentation/Archive/9.1/project-begin.view?. Retrieved 13 June 2019. 
  20. ↑ "Get Started With LabKey Server 10.1". LabKey Corporation. 10 March 2010. https://www.labkey.org/Documentation/Archive/10.1/project-begin.view?. Retrieved 13 June 2019. 
  21. ↑ "Get Started With LabKey Server v11.1". LabKey Corporation. 12 April 2011. https://www.labkey.org/Documentation/Archive/11.1/project-begin.view?. Retrieved 13 June 2019. 
  22. ↑ "LabKey Server v14.2 Now Available". LabKey Corporation. https://www.labkey.org/home/announcements-thread.view?rowId=9497. Retrieved 12 August 2014. 
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