{{Infobox software
| name = LabKey Server
| title = LabKey Server
| logo = 
| screenshot = 
| caption =
| collapsible =
| author =
| developer = [[LabKey Corporation]] and the LabKey Software Foundation
| 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>
| discontinued =
| frequently updated = yes
| 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>
| operating system = Cross-platform
| platform =
| size =
| language =
| status =
| 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>
| website = [https://www.labkey.org/ 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.<ref>{{cite web |url=http://labkey.com/server/labkey-server |title=LabKey Server |publisher=LabKey Corporation |accessdate=20 April 2012}}</ref>

[[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.<ref name="LKServ">{{cite web_short |url=http://labkey.com/services |title=LabKey Professional Services |publisher=LabKey Corporation |accessdate=20 April 2012}}</ref>

==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) [[caBIG]] 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>

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> 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>

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==

LabKey Server provides a secure data 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.

The platform also provides domain-specific support for several areas of research, 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; certified as "Silver-Level Compliant Data Service" with the [[caBIG]] standard
* '''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

{{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_short|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_short|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_short|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_short|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_short|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 =
| usage_cost =
| industries = biotechnology, clinical research, life sciences, pharmaceutical
}}
|-
|}

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

==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 ''[https://www.labkey.org/wiki/home/Documentation/page.view?name=beforeInstall Before You Install]'' page of the software documentation.

==Videos, screenshots, and other media==

===Videos===

The following demonstration videos are available for LabKey Server; the most current list is available [https://www.labkey.org/wiki/home/Documentation/page.view?name=videos on this page:]

* [http://labkey.wistia.com/medias/yu2etb68tq Extract-Transform-Load (ETL) Using LabKey Server]
* [http://labkey.wistia.com/medias/yed2addtyl Specimen Management Using LabKey Server]
* [http://fast.wistia.net/embed/iframe/bjioou5346?popover=true LabKey User Conference 2013: User Applications: The Hutch Integrated Data Repository Archive]
* [http://fast.wistia.net/embed/iframe/2rl2um06zb?popover=true LabKey User Conference 2013: User Applications: ITN Trialshare]
* [http://fast.wistia.net/embed/iframe/baxqwrmofc?popover=true LabKey User Conference 2013: User Applications: Using LabKey and the R statistical language to facilitate data integration and reproducible research within the Human Immunology Project Consortium]
* [http://fast.wistia.net/embed/iframe/h4hjg93g3f?popover=true LabKey User Conference 2013: User Applications: JDRF/nPOD DataShare: Accelerating Type 1 Diabetes Basic Science Research]
* [http://fast.wistia.net/embed/iframe/4of4nb8rm0?popover=true LabKey User Conference 2013: User Applications: The Use of LabKey Server in a globally distributed research project (South Asia International Center of Excellence for Malaria Research)]
* [http://labkey.wistia.com/medias/w4e1yraxh8 REDCap Integration with LabKey Server]
* [http://labkey.wistia.com/medias/yu3ghwjuox Navigate LabKey Projects and Folders]
* [http://labkey.wistia.com/medias/ri1d4kthf6 R Views with knitr]
* [http://labkey.wistia.com/medias/966zgaqq6q Survey Designer - 13.1 Release Video]
* [http://labkey.wistia.com/medias/xro7g9h36a Survey Designer - Continued]
* [http://labkey.wistia.com/medias/jxmb6vvoax Security: Linked and Filtered Schemas]
* [http://labkey.wistia.com/medias/fskrzfi2dv Panorama Proteomics Webinar]
* [http://labkey.wistia.com/medias/2fb5tr9rr0 Pathology Viewer - 13.1 Sprint Demo]
* [http://labkey.wistia.com/medias/xro7g9h36a Survey Designer - 13.1 Sprint Demo]
* [http://labkey.wistia.com/medias/m6u88r6owo Visualization Webinar - Jan 2013 - part 1 of 3]
* [http://labkey.wistia.com/medias/4pqpcziky7 Visualization Webinar - Jan 2013 - part 2 of 3]
* [http://labkey.wistia.com/medias/8rn2sgi7pz Visualization Webinar - Jan 2013 - part 3 of 3]
* [http://labkey.wistia.com/medias/8bmz0n4b96 LabKey User Conference 2012: Introduction to LabKey Server]
* [http://labkey.wistia.com/medias/6fce0qnw6z LabKey User Conference 2012: History of LabKey Server]
* [http://labkey.wistia.com/medias/1dn4nqjhds LabKey User Conference 2012: LabKey Security]
* [http://labkey.wistia.com/medias/kerqr7xc1a LabKey User Conference 2012: LabKey Server Assays - usage and development]
* [http://labkey.wistia.com/medias/hqne39wrgv LabKey User Conference 2012: Beyond the grid: using the LabKey reporting system to visualize, analyze, and present data in meaningful ways]
* [http://labkey.wistia.com/medias/z8afu0k15l LabKey User Conference 2012: Pipelines]
* [http://labkey.wistia.com/medias/vh1ordxxsr LabKey User Conference 2012: Client APIs]
* [http://labkey.wistia.com/medias/2xgms9qbwh LabKey User Conference 2012: User Applications: Adapting LabKey Server for novel applications (Infectious Disease Research Institute)]
* [http://labkey.wistia.com/medias/vp9wxevsr8 LabKey User Conference 2012: User Applications: ATLAS: Data Sharing in HIV Research]
* [http://labkey.wistia.com/medias/fjwa6u309v LabKey User Conference 2012: User Applications: The CDS as a case study]
* [http://www.youtube.com/watch?v=GZoBxLwmqY4&feature=youtu.be FCS Express Data Exports]
* [http://labkey.wistia.com/medias/1r0sdfz9bh Managing Protected Health Information (PHI)]
* [http://labkey.wistia.com/medias/sbmxvyfx7f Assessing data with quick charts]
* [http://labkey.wistia.com/medias/eqderuxwg6 Study Administration - organizing data]
* [http://labkey.wistia.com/medias/cf86822331 Security: Sharing data with another lab]
* [http://labkey.wistia.com/medias/c73a1aeff7 Participant lists - browse with faceted filtering]
* [http://labkey.wistia.com/medias/03bcfb374d Participant reports]
* [http://labkey.com/videos/top-level-videos/07022012-277 Visualize group data trends]
* [http://labkey.com/videos/top-level-videos/07022012-278 Ancillary studies]
* [http://labkey.com/videos/top-level-videos/07022012-279 Data browser]
* [http://labkey.com/videos/top-level-videos/03122011-272 LabKey at the Cascadia Proteomics Symposium]
* [http://labkey.com/videos/top-level-videos/30012011-260 Time charts: Comparing multiple measures on one chart]
* [http://labkey.com/videos/top-level-videos/30012011-263 Specimens: Tracking participant consent]
* [http://labkey.com/videos/top-level-videos/30012011-262 Security: Study demonstration mode]
* [http://labkey.com/videos/delivering-diagnostic-results Delivering diagnostic results]
* [http://labkey.com/videos/unlocking-spreadsheet-data-with-labkey Unlocking spreadsheet data #1: The problem]
* [http://labkey.com/videos/unlocking-spreadsheet-data-2-projects-and-sample-sets Unlocking spreadsheet data #2: Projects and sample sets]
* [http://labkey.com/videos/unlocking-spreadsheet-data-3-upload-and-search-files Unlocking spreadsheet data #3: Upload and search files]
* [http://labkey.com/videos/unlocking-spreadsheet-data-4-import-assay-results Unlocking spreadsheet data #4: Import assay results]
* [http://labkey.com/videos/unlocking-spreadsheet-data-5-integrate-and-analyze Unlocking spreadsheet data #5: Integrate and analyze]

===Screenshots===

The following screenshots are available for LabKey Server:

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

===Demos and live examples===

* [https://www.labkey.org/wiki/home/Documentation/page.view?name=tutorials Live demos and tutorials]
* [https://www.labkey.org/wiki/home/Documentation/page.view?name=showcase Live examples of LabKey Server]

==Entities using LabKey Server==

Examples of entities using LabKey Server include:

AdaptiveTCR, Bill & Melinda Gates Foundation, Fred Hutchinson Cancer Research Center, Harvard Partners, Institute of Molecular and Cell Biology – Singapore, Katze Lab at University of Washington, National Institute of Allergy and Infectious Diseases at Duke University, Stanford Canary Center for Cancer Early Detection, Statistical Center for HIV/AIDS Research & Prevention, USC Center for Applied Molecular Medicine

Source: The ''[https://www.labkey.org/wiki/home/Documentation/page.view?name=showcase Showcase of Live Sites]'', ''[https://www.labkey.org/Project/home/CPAS/begin.view LabKey CPAS Overview]'', and ''[http://labkey.com/company/our-clients Our Clients]'' pages

==See also==

* [[LabKey Corporation]]

==Further reading==

* {{cite web |url=https://www.labkey.org/project/home/Documentation/begin.view? |title=LabKey Server documentation |publisher=LabKey Software Foundation}}
* {{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=BMC Bioinformatics |year=2011 |volume=12 |issue=71 |title=LabKey Server: An open source platform for scientific data integration, analysis and collaboration |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 |url=http://www.biomedcentral.com/1471-2105/12/71 |doi=10.1186/1471-2105-12-71}}

==External links==

* [http://labkey.com/ LabKey] corporate site
* [http://freecode.com/projects/labkey-server LabKey Server] at Freecode
* [https://www.labkey.org/project/home/Documentation/Archive/begin.view? LabKey Server and CPAS] archived documentation
* [https://www.labkey.org/announcements/home/begin.view LabKey Server and CPAS] archived news

==References==
<references />


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

LabKey Server

2013-11-11T01:01:43Z

Labkeymohara: /* Videos */

{{Infobox software
| name = LabKey Server
| title = LabKey Server
| logo = 
| screenshot = 
| caption =
| collapsible =
| author =
| developer = [[LabKey Corporation]] and the LabKey Software Foundation
| 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>
| discontinued =
| frequently updated = yes
| 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>
| operating system = Cross-platform
| platform =
| size =
| language =
| status =
| 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>
| website = [https://www.labkey.org/ 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.<ref>{{cite web |url=http://labkey.com/server/labkey-server |title=LabKey Server |publisher=LabKey Corporation |accessdate=20 April 2012}}</ref>

[[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.<ref name="LKServ">{{cite web_short |url=http://labkey.com/services |title=LabKey Professional Services |publisher=LabKey Corporation |accessdate=20 April 2012}}</ref>

==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) [[caBIG]] 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>

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> 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>

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==

LabKey Server provides a secure data 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.

The platform also provides domain-specific support for several areas of research, 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; certified as "Silver-Level Compliant Data Service" with the [[caBIG]] standard
* '''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

{{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_short|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_short|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_short|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_short|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_short|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 =
| usage_cost =
| industries = biotechnology, clinical research, life sciences, pharmaceutical
}}
|-
|}

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

==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 ''[https://www.labkey.org/wiki/home/Documentation/page.view?name=beforeInstall Before You Install]'' page of the software documentation.

==Videos, screenshots, and other media==

===Videos===

The following demonstration videos are available for LabKey Server:

* [http://labkey.wistia.com/medias/w4e1yraxh8 REDCap Integration with LabKey Server]
* [http://labkey.wistia.com/medias/yu3ghwjuox Navigate LabKey Projects and Folders]
* [http://labkey.wistia.com/medias/ri1d4kthf6 R Views with knitr]
* [http://labkey.wistia.com/medias/966zgaqq6q Survey Designer - 13.1 Release Video]
* [http://labkey.wistia.com/medias/xro7g9h36a Survey Designer - Continued]
* [http://labkey.wistia.com/medias/jxmb6vvoax Security: Linked and Filtered Schemas]
* [http://labkey.wistia.com/medias/fskrzfi2dv Panorama Proteomics Webinar]
* [http://labkey.wistia.com/medias/2fb5tr9rr0 Pathology Viewer - 13.1 Sprint Demo]
* [http://labkey.wistia.com/medias/xro7g9h36a Survey Designer - 13.1 Sprint Demo]
* [http://labkey.wistia.com/medias/m6u88r6owo Visualization Webinar - Jan 2013 - part 1 of 3]
* [http://labkey.wistia.com/medias/4pqpcziky7 Visualization Webinar - Jan 2013 - part 2 of 3]
* [http://labkey.wistia.com/medias/8rn2sgi7pz Visualization Webinar - Jan 2013 - part 3 of 3]
* [http://www.youtube.com/watch?v=GZoBxLwmqY4&feature=youtu.be FCS Express Data Exports]
* [http://labkey.wistia.com/medias/1r0sdfz9bh Managing Protected Health Information (PHI)]
* [http://labkey.wistia.com/medias/sbmxvyfx7f Assessing data with quick charts]
* [http://labkey.wistia.com/medias/eqderuxwg6 Study Administration - organizing data]
* [http://labkey.wistia.com/medias/cf86822331 Security: Sharing data with another lab]
* [http://labkey.wistia.com/medias/c73a1aeff7 Participant lists - browse with faceted filtering]
* [http://labkey.wistia.com/medias/03bcfb374d Participant reports]
* [http://labkey.com/videos/top-level-videos/07022012-277 Visualize group data trends]
* [http://labkey.com/videos/top-level-videos/07022012-278 Ancillary studies]
* [http://labkey.com/videos/top-level-videos/07022012-279 Data browser]
* [http://labkey.com/videos/top-level-videos/03122011-272 LabKey at the Cascadia Proteomics Symposium]
* [http://labkey.com/videos/top-level-videos/30012011-260 Time charts: Comparing multiple measures on one chart]
* [http://labkey.com/videos/top-level-videos/30012011-263 Specimens: Tracking participant consent]
* [http://labkey.com/videos/top-level-videos/30012011-262 Security: Study demonstration mode]
* [http://labkey.com/videos/delivering-diagnostic-results Delivering diagnostic results]
* [http://labkey.com/videos/unlocking-spreadsheet-data-with-labkey Unlocking spreadsheet data #1: The problem]
* [http://labkey.com/videos/unlocking-spreadsheet-data-2-projects-and-sample-sets Unlocking spreadsheet data #2: Projects and sample sets]
* [http://labkey.com/videos/unlocking-spreadsheet-data-3-upload-and-search-files Unlocking spreadsheet data #3: Upload and search files]
* [http://labkey.com/videos/unlocking-spreadsheet-data-4-import-assay-results Unlocking spreadsheet data #4: Import assay results]
* [http://labkey.com/videos/unlocking-spreadsheet-data-5-integrate-and-analyze Unlocking spreadsheet data #5: Integrate and analyze]
* [https://www.labkey.org/wiki/home/Documentation/page.view?name=videos113#homepage 11.3 Video Demonstrations: New User Interface Features]
* [https://www.labkey.org/wiki/home/Documentation/page.view?name=videos113#timechart 11.3 Video Demonstrations: Visualizing Group Data Trends]
* [https://www.labkey.org/wiki/home/Documentation/page.view?name=videos113#ancillary 11.3 Video Demonstrations: Ancillary Studies]

===Screenshots===

The following screenshots are available for LabKey Server:

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

===Demos and live examples===

* [https://www.labkey.org/wiki/home/Documentation/page.view?name=tutorials Live demos and tutorials]
* [https://www.labkey.org/wiki/home/Documentation/page.view?name=showcase Live examples of LabKey Server]

==Entities using LabKey Server==

Examples of entities using LabKey Server include:

AdaptiveTCR, Bill & Melinda Gates Foundation, Fred Hutchinson Cancer Research Center, Harvard Partners, Institute of Molecular and Cell Biology – Singapore, Katze Lab at University of Washington, National Institute of Allergy and Infectious Diseases at Duke University, Stanford Canary Center for Cancer Early Detection, Statistical Center for HIV/AIDS Research & Prevention, USC Center for Applied Molecular Medicine

Source: The ''[https://www.labkey.org/wiki/home/Documentation/page.view?name=showcase Showcase of Live Sites]'', ''[https://www.labkey.org/Project/home/CPAS/begin.view LabKey CPAS Overview]'', and ''[http://labkey.com/company/our-clients Our Clients]'' pages

==See also==

* [[LabKey Corporation]]

==Further reading==

* {{cite web |url=https://www.labkey.org/project/home/Documentation/begin.view? |title=LabKey Server documentation |publisher=LabKey Software Foundation}}
* {{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=BMC Bioinformatics |year=2011 |volume=12 |issue=71 |title=LabKey Server: An open source platform for scientific data integration, analysis and collaboration |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 |url=http://www.biomedcentral.com/1471-2105/12/71 |doi=10.1186/1471-2105-12-71}}

==External links==

* [http://labkey.com/ LabKey] corporate site
* [http://freecode.com/projects/labkey-server LabKey Server] at Freecode
* [https://www.labkey.org/project/home/Documentation/Archive/begin.view? LabKey Server and CPAS] archived documentation
* [https://www.labkey.org/announcements/home/begin.view LabKey Server and CPAS] archived news

==References==
<references />


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