|Developer(s)||LabKey Corporation and the LabKey Software Foundation|
|Initial release||April 16, 2007|
[ (November 17, 2018 ) ±]
|Type||Laboratory informatics software|
|License(s)||Apache Software License|
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.
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.
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. 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. Initial development was funded by the NCI and the nonprofit organization Canary Foundation.
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.
The first public release of the software came on November 23, 2005, in the form of CPAS 1.1. A few weeks later the team released the source code to coincide with the the January 1, 2006 print publication of the groups corresponding paper in the Journal of Proteome Research, making it officially an open-source release. 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. 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.   The 2.x incrementation ended with version 2.3 in February 2008. 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). Version 9.1 of LabKey was released on April 2, 2009, with 10.1 arriving in March 2010 and 11.1 releasing in April 2011. July 2014 saw the arrival of the 30th official, public release of the platform, v14.2. 
LabKey Server 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.
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
As of 2014[update], 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.
| The following feature list(s) is/are derived solely from public, freely-available online information the vendor provides. A lack of a "Y" does not necessarily mean that the product doesn't have that feature. The lack of a "Y" could mean:
LabKey Server is free and open-source. For more about LabKey Server's license and free nature, please reference LabKey Server's FAQ.
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 Before You Install page of the software documentation.
Videos, screenshots, and other media
Downloads of the free open-source community edition can be found 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, click here.
- LabKey Server Overview (March 2014)
- Extract-Transform-Load (ETL) Using LabKey Server
- Specimen Management Using LabKey Server
- Import Excel Spreadsheets with the Data Processing Pipeline
- LabKey User Conference 2013: User Applications: The Hutch Integrated Data Repository Archive
- LabKey User Conference 2013: User Applications: ITN Trialshare
- 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
- LabKey User Conference 2013: User Applications: JDRF/nPOD DataShare: Accelerating Type 1 Diabetes Basic Science Research
- 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)
- REDCap Integration with LabKey Server
- Navigate LabKey Projects and Folders
- R Views with knitr
- Survey Designer - 13.1 Release Video
- Survey Designer - Continued
- Security: Linked and Filtered Schemas
- Panorama Proteomics Webinar
- Pathology Viewer - 13.1 Sprint Demo
- Survey Designer - 13.1 Sprint Demo
- Visualization Webinar - Jan 2013 - part 1 of 3
- Visualization Webinar - Jan 2013 - part 2 of 3
- Visualization Webinar - Jan 2013 - part 3 of 3
- LabKey User Conference 2012: Introduction to LabKey Server
- LabKey User Conference 2012: History of LabKey Server
- LabKey User Conference 2012: LabKey Security
- LabKey User Conference 2012: LabKey Server Assays - usage and development
- LabKey User Conference 2012: Beyond the grid: using the LabKey reporting system to visualize, analyze, and present data in meaningful ways
- LabKey User Conference 2012: Pipelines
- LabKey User Conference 2012: Client APIs
- LabKey User Conference 2012: User Applications: Adapting LabKey Server for novel applications (Infectious Disease Research Institute)
- LabKey User Conference 2012: User Applications: ATLAS: Data Sharing in HIV Research
- LabKey User Conference 2012: User Applications: The CDS as a case study
- FCS Express Data Exports
- Managing Protected Health Information (PHI)
- Assessing data with quick charts
- Study Administration - organizing data
- Security: Sharing data with another lab
- Participant lists - browse with faceted filtering
- Participant reports
- Visualize group data trends
- Ancillary studies
- Data browser
- LabKey at the Cascadia Proteomics Symposium
- Time charts: Comparing multiple measures on one chart
- Specimens: Tracking participant consent
- Security: Study demonstration mode
- Delivering diagnostic results
- Unlocking spreadsheet data #1: The problem
- Unlocking spreadsheet data #2: Projects and sample sets
- Unlocking spreadsheet data #3: Upload and search files
- Unlocking spreadsheet data #4: Import assay results
- Unlocking spreadsheet data #5: Integrate and analyze
The following screenshots are available for LabKey Server:
Demos and live 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).
- "LabKey Server documentation". LabKey Software Foundation. https://www.labkey.org/project/home/Documentation/begin.view?.
- 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 (January 2006). "Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments". Journal of Proteome Research 5 (1): 112–21. PMID 16396501. http://www.ncbi.nlm.nih.gov/pubmed/16396501.
- 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 (2011). "LabKey Server: An open source platform for scientific data integration, analysis and collaboration". BMC Bioinformatics 12 (71). doi:10.1186/1471-2105-12-71. PMC PMC3062597. PMID 21385461. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=PMC3062597.
- LabKey Software corporate site
- LabKey Server open source home
- LabKey Server at Freecode
- LabKey Server and CPAS archived documentation
- LabKey Server and CPAS archived news
- "LabKey Software Foundation - News". LabKey Software Foundation. https://www.labkey.org/announcements/home/begin.view. Retrieved 20 April 2012.
- "Install LabKey Manually". LabKey Software Foundation. https://www.labkey.org/wiki/home/Documentation/page.view?name=manualInstall. Retrieved 17 November 2012.
- "LabKey Frequently Asked Questions". LabKey Software Foundation. https://www.labkey.org/wiki/home/page.view?name=HomeFAQ. Retrieved 20 April 2012.
- "LabKey Server Documentation". LabKey Software Foundation. https://www.labkey.org/project/home/Documentation/begin.view?. Retrieved 12 August 2014.
- "LabKey Server". LabKey Corporation. http://www.labkey.com/products-services/labkey-server/. Retrieved 02 May 2016.
- "Products and Services" LabKey Corporation. Retrieved 02 May 2016.
- "Center, NCI launch open-source software for proteomics analysis". Fred Hutchinson Cancer Research Center. 5 January 2006. http://www.fhcrc.org/content/public/en/news/center-news/2006/01/proteomics-software.html. Retrieved 20 April 2012.
- Nelson, Elizabeth (2 January 2011). "A Seattle Version of the Silicon Valley Garage". LabKey Corporation. http://labkey.com/blog/2011/01/tools-%E2%80%B9-labkey-blog-%E2%80%94-wordpress. Retrieved 20 April 2012.
- "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.
- 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.
- "LabKey CPAS Overview". LabKey Software Foundation. https://www.labkey.org/Project/home/CPAS/begin.view. Retrieved 20 April 2012.
- 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.
- "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.
- "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.
- "Get Started With LabKey Server 8.1". LabKey Software Foundation. 1 May 2008. https://www.labkey.org/project/home/Documentation/Archive/8.1/begin.view?. Retrieved 20 April 2012.
- "Get Started With LabKey Server 9.1". LabKey Software Foundation. 2 April 2009. https://www.labkey.org/project/home/Documentation/Archive/9.1/begin.view?. Retrieved 20 April 2012.
- "Get Started With LabKey Server 10.1". LabKey Software Foundation. 10 March 2010. https://www.labkey.org/project/home/Documentation/Archive/10.1/begin.view?. Retrieved 20 April 2012.
- "Get Started With LabKey Server v11.1". LabKey Software Foundation. 12 April 2011. https://www.labkey.org/project/home/Documentation/Archive/11.1/begin.view?. Retrieved 20 April 2012.
- "LabKey Server v14.2 Now Available". LabKey Software Foundation. https://www.labkey.org/announcements/home/thread.view?rowId=9497. Retrieved 12 August 2014.
- "LabKey Software Foundation - Studies". LabKey Corporation. https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=study. Retrieved 28 January 2012.
- "LabKey Software Foundation - Import a Specimen Archive". LabKey Corporation. https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=importSpecimenData. Retrieved 28 January 2012.
- "LabKey Server". LabKey Corporation. http://www.labkey.com/server/labkey-server. Retrieved 28 January 2012.
- "LabKey Software Foundation - Administration". LabKey Corporation. https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=adminServer. Retrieved 28 January 2012.
- "LabKey Software Foundation - Backup and Maintenance". LabKey Corporation. https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=dbBackup. Retrieved 28 January 2012.