LabKey Server

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

24.3.0  (March 25, 2024; 8 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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