LabKey Server

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

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

[±]
Preview release 20.11 [±]
Written in Java[2]
Operating system Cross-platform
Type Laboratory informatics software
License(s) Apache Software License[3]
Website 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 Corporation, the company that develops the software, also 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 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.[8][10]

The first public release of the software came on November 23, 2005, in the form of CPAS 1.1.[9][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.[12] 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.[13] 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][14] [4] The 2.x incrementation ended with version 2.3 in February 2008.[1] The subsequent release after version 2.3 was 8.1 on May 1, 2008; 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).[15] Version 9.1 of LabKey was released on April 2, 2009[16], with 10.1 arriving in March 2010[17] and 11.1 releasing in April 2011.[18] July 2014 saw the arrival of the 30th official, public release of the platform, v14.2. [19]

Features

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.

The platform includes tools for electronic data capture (EDC), a file management system that provides upload and search capabilities, and a flexible, relational data store that supports integration and aggregation of results. A secure query service ensures that users can only view data that they have permission to see, no matter how they access the data (via the API, visualizations, SQL queries, or otherwise). Users can define new data types via the user interface, as well as associated metadata and wizards for data collection. They can bring data into the system through spreadsheet import wizards or extract-transform-load (ETL) tools; alternatively, the system can connect dynamically to external data sources, leaving data in place. A customizable data processing pipeline allows the upload and processing of the large data files common to biomedical research.[4]

Visualization and analysis tools include a graphical view designer, a built-in R interface, charting tools, and a SQL query designer. API libraries in a variety of familiar languages support customization and extension. Developers can add entire modules or simply include API-enhanced content (e.g., R visualizations) in wikis or HTML pages. LabKey Server readily integrates with and extends existing systems that are based on databases and/or spreadsheets.[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

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.

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:
  • the vendor chose to not put relevant feature information online despite its existence in the product.
  • the vendor chooses to make the feature information available only to those who create an account or call/e-mail.
  • the feature information exists online to the public, but a URL could not be found to cite the existence of the feature.
  • the feature does not exist for the product.
A vendor's product may receive more confirmed features with the addition of more public information to the vendor's site and/or by providing a URL to a page or document that can act as a citation for the existence of the feature. Prospective buyers are highly recommended to contact the vendor directly to verify features as this list isn't authoritative, and product upgrades and changes happen rapidly in some cases.


Product: LabKey Server
Sample, inventory, and data management
Sample login and management?Y[20]
Sample tracking?Y[20]
Sample and/or result batching?Y[21]
Task and event scheduling?Y[20]
Option for manual result entry?
Multiple data viewing methods?Y[20]
Data and trend analysis?Y[22]
Data and equipment sharing?Y[22]
Customizable fields and/or interface?Y[23]
Query capability?Y[22]
Import data?Y[22]
Internal file or data linking?
External file or data linking?
ELN support or integration?
Export data to MS Excel?Y[22]
Raw data management?
Data warehouse?Y[22]
Deadline control?
Production control?
Project and/or task management?Y[23]
Inventory management?
Document creation and/or management?Y[20]
Case management?Y[20]
Workflow management?
Specification management?
Customer and supplier management?
Billing management?
Quality, security, and compliance
Regulatory compliance?
QA / QC functions?
Performance evaluation?
Audit trail?Y[22]
Chain of custody?
Configurable roles and security?Y[22]
Data normalization?
Data validation?Y[22]
Data encryption?
Version control?
Automatic data backup?Y[24]
Environmental monitoring?
Reporting, barcoding, and printing
Custom reporting?
Report printing?
Label support?
Barcode support?
Export to PDF?
Export to MS Word?
Export to HTML and/or XML?
Fax integration?
Email integration?Y[23]
Base functionality
Administrator management?Y[22]
Modular?
Instrument interfacing and management?
Mobile device integration?
Alarms and/or alerts?
Work-related time tracking?
Voice recognition system?
External monitoring?
Messaging?
Multilingual?
Network-capable?
Web client or portal?Y[22]
Online or integrated help?
Software as a service delivery model?Y[25]
Usage-based cost?
Industries served
biotechnology, clinical research, life sciences, pharmaceutical

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 Software offers various professional services related to their product, including SaaS-based web hosting.[25] However, public pricing of its services is not available at this time.

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 Before You Install page of the software documentation.

Videos, screenshots, and other media

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 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).

Sources: LabKey Server Users, Showcase of Live Sites, and LabKey Server Overview pages

See also

Further reading


External links

References

  1. ↑ 1.0 1.1 1.2 1.3 "LabKey Software Foundation - News". LabKey Software Foundation. https://www.labkey.org/announcements/home/begin.view. Retrieved 20 April 2012. 
  2. ↑ "Install LabKey Manually". LabKey Software Foundation. https://www.labkey.org/wiki/home/Documentation/page.view?name=manualInstall. Retrieved 17 November 2012. 
  3. ↑ "LabKey Frequently Asked Questions". LabKey Software Foundation. https://www.labkey.org/wiki/home/page.view?name=HomeFAQ. Retrieved 20 April 2012. 
  4. ↑ 4.0 4.1 4.2 4.3 "LabKey Server Documentation". LabKey Software Foundation. https://www.labkey.org/project/home/Documentation/begin.view?. Retrieved 12 August 2014. 
  5. ↑ "LabKey Server". LabKey Corporation. http://labkey.com/server/labkey-server. Retrieved 20 April 2012. 
  6. ↑
  7. ↑ 7.0 7.1 "Center, NCI launch open-source software for proteomics analysis". Fred Hutchinson Cancer Research Center. 5 January 2006. http://www.fhcrc.org/content/public/en/news/center-news/2006/01/proteomics-software.html. Retrieved 20 April 2012. 
  8. ↑ 8.0 8.1 8.2 Nelson, Elizabeth (2 January 2011). "A Seattle Version of the Silicon Valley Garage". LabKey Corporation. http://labkey.com/blog/2011/01/tools-%E2%80%B9-labkey-blog-%E2%80%94-wordpress. Retrieved 20 April 2012. 
  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. https://www.labkey.org/Project/home/CPAS/begin.view. Retrieved 20 April 2012. 
  12. ↑ Snelling, George (8 December 2005). "CPAS 1.1 Source Code Released". LabKey Software Foundation. https://www.labkey.org/announcements/home/thread.view?rowId=35. Retrieved 20 April 2012. 
  13. ↑ "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. 
  14. ↑ "Computational Proteomics Laboratory". Fred Hutchinson Cancer Research Center. http://proteomics.fhcrc.org/CPL/home.html. Retrieved 20 April 2012. 
  15. ↑ "Get Started With LabKey Server 8.1". LabKey Software Foundation. 1 May 2008. https://www.labkey.org/project/home/Documentation/Archive/8.1/begin.view?. Retrieved 20 April 2012. 
  16. ↑ "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. 
  17. ↑ "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. 
  18. ↑ "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. 
  19. ↑ "LabKey Server v14.2 Now Available". LabKey Software Foundation. https://www.labkey.org/announcements/home/thread.view?rowId=9497. Retrieved 12 August 2014. 
  20. ↑ 20.0 20.1 20.2 20.3 20.4 20.5 "LabKey Software Foundation - Studies". LabKey Corporation. https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=study. Retrieved 28 January 2012. 
  21. ↑ "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. 
  22. ↑ 22.00 22.01 22.02 22.03 22.04 22.05 22.06 22.07 22.08 22.09 22.10 "LabKey Server". LabKey Corporation. http://www.labkey.com/server/labkey-server. Retrieved 28 January 2012. 
  23. ↑ 23.0 23.1 23.2 "LabKey Software Foundation - Administration". LabKey Corporation. https://www.labkey.org/wiki/home/Documentation/Archive/11.1/page.view?name=adminServer. Retrieved 28 January 2012. 
  24. ↑ "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. 
  25. ↑ 25.0 25.1 "Try LabKey Server". LabKey Corporation. https://labkey.com/forms/try-labkey-server. Retrieved 28 July 2014. 
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