LabKey Server

LabKey Server

Developer(s)	LabKey Corporation and the LabKey Software Foundation
Initial release	April 16, 2007 (2007-04-16)
Stable release	24.3.0  (March 25, 2024 (2024-03-25)) [±]
Preview release	20.11 [±]
Written in	Java
Operating system	Cross-platform
Type	Laboratory informatics software
License(s)	Apache Software License
Website	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.

LabKey Corporation, the company the develops the software, also sells a number of professional services, including SaaS hosting, installations and upgrade assistance, training programs, customization, consulting, and support.

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 efforts such as the Human Genome Project 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 version 2.0, released on April 16, 2007, came a renaming of the product to what is still known today as LabKey Server. 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. 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.

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, though the increment jump was never publicly explained.

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. 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.

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. 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, 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

Product: LabKey Server

Sample, inventory, and data management Sample login and management? Y Sample tracking? Y Sample and/or result batching? Y Task and event scheduling? Y Option for manual result entry? Multiple data viewing methods? Y Data and trend analysis? Y Data and equipment sharing? Y Customizable fields and/or interface? Y Query capability? Y Import data? Y Internal file or data linking? External file or data linking? ELN support or integration? Export data to MS Excel? Y Raw data management? Data warehouse? Y Deadline control? Production control? Project and/or task management? Y Inventory management? Document creation and/or management? Y Case management? Y Workflow management? Specification management? Customer and supplier management? Billing management? Quality, security, and compliance Regulatory compliance? QA / QC functions? Performance evaluation? Audit trail? Y Chain of custody? Configurable roles and security? Y Data normalization? Data validation? Y Data encryption? Version control? Automatic data backup? Y 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 Base functionality Administrator management? Y 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 Online or integrated help? Software as a service delivery model? Y Usage-based cost? Industries served biotechnology, clinical research, life sciences, pharmaceutical

Pricing

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

LabKey also offers various professional services related to their product, including SaaS-based web hosting. 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.

• 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

Screenshots

The following screenshots are available for LabKey Server:

• All screenshots for LabKey Server on Freecode

Demos and live examples

• Live demos and tutorials
• Live examples of LabKey Server

Entities using LabKey Server

Examples of entities using LabKey Server include:

Immune Tolerance Network (ITN), Fred Hutchinson Cancer Research Center, Statistical Center for HIV/AIDS Research & Prevention, HIV Vaccine Trials Network, Collaboration for AIDS Vaccine Discovery, Human Immunology Project Consortium, Juvenile Diabetes Research Foundation (JDRF) Network for Pancreatic Organ Donors (nPOD), NWBioTrust, Katze Lab at University of Washington, Harvard Partners, Institute of Molecular and Cell Biology – Singapore, National Institute of Allergy and Infectious Diseases at Duke University, Stanford Canary Center for Cancer Early Detection, USC Center for Applied Molecular Medicine, TB Systems Biology Program at Broad Institute, Oregon National Primate Research Center, Wisconsin National Primate Research Center, Infectious Disease Research Institute

Source: The Showcase of Live Sites, LabKey CPAS Overview, and Our Clients pages

See also

• LabKey Corporation

Further reading

• "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. http://www.biomedcentral.com/1471-2105/12/71. 

External links

• LabKey Software corporate site
• LabKey Server at Freecode
• LabKey Server and CPAS archived documentation
• LabKey Server and CPAS archived news