LabKey Server

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LabKey Server is free, open source software available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based querying, reporting, and collaborating across a range of data sources. Specific scientific applications and workflows can be added on top of the basic platform and leverage a data processing pipeline.

License

The LabKey Software Foundation licenses LabKey Server and its documentation for free under the Apache License. ^[1]

Languages and Extensibility

The base platform is written in Java. It can be extended through the addition of Java-based modules or simple, file-based modules written in HTML, XML and JavaScript.^[2] The platform can also be extended using LabKey Server's Java, JavaScript, R and SAS client libraries.^[3]

History

LabKey Server was spun out of the Computational Proteomics Lab at the Fred Hutchinson Cancer Research Center after contributors realized that the software could be beneficial to the broader scientific community. The software was originally called the Computational Proteomics Analysis System (CPAS).^[4] ^[5] ^[6]

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 in 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.

Users

Users range from individual labs to large research consortia. Current users include:^[7]

Fred Hutchinson Cancer Research Center
Statistical Center for HIV/AIDS Research and Prevention (SCHARP)
Center for HIV-AIDS Vaccine Immunology (CHAVI) at Duke University
Collaboration for AIDS Vaccine Discovery (CAVD), funded by the Gates Foundation
International AIDS Vaccine Initiative (IAVI)
Cedars-Sinai Medical Center
Harvard Partners
University of Washington
University of Michigan
University of Kentucky
University of Wisconsin

Publications

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, 2006. ^[8]
Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials. Cytometry Part A, 2008. ^[9]
The Best of Both Worlds: Integrating a Java Web Application with SAS® Using the SAS/SHARE® Driver for JDBC. SAS Global Forum, 2010. ^[10]

References

External Links

LabKey Server. The official web site for the LabKey Software Foundation includes documentation and community support forums.
LabKey Software. LabKey Software provides professional customization and support for LabKey Server.
SCHARP
CHAVI
CAVD
IAVI

[1] ttp://www.labkey.org/wiki/home/page.view?name=HomeFAQ

[2] ttp://www.labkey.org/wiki/home/Documentation/page.view?name=buildingModule

[3] ttp://www.labkey.org/wiki/home/Documentation/page.view?name=viewApis

[4] ttp://proteomics.fhcrc.org/CPL/home.html

[5] ttp://www.fhcrc.org/about/pubs/center_news/2005/mar17/sart1.html

[6] ttp://www.fhcrc.org/about/pubs/center_news/2006/jan5/br4.html

[7] ttp://labkey.com/about/clients.html

[8] ttp://pubs.acs.org/cgi-bin/abstract.cgi/jprobs/2006/5/i01/abs/pr0503533.htm

[9] ttp://www3.interscience.wiley.com/cgi-bin/fulltext/120748129/HTMLSTART

[10] ttp://labkey.com/resources/publications/Integrating_a_Java_Web_Application_with_SAS.pdf

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