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LabKey Server
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<h2 id="license">License</h2> <p>LabKey licenses LabKey Server and its documentation for free under the <a href="/facts/Apache_License/5AeIjas8">Apache License</a>.<a class="footnote-ref" id="fnref:1" href="#fn:1"><sup>1</sup></a> </p> <h2 id="languages-and-extensibility">Languages and extensibility</h2> <p>The base platform is written in <a href="/facts/Java_(programming_language)/9ScgFyAL">Java</a>. It can be extended through the addition of Java-based modules or simple, file-based modules written in <a href="/facts/HTML/sSc3fT78">HTML</a>, <a href="/facts/XML/clNgUfWk">XML</a> and <a href="/facts/JavaScript/XhhIIEsl">JavaScript</a>.<a class="footnote-ref" id="fnref:2" href="#fn:2"><sup>2</sup></a> The platform can also be extended using LabKey Server's <a href="/facts/Java_(software)/9ScgFyAL">Java</a>, <a href="/facts/JavaScript/XhhIIEsl">JavaScript</a>, <a href="/facts/R_(programming_language)/LSrkr8K8">R</a>, <a href="/facts/Python_(programming_language)/YbuGqofa">Python</a>, <a href="/facts/Perl/fx31kjlT">Perl</a> and <a href="/facts/SAS_(software)/7y2ulIMX">SAS</a> client libraries.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a> </p> <h2 id="history">History</h2> <p>LabKey Server, originally known as the Computational Proteomics Analysis System (CPAS), was developed at the <a href="/facts/Fred_Hutchinson_Cancer_Research_Center/lRer5Qo1">Fred Hutchinson Cancer Research Center</a> to manage high volumes of data generated at the Fred Hutch Computational Proteomics Lab. In 2005, a small team spun out of the Hutch and began operating independently as LabKey Software after contributors realized that the software could be beneficial to the broader scientific community.<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a><a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a><a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> </p> <h2 id="core-components">Core Components</h2> <p>LabKey Server provides a secure data repository for all types of biomedical data, including <a href="/facts/Mass_spec/RH5WBHJ2">mass spectrometry</a>, <a href="/facts/Flow_cytometry/M2IvPdL8">flow cytometry</a>, <a href="/facts/DNA_microarray/hofkMvou">microarray</a>, <a href="/facts/Microplate/lofVk1Xc">microplate</a>, <a href="/facts/ELISPOT/zo2eKIYV">ELISpot</a>, <a href="/facts/ELISA/8yvpYDtH">ELISA</a>, <a href="/facts/Neutralizing_antibody/efmyIPAV">NAb</a> and <a href="/facts/Observational_study/zEhxI4eh">observational study</a> information. A customizable data processing pipeline allows the upload and processing of the large data files common in biomedical research. </p><p>The platform also provides domain-specific support for several areas of research, including: </p> <ul><li>Observational Studies. Supports management of <a href="/facts/Longitudinal_studies/snyWEsXK">longitudinal</a>, large-scale studies of participants, subjects or animals over time. Allows the integration of clinical data with assay results.</li> <li>Proteomics. Allows the processing of high-throughput mass spectrometry data using tools such as the <a href="/facts/Mass_spectrometry_software/Nmv3GbXB">X! Tandem</a> search engine, the <a href="/facts/Trans-Proteomic_Pipeline/ChI3sd3L">Trans-Proteomic Pipeline</a>, <a href="/facts/Mascot_(software)/lpX47FRS">Mascot</a> and <a href="/facts/Sequest/MJr7aqY6">Sequest</a>. Certified as "Silver-Level Compliant Data Service" with the <a href="/facts/CaBIG/4x065HVR">caBIG</a> standard.</li> <li>Flow Cytometry. Supports automated quality control, centralized data management and web-based data sharing. Integrates with <a href="/facts/FlowJo/g9bkoQGm">FlowJo</a>.</li></ul> <h2 id="zika-open-research-portal">Zika Open Research Portal</h2> <p>In 2016, LabKey and Professor Dave O'Connor of the <a href="/facts/University_of_Wisconsin%25E2%2580%2593Madison/Rfj54YvS">University of Wisconsin–Madison</a> launched the Zika Open Research Portal <a href="http://zika.labkey.com">[1]</a> using LabKey Server. The portal provides direct access to experiment data being produced by members of the Zika Experimental Science Team (ZEST). The portal received attention from the scientific community for being the first platform of its kind to share real-time research data.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a><a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> </p> <h2 id="open-source-software">Open Source Software</h2> <p>Labkey is licensed in a variety of manners. Source-code is provided for a core set of features with the Community Edition, and there are also Premium Editions available.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> </p> <h2 id="users">Users</h2> <p>Users range from individual labs to large research consortia. In 2017, the program's users included the following:<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> </p> <ul><li><a href="/facts/Cedars-Sinai_Medical_Center/cQcdlRga">Cedars-Sinai Medical Center</a></li> <li>Center for HIV-AIDS Vaccine Immunology (CHAVI) at <a href="/facts/Duke_University/BFMHVjsB">Duke University</a></li> <li>Collaboration for AIDS Vaccine Discovery (CAVD), funded by the <a href="/facts/Gates_Foundation/IW7prjCH">Gates Foundation</a></li> <li>Fred Hutchinson Cancer Research Center</li> <li><a href="/facts/Genomics_England/o4uKIwYz">Genomics England</a></li> <li>International AIDS Vaccine Initiative (IAVI)</li> <li>Infectious Disease Research Institute (IDRI)</li> <li><a href="/facts/Institute_of_Molecular_and_Cell_Biology_(Singapore)/0PxNfM61">Institute of Molecular and Cell Biology (Singapore)</a></li> <li>Just Biotherapeutics</li> <li><a href="/facts/NIMML/RKbev6JM">NIMML</a></li> <li>Oregon <a href="/facts/National_Primate_Research_Center/QKc9rle8">National Primate Research Center</a></li> <li><a href="/facts/Partners_Harvard_Medical_International/am5xXrlJ">Harvard Partners</a></li> <li>Statistical Center for HIV/AIDS Research and Prevention (SCHARP)</li> <li>Southwest <a href="/facts/National_Primate_Research_Center/QKc9rle8">National Primate Research Center</a></li> <li><a href="/facts/University_of_Washington/36PG6qkG">University of Washington</a></li> <li><a href="/facts/University_of_Michigan/6e1Ea5xh">University of Michigan</a></li> <li><a href="/facts/University_of_Kentucky/AdJlvQ7w">University of Kentucky</a></li> <li><a href="/facts/University_of_South_Florida/AbTxgUXq">University of South Florida</a></li> <li><a href="/facts/University_of_Wisconsin/Rfj54YvS">University of Wisconsin</a></li> <li>Tulane <a href="/facts/National_Primate_Research_Center/QKc9rle8">National Primate Research Center</a></li> <li>Wisconsin <a href="/facts/National_Primate_Research_Center/QKc9rle8">National Primate Research Center</a></li></ul> <h2 id="publications">Publications</h2> <ul><li>Nelson, Elizabeth K; Piehler, Britt; Eckels, Josh; Rauch, Adam; Bellew, Matthew; Hussey, Peter; Ramsay, Sarah; Nathe, Cory; Lum, Karl; Krouse, Kevin; Stearns, David; Connolly, Brian; Skillman, Tom; Igra, Mark (2011). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062597">"LabKey Server: An open source platform for scientific data integration, analysis and collaboration"</a>. <i>BMC Bioinformatics</i>. 12: 71. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1186%2F1471-2105-12-71">10.1186/1471-2105-12-71</a>. <a href="/facts/PMC_(identifier)/dX1zMt71">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062597">3062597</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/21385461">21385461</a>.</li> <li>Rauch, Adam; Bellew, Matthew; Eng, Jimmy; Fitzgibbon, Matthew; Holzman, Ted; Hussey, Peter; Igra, Mark; MacLean, Brendan; et al. (2006). "Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments". <i>Journal of Proteome Research</i>. 5 (1): 112–21. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1021%2Fpr0503533">10.1021/pr0503533</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/16396501">16396501</a>.</li> <li>Shulman, Nicholas; Bellew, Matthew; Snelling, George; Carter, Donald; Huang, Yunda; Li, Hongli; Self, Steven G.; McElrath, M. Juliana; De Rosa, Stephen C. (2008). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2591089">"Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials"</a>. <i>Cytometry Part A</i>. 73A (9): 847–56. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1002%2Fcyto.a.20600">10.1002/cyto.a.20600</a>. <a href="/facts/PMC_(identifier)/dX1zMt71">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2591089">2591089</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/18615598">18615598</a>.</li> <li><a href="http://labkey.com/resources/publications/Integrating_a_Java_Web_Application_with_SAS.pdf">"The Best of Both Worlds: Integrating a Java Web Application with SAS Using the SAS/SHARE Driver for JDBC"</a> (PDF).</li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="http://www.labkey.com">LabKey</a>. The official web site for LabKey. Learn about products, features, and professional customization.</li> <li><a href="http://www.labkey.org">LabKey Support Portal</a>. Find support including <a href="http://www.labkey.org/project/home/Documentation/start.view?">documentation</a> and <a href="http://www.labkey.org/wiki/home/page.view?name=support">community forums</a>.</li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>"LabKey Frequently Asked Questions: /home". Labkey.org. Retrieved 2010-05-29. <a href="http://www.labkey.org/Documentation/wiki-page.view?name=HomeFAQ" target="_blank">http://www.labkey.org/Documentation/wiki-page.view?name=HomeFAQ</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>"Building Modules: /home/Documentation". Labkey.org. Retrieved 2010-05-29. <a href="http://www.labkey.org/wiki/home/Documentation/page.view?name=buildingModule" target="_blank">http://www.labkey.org/wiki/home/Documentation/page.view?name=buildingModule</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>"LabKey API: /Documentation". Labkey.org. Retrieved 2010-05-29. <a href="http://www.labkey.org/Documentation/wiki-page.view?name=viewApis" target="_blank">http://www.labkey.org/Documentation/wiki-page.view?name=viewApis</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>"Computational Proteomics Laboratory". Proteomics.fhcrc.org. Archived from the original on 2010-06-16. Retrieved 2010-05-29. <a href="https://web.archive.org/web/20100616200723/http://proteomics.fhcrc.org/CPL/home.html" target="_blank">https://web.archive.org/web/20100616200723/http://proteomics.fhcrc.org/CPL/home.html</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Wizards computational science. <a href="https://archive.today/20120804224849/http://www.fhcrc.org/content/public/en/news/center-news/2005/03/wizards-computational-science.html" target="_blank">https://archive.today/20120804224849/http://www.fhcrc.org/content/public/en/news/center-news/2005/03/wizards-computational-science.html</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>"Center News - 1/5/06 - Center, NCI launch open-source software for proteomics analysis". Fhcrc.org. 2006-01-05. Retrieved 2010-05-29. <a href="http://www.fhcrc.org/about/pubs/center_news/2006/jan5/br4.html" target="_blank">http://www.fhcrc.org/about/pubs/center_news/2006/jan5/br4.html</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Butler, Declan (2016-02-23). "Zika researchers release real-time data on viral infection study in monkeys". Nature. Nature News. doi:10.1038/nature.2016.19438. S2CID 168146966. Retrieved 2016-02-23. <a href="http://www.nature.com/news/zika-researchers-release-real-time-data-on-viral-infection-study-in-monkeys-1.19438" target="_blank">http://www.nature.com/news/zika-researchers-release-real-time-data-on-viral-infection-study-in-monkeys-1.19438</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>"Zika Data From the Lab, and Right to the Web". New York Times. 2016-07-18. Retrieved 2016-07-18. <a href="https://www.nytimes.com/2016/07/19/health/zika-data-monkey-studies.html?_r=0" target="_blank">https://www.nytimes.com/2016/07/19/health/zika-data-monkey-studies.html?_r=0</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>"LabKey Server - Research's Most Flexible Software Platform for Insight". <a href="https://www.labkey.com/products-services/labkey-server#server-editions" target="_blank">https://www.labkey.com/products-services/labkey-server#server-editions</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>"Our Clients | LabKey Software". Labkey.com. Retrieved 2010-05-29. <a href="https://www.labkey.com/resources/clients/" target="_blank">https://www.labkey.com/resources/clients/</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> </ol>