computer science

LabKey Server

LabKey Server is a computer science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand LabKey Server rather than just read about it. In short: LabKey Server is a software suite 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.

Key takeaways

LabKey Server belongs to computer science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect LabKey Server to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of LabKey Server from memory before moving on to harder problems.

Reference excerpt

LabKey Server is a software suite 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 LabKey licenses LabKey Server and its documentation for free under the Apache License.

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. The platform can also be extended using LabKey Server's Java, JavaScript, R, Python, Perl and SAS client libraries.

History LabKey Server, originally known as the Computational Proteomics Analysis System (CPAS), was developed at the Fred Hutchinson Cancer Research Center 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.

Core Components 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.

Zika Open Research Portal In 2016, LabKey and Professor Dave O'Connor of the University of Wisconsin–Madison launched the Zika Open Research Portal [1] 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.

Open Source Software 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.

Users Users range from individual labs to large research consortia. In 2017, the program's users included the following:

Cedars-Sinai Medical Center Center for HIV-AIDS Vaccine Immunology (CHAVI) at Duke University Collaboration for AIDS Vaccine Discovery (CAVD), funded by the Gates Foundation Fred Hutchinson Cancer Research Center Genomics England International AIDS Vaccine Initiative (IAVI) Infectious Disease Research Institute (IDRI) Institute of Molecular and Cell Biology (Singapore) Just Biotherapeutics NIMML Oregon National Primate Research Center Harvard Partners Statistical Center for HIV/AIDS Research and Prevention (SCHARP) Southwest National Primate Research Center University of Washington University of Michigan University of Kentucky University of South Florida University of Wisconsin Tulane National Primate Research Center Wisconsin National Primate Research Center

Publications 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). "LabKey Server: An open source platform for scientific data integration, analysis and collaboration". BMC Bioinformatics. 12: 71. doi:10.1186/1471-2105-12-71. PMC 3062597. PMID 21385461. 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". Journal of Proteome Research. 5 (1): 112–21. doi:10.1021/pr0503533. PMID 16396501. Shulman, Nicholas; Bellew, Matthew; Snelling, George; Carter, Donald; Huang, Yunda; Li, Hongli; Self, Steven G.; McElrath, M. Juliana; De Rosa, Stephen C. (2008). "Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials". Cytometry Part A. 73A (9): 847–56. doi:10.1002/cyto.a.20600. PMC 2591089. PMID 18615598. "The Best of Both Worlds: Integrating a Java Web Application with SAS Using the SAS/SHARE Driver for JDBC" (PDF).

References

External links LabKey. The official web site for LabKey. Learn about products, features, and professional customization. LabKey Support Portal. Find support including documentation and community forums.

Worked examples

Example 1 — a first encounter with LabKey Server

Start with the simplest possible case. Write down what LabKey Server claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In computer science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to LabKey Server before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about LabKey Server ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of LabKey Server

In research: LabKey Server appears in computer science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses LabKey Server in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: LabKey Server is common in secondary-school and first-year university syllabi. It links to neighbouring topics Free bioinformatics software, Mass spectrometry software, Proteomics, so understanding it makes those chapters shorter.
In everyday life: Look for LabKey Server outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study LabKey Server in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what LabKey Server means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain LabKey Server out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is LabKey Server in simple terms?

Why does LabKey Server matter?

Because it connects several computer science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study LabKey Server?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on LabKey Server.