Professor David O’Connor’s lab at the University of Wisconsin uses LabKey Server as its “operating system,” speeding its efforts to understand how genetics affects immunity to viruses such as HIV/SIV.
The lab uses LabKey Server SDMS software to manage its extensive list of experiments, Illumina sequencing data, purchases, oligonucleotides, freezer samples, and other lab inventory, as well as to provide basic electronic lab notebook (ELN) functionality. Data, files, protocols, grant information, and experiment descriptions recorded on the server can be searched and queried, allowing lab members to look across experiments performed over more than ten years to find what they need quickly. Further, the server hosts an informational portal for an NIH-funded contract on major histocompatibility complex (MHC) genetics, allowing different subsets of data to be exposed to the scientific community and the funding agency.
Server SDMS enables the lab to automate genotyping workflows for efficiency and consistency; perform a comprehensive review of available genomic and clinical information for primate subjects; and gain analysis, querying, visualization, export, and search capabilities across many different data types. Today, the system helps the lab track data and metadata for tens of thousands of experiments, eliminate manual workflows, and securely share data with collaborators.
In February of 2016, the O’Connor lab became the first group to make real-time Zika data publicly available via their LabKey Server. Results are updated daily and are accessible online through the Zika experimental science team (ZEST) data portal.
Zika researchers release real-time data on viral infection study in monkeys (Nature, 23 Feburary 2016)
Presentation: Managing Next Generation Sequencing and Multiplexed Genotyping Data Using Open Source LabKey Server