Researchers can engage the U-BRITE Data Portal via a number of different Repositories we describe below.
Omics Data Repository
The Omics Data Repository is for managing data at the “files and folders” level of abstraction. Researchers can interact with their own “omics” data, which is often made available as flat files that fit this abstraction, or discover other locally cached omics data of interest here in this repository.
Currently, the Omics Data Repository is implemented on top of managed, high-performance, parallel storage connected to UAB’s Cheaha supercomputer.
The Source Code Repository is for version control of source code and other research artifacts to better facilitate team science and reproducible research.
In particular, we help connect research teams to git-based IT infrastructure, training in modern practices, and tooling for interacting with the extensive git ecosystem. This encourages and enables the participation of the entire team, not just a handful of investigators, in the R&D process and promotes sharing of web notebooks, pipelines, and other research products within and among research teams.
Currently, the Source Code Repository is implemented on a UAB-local instance of GitLab, maintained and supported by Research Computing.
The i2b2 system and the Enterprise Clinical Data Warehouse offer a full range of self service and analyst supported data access and services to support the research process with data from inpatient and outpatient clinical operations. CCTS Informatics and the UAB Informatics Institute provides investigators with access to UAB electronic health record data via either (1) our self-service i2b2 tool or (2) an Electronic Data Warehouse (EDW) analyst.
The i2b2 system offers investigators real time, self service access to not only aggregate counts of patients for research feasibility, but also to detailed patient level data. Specifically, investigators are able to download all diagnosis, labs, medications, encounters, cancer registry data elements, and many other clinical facts on a population of patients identified by an i2b2 query. This type of data download is automatically considered to be exempt from IRB review based on the design and extended functionality of i2b2.
The Documentation Repository is for organizing and sharing documents, such as standard operating procedures (SOP), data management and analysis protocols, reports, grant proposals, manuscripts, and other important files related to R&D processes, in a modern research team.
Currently, the Documentation Repository is implemented with UAB’s Box, which provides an enterprise cloud platform for secure content management — in particular, a shared files and folders abstraction that should be familiar to most investigators, desktop integration with MS Office, Box Sync and Box Drive, and a flexible sharing and permissions model that facilitates team collaboration.
Indeed, the U-BRITE team itself uses the Documentation Repository for organizing slides, meeting minutes, design and data governance documents, implementation plans, case studies, and other aspects of coordinating new and ongoing U-BRITE development.
- Access UAB Box at https://uab.box.com.