Analysis Gateway


Researchers can engage the U-BRITE Analysis Gateway via a number of different abstractions we describe below.

Jupyter Notebook

The Jupyter Notebook is “an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more“.

We recommend that research teams consider doing their scripting in these “data science notebooks”, an abstraction that may improve shareability and reproducibility of data analyses and research results.

Reusable Pipelines Directory

Many bioinformatics practitioners and their respective research teams here at UAB have been hard at work developing, documenting, and publishing data analysis pipelines that can be co-developed with, or shared with, and re-used by other teams.

The Reusable Pipelines Directory attempts to catalog and link to pipelines of interest to the U-BRITE target audience.

Smart API Directory

As data analysis pipelines are developed, it is often desirable to make use of existing libraries of code rather than writing new code that may not be as well-tested or documented. As more of these libraries are made available as modern web services, authors of new pipelines can call them over the network via a web service interface (often a REST API), even if those services are implemented in a different programming language than that of the pipeline. This approach promotes further re-use of existing code and can greatly expand the number of “building blocks” available to the pipeline author.

The Smart API Directory attempts to catalog and link to APIs (Application Programming Interfaces) of interest, including those written by the U-BRITE team.