JBrowse PSB 2020

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Overview

In this workshop, we present an introduction to the JBrowse genome browser. We will cover new functionality of JBrowse 2, which is downloadable as a desktop application, and provides new modalities for genome browsing including complex structural variant views and Circos views. It also contains connections to datasets for human datasets and common model organisms using trackhubs and data APIs.

Relevance to PSB

The JBrowse JavaScript genome browser is a very widely used genome browser, deployed at thousands of sites with around 30,000 monthly active users (source: Google Analytics). We are now presenting a preview of JBrowse 2, a ground up rewrite of JBrowse that enables new visualization modalities including multiple-linear views and circos views, which opens up the doors to synteny views, structural variant comparisons, and more. JBrowse 2 preserves the capabilities of JBrowse (especially the ability to interface with many data sources) but moving to a more modular architecture and a React-style model where the rendered DOM is a function of application state. Many new features are available in JBrowse 2 and this part of the workshop will introduce them for the first time.


Intended Audience

JBrowse is sufficiently easy to install that a biologist, bioinformatics researcher, or bioinformatics developer can easily set up and configure a JBrowse server after the initial hurdles of learning about configuration options and file formats are overcome. This talk is intended to introduce the more advanced features of JBrowse, and provide a preview of the JBrowse 2 application.

Workshop Schedule

Time Presenter Topic
10 minutes Ian Holmes Welcome, JBrowse and JBrowse 2 overview
60 minutes Colin Diesh and Garrett Stevens JBrowse 2 architecture, SV inspector, and detailed overview of JBrowse 2
20 minutes Ian Holmes Coverage of the JBrowse ecosystem, including plugins, JBrowse Connect, Apollo, and the future.