JBrowse PSB 2020

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In this workshop, we present an introduction to the JBrowse genome browser using a preconfigured VirtualBox appliance that attendees will be able to use with their own computers to participate. We will cover installing and configuring JBrowse for a variety of common data formats including FASTA, GFF3, BAM, BigWig, VCF, and CRAM. We will also cover setting up JBrowse Connect, a server-side component for integrating computational analysis resources such as Galaxy into your JBrowse instance, and review new features such as the Apollo genome curation tool, the human genome data release, and JBrowse 2, which will see its first official release shortly before the workshop.

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). JBrowse can be deployed as a “static site” (i.e. no server CPU usage beyond delivering static files to the client), on cheap or cloud storage (including e.g. from an Amazon S3 bucket), making it the ideal secure and cost-efficient mode of presenting results of high-throughput genome analyses, for personalized genome medicine, and for many other applications in computational genomics. The Apollo genome annotation editor allows community and/or crowdsourced curation of gene structures and feature annotations over the web. The features of JBrowse being published in 2019 (including a new version of Apollo, the JBrowse 2 codebase which fundamentally pushes bioinformatics analysis into the browser, the integration with Galaxy, and other features) are highly relevant as visualization and analysis front-ends to bioinformatics researchers, and a natural fit to trainees, graduate students, postdocs, and industry attendees of the PSB conference.

Tutorial Level

Beginner to Intermediate. Students should be comfortable performing simple command line tasks like moving files and running scripts.

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 help them over those hurdles and to introduce the more advanced features of JBrowse, the preconfigured datasets and auxiliary applications like JBrowse Connect, and the features coming in JBrowse 2.

Prerequisite Software and VirtualBox Images

Prerequisite software for JBrowse will be pre-installed on VirtualBox images on USB drives that will be distributed to workshop attendees. Participants using these VirtualBox images will be able to setup and configure JBrowse during the workshop.

After the workshop, a VirtualBox system image with JBrowse prerequisite software pre-installed will be made available on JBrowse tutorial page at GMOD.org JBrowse#Tutorials. Users will be able to use this image to walk through the material presented at this workshop.

Workshop Schedule

Time Presenter Topic
10 minutes Ian Holmes Welcome, JBrowse overview
60 minutes Colin Diesh and Garrett Stevens JBrowse2 architecture, SV inspector, and new cool stuff in JBrowse1
20 minutes Ian Holmes JBrowse Connect and functional annotation in Apollo

JBrowse 2

JBrowse 2 is a radical redesign of JBrowse from the ground up, preserving 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.

JBrowse Human Instance

JBrowse is increasingly used by labs working in cancer genomics to visualize variants including structural variants such as gene fusions. JBrowse 2 will include new UI features to visualize these. The JBrowse team has assembled a reference instance of human genome data that can be used for human genome analyses, encompassing data from Ensembl, ENCODE, UCSC, the 1000 genomes project, COSMIC, and other sources. This part of the workshop will include a tour of this data bundle, with a guide to deploying it for human-centered applications in biomedicine, especially cancer research.