Difference between revisions of "JBrowse PSB 2020"

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Revision as of 22:46, 31 July 2019

Overview

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

Times based on 9am-10:30am time slot.

Time Presenter Topic
9am-9:10am Ian Holmes Welcome, JBrowse overview
9:10am-9:25am Rob Buels JBrowse 2: A component architecture for building genome browser apps
9:25am-10:00am Scott Cain JBrowse setup and usage tutorial
10:00am-10:15am Ian Holmes JBrowse, Apollo, and Galaxy: beyond browsing to interactive editing
10:15am-10:30am Shihab Dider JBrowse hg38 human instance & associated data

Tutorial Summary

The 9:25-10:00 section of the workshop will be based on the successful JBrowse tutorial workshop presented by Scott Cain at the January 2019 Plant and Animal Genomes conference, updated and extended to include the new JBrowse features appearing throughout 2019, and streamlined reflecting the probable greater familiarity of PSB attendees with some of the basic bioinformatics issues and shorter timeframe. A detailed plan of the previously presented version of this workshop can be found at JBrowse_Tutorial_PAG_2019

Key points will include:

  • Instructions on how to download, install, configure, and test a JBrowse installation
  • The three basic steps: load reference sequences, index tracks, build the name index
  • Overview of data sources: GFF, BED, BAM, VCF, CRAM, Wiggle/BigWig
  • Overview of track types and options: SVG, Canvas, HTML, paired reads, coverage
  • Changing the appearance and dynamic behavior of tracks
  • Overview of the JBrowse plugin ecosystem: installing plugins, the plugin repository, notable and significant plugins
  • Advanced features of the user interface: highlighting regions and features, opening local files (and the standalone JBrowse desktop app), finding set intersections and unions using “combination tracks”

Connecting to Galaxy

This part of the workshop will describe the JBrowse Connect platform for initiating and managing tasks through the JBrowse UI, and will walk through the specific example of proxying a Galaxy BLAST workflow into the JBrowse app, so that users can BLAST data against the reference genome.

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.