Genome Browser in a Box User's Guide

Contents

What is Genome Browser in a Box (GBiB)?
Getting Started: Setting up Genome Browser in a Box
Using Genome Browser in a Box
Improving speed and performance
Updating Genome Browser in a Box
Viewing your own data
Sharing Genome Browser in a Box with others
User accounts and sessions
Troubleshooting common problems
Genome Browser in a Box commands
Licensing information

Other resources:

What is Genome Browser in a Box?

Genome Browser in a Box (GBiB) is a "virtual machine" of the entire UCSC Genome Browser website that is designed to run on most PCs (Windows, Mac OSX or Linux). GBiB allows you to access much of the UCSC Genome Browser's functionality from the comfort of your own computer. It is particularly directed at individuals who want to use the Genome Browser toolset to view protected data. If it is not human sequencing reads, it usually does not fall under medical data privacy rules, and you should most likely not use GBiB but rather assembly hubs or track hubs. See our mirror page for adiscussion of the advantages/disadvantages of the different methods to customize your genome data display.

Differences between GBiB and the Genome Browser

While GBiB and the Genome Browser are similar in many ways, there are key differences. In particular, GBiB makes it much easier to visualize sensitive or protected data. Prior to the introduction of GBiB, it was necessary to upload your data to the UCSC Genome Browser website or place the data files on a publicly accessible web server and supply the URL to UCSC in order to view your own data with the Genome Browser. GBiB removes these requirements: none of your data must be uploaded to the UCSC servers, allowing you to use the Genome Browser on personal datasets in situations where it's infeasible to load the data onto a public web server.

Rather than installing the entire UCSC genome annotation database (several terabytes of data), GBiB instead depends upon remote connections to various UCSC servers for much of its functionality and data. It connects to the UCSC download server to obtain genomic sequences, liftOver files, and many of the other large data files, and connects to one of UCSC's public MySQL servers to download data displayed by the various annotation tracks. A few Genome Browser tracks are unavailable on the UCSC public MySQL servers due to agreements with the data distributors (DECIPHER and LOVD Variants), and thus are unavailable for use with GBiB.

The majority of protected data use in the research community currently focuses on the human genomes, primarily the hg19 (GRCh37) assembly and with a growing body of annotation on the newer hg38 (GRCh38) assembly. As a result, GBiB is currently optimized for use with the hg19 assembly. Many other recent genome assemblies can also be viewed, but access may be slower than for optimized assemblies. Access speed may also be impacted by your connection distance from the UCSC server. To improve performance in these situations, GBiB includes a simple tool that allows you to download ("mirror") selected genome annotation tracks to your machine. You can find more information about this tool in the Improving Speed and Performance section.

For more background on GBiB see:

Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics. 2015 Mar 1;31(5):764-6. PMID: 25348212; PMC: PMC4341066

Getting Started: Setting up Genome Browser in a Box

System requirements

GBiB will run on most modern PCs and major operating systems that meet these basic requirements: