BOSC 2007 - Ajax GBrowse

These slides were originally presented using the Fuller Screen Firefox addon

AJAX GBrowse:
Genome Browser Improvements and Community Genome Annotation

Mitchell Skinner
Holmes Lab
University of California, Berkeley

Goal: Google Maps for the Genome + Wikipedia for the Genome

	Maps	Genomes
Traditional (static, CGI-based page refresh)	original Yahoo Maps	UCSC Genome Browser, GBrowse
Improved (dynamic, faster, better UI)	Google Maps	AJAX GBrowse

The user interface improvements are the first step toward building a community annotation framework (a genome wiki).

Ajax GBrowse

Built using GBrowse and Bioperl's Bio::Graphics
Bio::Graphics lays out locally

Ajax GBrowse

Built using GBrowse and Bioperl's Bio::Graphics
Bio::Graphics lays out locally

Rendering Tiles

For each track, for each zoom level:

Chromosome-wide layout
Break it into pieces and render one tile at a time.

Rendering Tiles - expensive

D. melanogaster genome: ~120 million bases
max zoom: 10 pixels/base

=> 1.2 billion pixels wide,
10s to 100s of pixels high
per track

For the entire Drosophila genome, all 10 tracks, all zoom levels

Space for tiles: 15gb
Rendering time: 15hours

Rendering Tiles - optimizations

Space

hard-linking identical tiles

Time

GD:

memset for filling rectangles
memcpy for creating tiles from larger image

Space & Time: Render on demand

still requires substantial up-front work

A pixel-based approach is inherently expensive.

Client-side rendering?

SVG

not in IE
Scalable?

Client-side rendering?

SVG

not in IE
Scalable?

Client-side rendering: HTML

Rectangle - works for genomic features
Pretty fancy rectangle

Zooming: position/size by percentage
Can also use images

Client-side rendering advantages

much less space/CPU usage on the server
useful amounts of data can be cached on the client

May even enable off-line usage

client could do a lot more

highlight features
show subsets of features
edit features

facilitates collaborative editing of annotations (a genome wiki)

Can show image-based, pre-rendered tracks and HTML-based, client-rendered tracks in the same browser instance

What we've done

Google-maps style image browser
Client-rendered
Basic persistent feature upload

Crucial to community annotation

Where we're going

Full genome browser functionality

Search, overview, ...

Community Annotation

More extensive feature upload (e.g. more file formats, more control over the appearance of uploaded tracks)
Editing (genome wiki?)

Open source project, part of GMOD: gmod.org
(see "ajax" subdirectory in CVS)

For more: genome.biowiki.org

Thanks:

Ian Holmes
Andrew Uzilov
Lincoln Stein
Chris Mungall
Steve Taylor
GMOD
IHH, AVU, and MES supported in part by NIH/NHGRI 1R01GM076705-01

Why in a web browser?

No software to install

Java Web Start is nice but still more cumbersome than a web page

Much easier for a non-computer-savvy people
Web network effects: bookmarkable, linkable