I may as well come clean and admit that I'm developing a genome browser. What? Another genome browser? Why? You may well ask these questions. Well, it's a long story. But here is a completely non-exhaustive list of existing genome browsers.
- The classics: UCSC Genome Browser Home and paper and it's microbial sibling.
- Argo a Java rich-client genome browser built at the Broad Institute.
- Integrative Genomics Viewer also from Broad (see press release).
- Affymetrix spun out it's Integrated Genome Browser into an open source project, along with a library of re-usable components called GenoViz.
- GBrowse Lincoln Stein's Perl based genome browser, followed by the AJAXy javascripty JBrowse (with a paper, nicely written as usual from Lincoln Stein.).
- x:map an AJAX genome browser based on the Google Maps API.
- The biology of extemophiles lab at the University of Paris Sud have a nice little web based browser for Sulfolobus.
- NCBI has a new AJAX tool called Sequence Viewer
- Flash based OmicBrowse is apparently big in Japan.
- MochiView is really nice. Read the paper in BMC Biology.
- GenomeGraphs: integrated genomic data visualization with R
- GenomeView
- Visualization guru Ben Fry (of processing fame) wrote at least two:cd36 browser and a handheld genome browser
- A guy who calls himself Saaien Tist implemented a circular genome browser in ruby-processing
- Back in 2002, some canucks built BioViz an SVG based genome browser
- The Savant Genome Browser is a desktop visualization tool for genomic data. It was primarily developed for visualizing high throughput (aka next generation) sequencing data... Savant comes out of the Computational Biology Lab at the University of Toronto - also home of Cytoscape Web.
Note: updated in Sept. 2009 to reflect the fact that everyone and their uncle built a genome browser this past couple of years. See Brother, can you spare a genome browser?
Note: updated again in May of 2010 and again in Feb 2011 to add Savant.
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R Bloggers
Hi there, I'm the developer of the X:Map database and website, and I can't wait to see what you come up with :)
ReplyDeleteGenome browsers are a really interesting branch of user interface design in my opinion, as the data set is so huge, and people are split between those who want an extreme close-up view of a specific area, and those who want to be able to see a general overview of a region (and the surrounding features).
As you can tell from our site, we went more for the latter ;-)
Good luck with it!!
Tim
Hi Tim,
ReplyDeleteThanks for the encouragement. X:Map is very cool - I really like the approach of rendering the tiles in R. (That's how you guys do it, right?)
-chris
We have an R package 'exonmap' for doing data analysis, but the actual tiles are pre-rendered with a Java app I wrote.
ReplyDeleteNice compilation of browsers. Don't forget Ensembl.
ReplyDeleteHave you released your own browser yet? Do you still like protovis?
Hi Steve,
ReplyDeleteI like protovis a lot. I made a little experimental prototype of a genome browser in protovis. It's not too likely that I'll follow up on that, but I'm using protovis for other purposes in my current project.
My genome browser is released on the Gaggle Genome Browser website and written up in a paper as well.