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| Genome browser/wiki poster for Biology of Genomes 2007
See the RECOMB 2007 poster.
Note that the order of authors is different in this abstract.
The submitted abstract
A PROTOTYPE “GENOME WIKI” FOR COMMUNITY ANNOTATION
Mitch Skinner1, Andrew Uzilov1, Lincoln Stein2, Chris Mungall3, Ian Holmes1
1: Department of Bioengineering, University of California, Berkeley
2: Cold Spring Harbor Laboratory
3: Lawrence Berkeley National Laboratory
The current standard for genome browser software involves a user interface based on static web pages. These pages are created on a server from a pre-loaded database of genome features, then viewed remotely on a web browser.
It is desirable to improve on this general approach by adding two new kinds of feature:
1. Instant responsiveness. In current browsers, whenever the user requests an action (such as moving to a new genome location, zooming in/out, changing view properties, etc.) the server must perform various database and page-rendering operations. This causes a significant lag, even if only a small part of the view is changed.
2. Persistent community annotation. In a typical system, entry of new annotations is dependent on a database administrator. While some genome browsers allow user-generated annotations to be transiently displayed alongside “official” tracks, there is typically no mechanism for permanently entering new records over the web. This has the potential to slow down community annotation.
While somewhat independent, both of these features are typical of a new generation of “Web 2.0” applications. We are extending the GBrowse open-source genome browser to implement these ideas, using the recently-popularized AJAX (Asynchronous Java Script And XML) framework, whereby a carefully designated proportion of the computational load is shifted from the database server to the web-browsing client.
The new framework enables a much smoother interface, familiar to users of websites such as Google Maps. For example, chromosome views can be dynamically dragged in a continuous motion without noticeable delay. Similarly, tracks can be instantly collapsed or expanded, with no waiting time while the new view is downloaded over the network.
Our approach also empowers true community annotation, whereby users can add their own tracks to a genome browser for others to see, constituting a live “genome wiki”. We are currently porting all existing GBrowse functionality to this new system. As a demonstration we have working browsers for D.melanogaster and S.cerevisiae chromosomes viewable at http://genome.biowiki.org/.
-- Created by: AndrewUzilov on 17 Apr 2007
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