Introduction

SilverGene is a novel genomic visualiser hosted within most standard web browsers and written using the Microsoft Silverlight presentation technology. It delivers highly interactive exploration at arbitrary scales, the ability to work interchangeably with local or remotely accessed data, and developing support for publication and collaboration. SilverGene supports textual annotation of arbitrary genomic regions or features. These annotations, along with selected genomic data, may be saved for later perusal or shared with collaborators. In addition, SilverGene provides full text query of user annotations and genomic features, as well as the capability to support analysis tools such as motif searching  using the BioPatML pattern language (see Maetschke, Towsey and Hogan [2007] for details).

SilverGene was developed to address deficiencies in current genomic visualisation tools. Existing web-based genome browsers are tightly coupled to a specialised data source and do not allow the user to view data located on their own desktop. Further, these systems often rely on transmission of large images created on a remote server. SilverGene renders the sequence on the client side, providing a richer interactive experience with fewer delays due to transfer of large image files.

The SilverGene Beta is configured to run using the latest version of Microsoft Silverlight, currently Silverlight 2, Beta 2 (2.0.30523.8). If your browser is supported, and you do not have the latest version of the plugin, a link to the free download will appear when you navigate to SilverGene. After a quick download and installation process, you will be ready to go.

Features

See the Features page for more details on the capabilities of SilverGene.

How to use SilverGene

User's Manual - General guidance for the main features of SilverGene
Guided Tour - A step by step tour of how to use SilverGene
Case Study - Practical example of how SilverGene can be used in to explore a publication
Developer's Guide - Provides details about how to create and customise SilverGene pages
Implementation Details - Provides technical details about the implementation of SilverGene

 

Demonstrations

Main demo page- live version of SilverGene, displaying the complete genome of Chlamydia trachomatis - a bacterium of significant interest to our research group.  See Guided tour (above) for an exploration of this genome.
Widget mode- embedding a SilverGene "widget" within your webpage

A Silverlight3 version of SilverGene is currently under development and will be released after an end-user runtime for Silverlight3 becomes available.