Details of the Brassica / Arabidopsis Comparative Genome Viewer

There are currently several genome browsers available. While they are all useful and informative they have two main drawbacks: 1) distracting page reloads and 2) static displays. The Brassica / Arabidopsis Comparative Genome Viewer developed at the AAFC Saskatoon Research Centre overcomes both of these shortcomings through the use of SVG. All the data is scaled and translated on the client side so there is no need for the data to be reloaded each time the user desires a different view. This client side transformation dramatically improves the flow of browsing.

BioViz has been implemented using a multi-windowed format which provides the user with a great deal of flexibility when arranging the view of their data. The browser has been implemented using a client server methodology with the client side responsible for presentation of the data, and the server side responsible for retrieval of the appropriate data at the client's request. Use of the Adobe postURL and parseXML methods makes asynchronous data retrieval possible, allowing the user to request several pieces of supplementary information and continue working while the data loads. This results in a further improvement to the flow of browsing, especially on a slow network.

Implementation of BioViz application

The server side of the Viewer consists of a collection of Perl CGIs which are called by client requests via the postURL method. These scripts are responsible for gathering data from the appropriate source and turning it into SVG for display in the client. Possible sources include XML files, flat files, MySQL databases, and dynamically generated text reports. The SVG returned from the server is added to the GUI using the parseXML method available in the Adobe SVG plugin.

The client portion of the project is based on the CGUI (Custom Graphical User Interface) toolkit which provides the basic GUI elements used in the browser. This toolkit has been built using Javascript objects which allow the easy creation of the GUI elements. BioViz specific extensions are included in the BioViz package.

More Information

• BioViz: Genome Viewer - SVG Open - 2002
• The source for the toolkit can found here

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