Flash GViewer

[[[Image:gviewer_rat_human.jpg|Rat-Human Comparative Map]]]Description: Flash GViewer is a customizable Flash movie that can be easily
inserted into a web page to display each chromosome in a genome along
with the locations of individual features on the chromosomes. It is intended
to provide an overview of the genomic locations of a specific set of
features - eg. genes and QTLs associated with a specific phenotype,
etc. rather than as a way to view all features on the genome. The features
can hyperlink out to a detail page to enable to GViewer to be used
as a navigation tool. In addition the bands on the chromosomes can
link to defineable URL and new region selection sliders can be used
to select a specific chromosome region and then link out to a genome
browser for higher resolution information.

Current features (v0.4) include:

Uses a base map containing the chromosomes and banding pattern
of the desired organism. Perl scripts are available to take the UCSC
cytogenetic map files and convert them to the appropriate XML format.
This can also be used to portray any other custom backdrop for a
chromosome - colored segments corresponding to syntenic regions in
other organisms, colored according to feature density, etc.
Bands can link out to a URL defined in the base map (to allow users
to click to view a region in a genome browser, for example).
Annotations can come from a static XML file or can be dynamically
generated by a server-side script
Features appear at the appropriate position on the chromosome and
then dynamically move out to form a non-overlapping display.
Placing the mouse over individual features brings up a tooltip
displaying the feature's name, it also visually highlights the region
of the chromosome that the feature is aligned with
Clicking on a feature toggles the highlight display so it will
stay on when you move the mouse away. This can be used to turn on
the region highlights for multiple features to better visualize their
overlapping regions. Click again to turn each feature's highlight
off.

Clicking on a feature can open up a new browser window with a
cusomizable URL, eg a gene report page.
Clicking on a chromosome will expand that chromosome and enlarge
and label the features making them easier to view. Click the chromosome
again to return the whole genome view.
Turn on/off labels for zoom view and genome view (press i button
in bottom left corner). Click redraw to refresh the view to show/hide
labels.
(New in v0.4) Javascript can be used
to dynamically highlight displayed annotations by using triggering
javascript functions in the web page containing the flash movie.
Javascript can be used to query annotation data from the flash movie
and handle the returned data.
Customizable web interface and perl CGI script provided to allow
users to upload annotations and display them on the GViewer against
the base map of their choice.
(New in v0.4) Region selection sliders
in Zoom View allow the selection of a genomic region so you can
then click to open up a genome browser window for the specified
region.


Demo & Screenshots: A live version of the Flash movie is available on the Flash GViewer documentation, screenshots of the tool are provided below.

[[/files/gviewer_example1.jpg ]]

[[/files/gviewer_regionbar.jpg ]]

[[/files/gviewer_r_m_chr2.jpg ]]

[[/files/gviewer_example_hs.jpg ]]

[[/files/gviewer_human_mouse.jpg ]]

Requirements: To view the Flash GViewer on a web page requires the Macromedia Flash Plugin version 7, it can be downloaded from Macromedia here. To edit the source code (the .fla file in CVS) and publish modified versions of the .swf requires Macromedia Flash Professional v7.
Documentation: Installation instructions, explanations of the Flash HTML tags, the XML file formats for the base map and the annotations are listed in the Flash GViewer documentation.
Contact: [Simon Twigger].
Downloads: Via the web from sourceforge

Navigation menu