Firefox toolbar for the Gaggle

The Firegoose toolbar connects the Gaggle to the web. By downloading and installing this extension into your Firefox browser you can broadcast data between the Gaggle and web resources.

Supported web sites include KEGG pathways, EMBL STRING (a database of functional associations), DAVID (which enables clustering by functional annotations), and Entrez Gene and Protein. With a little scripting, the Firegoose can potentially exchange data with practically any bioinformatics website.

Warning: If you're having problems with Firegoose and Java 6 update 10 on Windows, a work-around can be found here. This issue seems to be fixed in Java 1.6.0_13.

The latest Java 7 update 13 breaks Firegoose. Install the latest version and it should address the problem.

• install
• help
  • Capture Selection
  • Tools Menu
  • help for target websites
• microformat
• microformat reference
• Embedded XML
• Wiki: feature requests and general notes.
• Bugs: create and acct, then file bug reports

Demo

• Quick Demo: a demo that quickly exercises a few features of Firegoose.
• Try the Demo: Halobacterium response to anoxic environments. Part 2 of the demo shows off the capabilities of the Firegoose.

For Data Providers

We encourage data providers to make their data available in the structured format of their choice and, equally importantly, to provide links from existing web interfaces to the underlying structured data.

Read more...

Source

Firegoose source is here:

• http://gaggle.systemsbiology.net/svn/gaggle/FireGoose/trunk/
• Using the svn command-line client: svn checkout http://gaggle.systemsbiology.net/svn/gaggle/FireGoose/trunk yourInstallationDirectory

An ant build script is included which will compile the Java component and package all files into an XPI file. The extension can then be installed in Firefox by pointing the browser to the XPI file or dragging the XPI file into the browser window.

Setting up your development environment to work on an extension is a little complicated. Look for help by searching for "firefox extension development".

Citation

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
J Christopher Bare, Paul T Shannon, Amy K Schmid and Nitin S Baliga
BMC Bioinformatics 2007, 8:456 doi:10.1186/1471-2105-8-456
Published:19 November 2007