Gaggle Components
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Data Standards
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Gaggle Genome Browser

What is it?

The Gaggle Genome Browser is an open source software tool for visualizing high-density data plotted against coordinates on the genome. Tiling arrays, ChIP-chip, and high-throughput sequencing are a few potential use-cases. The genome browser is designed to gracefully handle large datasets, allow easy import of user data, and interoperate with other bioinformatics tools through the Gaggle framework.

Demos

Finding protein-DNA binding sites with MeDiChI.

Launch demo genome browser with Halobacterium salinarum tiling array and ChIP-chip data.

Other web start packages containing prepackaged data from H. salinarum can be found on the Halo Gaggle page.

Bacillus anthracis RNA-seq data from Structure and complexity of a bacterial transcriptome.

DNA binding locations of CTCF and STAG1 in Human.

Features

  • Interactively pan and zoom across whole genome
  • Import genome from UCSC genome browser
  • Import genome from local files
  • Import data in GFF format
  • Render data tracks in several formats: scaling bubble plot, heatmap, segmentation, lines, markers, and bars.
  • Bookmark and annotate interesting regions and features
  • Link out to UCSC genome browser
  • Embedded Sqlite database
    • responsive UI for large datasets
    • ability to handle tracks that don't fit into memory
    • eases importing tracks and building datasets
    • smaller memory footprint

Documentation

Help is available on several aspects of the genome browser:

The wiki provides more information. For developers, see the design and architecture overview, schema and javadocs.

Support

For questions and support contact the Gaggle mailing lists.

Bugs / Feature requests

Please submit bugs and feature requests to our issue tracker. Anyone can create an account.

Source

Source code is available from our subversion repository. Please contact us to submit patches or contribute code.

http://gaggle.systemsbiology.net/svn/gaggle/genomebrowser/
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...check out more applications of GGB and screenshots.

Citation

Integration and visualization of systems biology data in context of the genome
J Christopher Bare, Tie Koide, David J Reiss, Dan Tenenbaum and Nitin S Baliga
BMC Bioinformatics 2010, 11:382 doi:10.1186/1471-2105-11-382
Published:19 July 2010

© 2006, Institute for Systems Biology, All Rights Reserved
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