Gaggle Components
Geese
Data Standards
Boss

Gaggle Genome Browser

Gaggle

The genome browser can share data with other software tools and data sources using the Gaggle integration framework.

Name lists

The genome browser can send and receive name lists. Upon receiving a name list, the browser will search for matching names in the currently loaded genome and select them.

Matrices

The genome browser can also send and receive matrices. A received matrix will be imported as a new track and plotted in the display. One subtlety is that names of rows must be mapped to coordinates on the genome. This can happen in one of several ways.

  • Matching by gene names.
  • Coordinates can be encoded in row names in this format: [seq][+/-]:[start]-[end]. This specifies the sequence, strand, start, and end for the feature.
  • A coordinate map can be created that maps arbitrary strings (probe IDs, for example) to coordinates.

Gaggle Broadcast Example

Using the DMV, we can broadcast track data into GGB. The following steps will broadcast a matrix track which will be displayed as a heatmap.

  1. start an empty DMV
  2. Download this tab delimited text file and load it into the DMV (File|Load tab-delimited matrix file)
  3. Start an empty genome browser
  4. At this point, a Gaggle boss should be running and both DMV and GGB connected to it. If not, start a boss and connect both programs. (Use menu item Gaggle|Connect to Boss).
  5. Download the Halobacterium sp. NRC-1 genome by clicking File|New Dataset, typing "halo", double-clicking Halobacterium sp. NRC-1 and clicking OK. See getting started for more details.
  6. Back in the DMV, click the 'all' button to select the whole matrix select the genome browser as the target and click 'M' to broadcast a matrix
  7. A dialog should appear titled "Receive Matrix Broadcast". Enter a name for your new track and click OK. You should see a heatmap track with data in both strands appear
© 2006, Institute for Systems Biology, All Rights Reserved
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