Gaggle Components
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Data Standards
Boss

Gaggle Genome Browser

Data Sources

Currently, the genome browser can import chromosome data forming the basis for its coordinate system from the UCSC Genome Browser. Track data can be imported from Gaggle broadcasts, files, R or directly into SQLite.

Files

GGB supports importing track data from tab-delimited text files in several formats including a variant of GFF. See documentation on file formats.

R Integration

Once we've gotten a dataset started, a nice way to add tracks is through the R interoperability library.

SQLite

For those proficient with SQL, adding data directly to the SQLite database might be the most convenient way to import data into the genome browser. If you go this route, you'll want to check out the description of the gaggle genome browser database schema.

Python or other scripting languages

SQLite bindings are almost certainly available for your favorite programming language. As an example, we've put together sample Python code for creating a gaggle genome browser data file from scratch, under /src/scripts in the SVN archive.

Gaggle

Tracks can be broadcast in through the Gaggle framework from other Gaggle enabled programs such as MeV and DMV. DMV (Data Matrix Viewer) is a simple spreadsheet-like program for working with tables of numeric data within the Gaggle. See the topic Gaggle integration for more information and an example.

Help

For support contact the Gaggle mailing lists.

© 2006, Institute for Systems Biology, All Rights Reserved
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