This page describes the usage of UTGB Toolkit.

• UTGB Quick Start

Drag & drop of tracks is supported in UTGB, and also you can resize the height of tracks by dragging the lower frame border of the tracks.

• Configuration button
• Opens the configuration panel for the track

• / Adjusts the height of the track
• Resizes the track frame height according to the track image size

• / Minimize/Restore track button
• Minimizes/Restore the height of the track frame

• Close Button
• Closes unnecessary tracks

The following keyboard shortcuts are provided for relocating the window location quickly:

Left		scroll left
Right		scroll right
Up		zoom out
Down		zoom in

Tracks displayed in UTGB can be configured by editing config/view/default-view.silk file. Each track configuration enclosed in track node has common parameters, class, name, pack and height. The class parameter must be present to specify a type of the track. Here is an example of a track configuration:

-track 
 # Track types. (e.g., ReadTrack, WigTrack, RefSeqTrack, RulerTrack, etc.)
 # Case differences and spacing will be ignored in this parameter. 
 -class: ReadTrack
 # Name of the track
 -name: BED Track
 # To pack track height. If pack value is true (default), the height of this track will be fit to its content height 
 -pack: true
 # Pixel height of the track. If pack is set to true, this field will be ignored.
 -height: 30
 # Track-specific properties. See the track catalog for details
 -property
  -path: (read file name)

The other parameters are optional but tracks usually have track-specific configuration parameters. For example, ReadTrack requires path value under property node to specify a data source to display. For details, see Track Catalog.

To set the default coordinate location in genome to display, use track group:

-track group
  -coordinate
    -species: human
    -ref: hg19
    -chr: chr1
    -start: 1
    -end: 10000

In UTGB, you can display data written in BED, SAM, BAM, WIG, FASTA format data. See the following page to create tracks for these data formats.

• Track Catalog

These documents are for programmers who want to develop your own tracks.

• How to use Eclipse for Web Application Development

• How to create a web action
• How to access databases
• Lens: How to map various data sources to objects

• How to create your own tracks

• FAQ: Frequently Asqued Questions

Here is the initial folder strucrture of the web application generated by UTGB shell:

README		Instruction file
config		configuration folder
db		database folder
eclipse		eclipse launch file folder
src		source codes
pom.xml		project description
war		temporary folder for GWT codes; containing javascript codes
target		work folder containing build classes, temporary files

• How to deploy your web application to a remote server

Silk is a compact text format for describing biological data.

• Silk format specification

• Build UTGB from Source Codes
• How to use Subversion with UTGB Shell