The ZENBU system is designed around the concept of user configurable visualization and processing. This is accomplished through a configuration saving and sharing system. The configurations in ZENBU are broken down into three main concepts: Tracks, Views, and Scripts.
Tracks are one of the central concepts in the ZENBU system.
A Track consists of three parts
- Data sources : a collection of one or more data sources which are pooled together to form a dynamic merged data source.
- Data processing : an optional script of data signal processing modules which manipulates and analyzes the data. This processing can be for either data visualization purposes or strictly for use in data exporting and offline analysis.
- Visualization parameters : a set of default visualization parameters which are used by the ZENBU genome browser visualization system when the track is loaded into a View.
Each Track in the system is internally identified based on its configuration content and a hashkey system. Anytime a user changes the definition of a Track, its configuration is different and receives a different hashkey. If two users happen to configure the same track, based on content description, they will be the same and get the same hashkey. This concept to Tracks-defined by their descriptions (not based on names or saving) is the foundation for the TrackCache system and enables the same TrackCache to be utilized by different users in different views.
In addition there is a Track Sharing system in place. This allows any user to name and describe their tracks to make it share with other users of the system. This is done in the track reconfiguration panel with the button labeled <share track>. This enables every user created Track to be referenced and reused. Although every different track configuration generates a new hashkey and track configuration within the TrackCache system, only those Tracks which are explicitly saved, can be searched for in the data explorer and shared as a predefined track.
A View is an ordered collection of Tracks with additional parameters.
These additional parameters include a Title and Description of the view, and every other user adjustable parameter of the ZENBU genome browser. In addition, a View can override any of the default visualization parameters from predefined Tracks which were loaded into the view.
A Script configuration is composed of a data processing script with additional parameters.
These parameters include a Title and Description of the script to allow for searching and sharing, and a set of recommended visualization parameters.
When a predefined script is loaded into a new or reconfigured Track, it will reset the visualization parameters to its recommendations. The user then has the option to override these visualization defaults and to even modify the script modules and parameters.
Saving and Sharing configurations
Every configuration is able to be saved by users of the systems. Saved configurations are appended with both a Title and a Description which are then searchable via the metadata searching systems in both the data explorer and ZENBU genome browser interfaces.