ZENBU genome browser
The ZENBU genome browser [gLyphs] is designed to provide an advanced tool for not only visualizing genomics data, but also for interactively processing the data. While most genome browsers provide static visualization images, data in the ZENBU system is dynamically manipulatable by the users of the system.
Views are collections of tracks
The ZENBU genome browser is launched with a previously saved view configuration. A view is simply a collection of tracks with a title and description. This can be considered like an interactive figure of a paper.
Any user who is loggged into the system can save and share views with other users. This is done through the save view 
button at the top of the genome browser.
The system will also automatically save temporary views as the user makes changes. This autosave enables the use of the web browser "back arrow" to undo changes. Although these temporary views are in the system with unique URLs, they are not permanent and will be deleted after a period of time. To ensure your view is permanent and can be re-accessed in the future, users should login and explicitly save the view.
Users can manipulate the order of tracks in their views through "click and drag" of the side-bar or title-bar.
Each view receives a unique URL for sharing with your collaborators via email or for bookmarking.
For example this URL links to the ZENBU genome browser view shown above
http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=l_D-jGt1IlehEahizVAMeB;loc=hg19::chr8:128746973..128755020
Multiple views on the same data
Unlike other genome browsers, ZENBU does not need to link the track visualization to specific upload file formats. This means with ZENBU, the user can upload their data once and then manipulate it in ZENBU to create many views with the same data. Where other genome browsers like UCSC or IGV require many different visualization file formats to support each different visualization track style, ZENBU can focus on a few common data interchange file formats (BAM, BED, GTF/GFF, OSCTable). This makes ZENBU more like a bioinformatics processing tool rather than just a visualization tool (genome browser).
Because the data is loaded once and visualization/processing is performed by ZENBU, the data content of all tracks is guaranteed to be synchronized and one can see exactly how each track was made by looking at the ZENBU data processing scripting in each track. This makes the tracks of ZENBU "data transparent"
In this example RNAseq data was loaded once from BAM files and then processed by ZENBU to create 7 different visualization tracks.
For many more examples of how ZENBU can process and visualize the same uploaded data into many different visualizations, please check out both the data processing sections and the experimental case studies sections of the documentation.
Tracks for data visualization and processing
The main aspect of the ZENBU genome browser is the concept of a track. The tracks in ZENBU are completely user definable and encapsulate the concepts of
- dynamic data source pooling to create a track virtual DataSource by choosing a collection (one or more) of primary data sources
- data processing
- data visualization
Data pooling
The ZENBU system allows for the dynamic creation of merged data sets referred to as data stream pools. This provides for a great deal of flexibility when configuring tracks. It no longer is necessary to pre-merge your datasets prior to upload. Data can be loaded in an atomic, singular manner and then ZENBU can perform the mix-and-matching of data sources when users configure their tracks.
A Data Stream Pool can also be though of as the virtual DataSource for a ZENBU track configuration
Dynamic track based data processing
One of unique features of the ZENBU system is the ability to apply data processing and analysis on-demand at query time and as part of the visualization process. This means that raw or unprocessed data can be loaded into the ZENBU system which translates it into the internal Data Model, and then ZENBU can perform many of the data manipulations and analysis that previously required bioinformatics experts with knowledge of the unix command line and a collection of bioinformatics tools.
The data processing system is applied on a track level at query time. This means that no intermediary result needs to be stored in a database or on disk. This allows the user to modify processing parameters and immediately see the effect of the change in the visualization. It also makes the system very fast since data is processed in memory and there is no overhead of reading and writing to slow disks.
Because data processing is applied on each track, and tracks are loaded independently, there is a level of parallelism inherent in the design of the system. The processed data result generated by ZENBU on-demand can also be downloaded into data files for further analysis by external systems like R, BioConductor, or BioPython.
Data processing is controlled through a Scripting system based on chaining Processing modules together in a manner similar to digital signal processing [1]
Visualization
The Tracks in the ZENBU gLyphs genome browser fall into three main categories of visualization styles
- Annotation tracks: where the data sources only contain genomic information and no expression
- Expression tracks: where expression level is displayed without feature boundaries in a style similar to the UCSC genome browser 'wiggle' but in an user interactive tool.
- Hybrid tracks: ZENBU enhanced visualization which allow for processed data to contain both genomic features and multi-experiment expression data
For details on all the different visualization styles and configuration options, please refer to the Track Visualization Styles section of the documentation.
Downloading processed track data
Since tracks contain dynamic pooling of data and data processing, the data output of a ZENBU track may be useful for bioinformaticians to utilize as part of external data analysis. To enable this each track has the ability to export its processed data into local files via the download data control 
For details please refer to the Data Download section of the documentation.
Experiment expression data graph
TODO
Adding tracks to the view
Creating new tracks
New tracks can be added to views through the configure new track control 
which brings up this "configure new track" interface
For details on Creating new tracks, please see the Configuring Tracks section of the documentation
Adding Predefined Tracks Into the View
Previous saved and shared tracks can be added into a view of the genome browser through the add predefined tracks control 
. Tracks are one of the types of configurations which can be saved and shared among users. This interface allows these previously saved and shared tracks to be added into ones view.
Clicking the "add predefined tracks" button brings uo this control panel
It provides the user with options to search the available tracks, filter based on which collaboration the track was shared with, and then select one-or-more tracks to add to your view
Saving and Sharing Views
Any user who is logged into the system can save and share view configurations with other users. This is done through the save view button at the top of the genome browser. This will bring up the "save configuration panel"
When saving a view, users can enter both a "configuration name" and a description of the view. All text entered will be searchable with the metadata search system at a later time in the data explorer.
The user must also select the user collaboration into which the view will be saved and shared with. Views are only shared into a single collaboration, but can latter be moved to a different collaboration through the editing panel which can be accessed in the data explorer views section
After saving, top of the genome browser view will display the new "configuration name" and description and a new unique URL is generated which allows direct access to this view.
Only users who have logged into the system can save and share views with others. Guests will be reminded to login before trying to save.
Exporting View as SVG Image
TODO
Controls and widgets
Track control widgets
The widgets and controls on each track which enables the user to modify and move the track.
- close track
which will delete the track from the view - reconfigure track
brings up the Reconfigure Track interface which allows users to reconfigure how the track is built. 
- copy track
which will duplicate a track in the view. This is very useful when used in combination with track-reconfiguration. It is sometimes easier to take an existing track and modify it to get your desired track-configuration, and this copy tool enables this. - download data
brings up the Download Track data interface. This enables users to download their processing results into several different file formats for use in external systems or for additional analysis. This panel also provides interfacing for user control of the TracCache building system - activate/deactivate track
changes the active state of a track. means the track is in an active/expanded state and clicking on the blue-circle will cause the track to deactivate and not draw its content. 
means the track is in a deactivated/compact state and click on the red-bar witll cause the track to become active.
There are several ways the user can change the genomic location of the Genome Browser
- searching for genes or annotations to refocus the view. This is part of the Metadata searching system which allows for complex multi-keyword queries with logic in order to find lists of potential gene targets.
For details please refer to the Region Location section of the documentation.
